Medicine in Omics最新文献

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Analysis of zebrafish homologs within the human genome provides valuable insights into exploring pan-cancer alternative splicing events as prognostic markers and therapeutic targets 分析人类基因组中的斑马鱼同源物为探索泛癌症选择性剪接事件作为预后标志物和治疗靶点提供了有价值的见解
Medicine in Omics Pub Date : 2025-07-08 DOI: 10.1016/j.meomic.2025.100046
Yanjun Liang , Xiao Zhu
{"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 ,&nbsp;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}
引用次数: 0
Multi-omics integration reveals chromatin-associated lncRNA prognostic model in lung adenocarcinoma: Bridging GWAS, transcriptome and clinical outcomes 多组学整合揭示染色质相关lncRNA在肺腺癌中的预后模型:连接GWAS、转录组和临床结果
Medicine in Omics Pub Date : 2025-06-26 DOI: 10.1016/j.meomic.2025.100045
Xiao Zhu , Zhuolong Xiong
{"title":"Multi-omics integration reveals chromatin-associated lncRNA prognostic model in lung adenocarcinoma: Bridging GWAS, transcriptome and clinical outcomes","authors":"Xiao Zhu ,&nbsp;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}
引用次数: 0
Neuroprotective effects of Persea americana and Tabebuia rosea ethanolic extracts against aluminum chloride-induced Alzheimer’s disease in rat model 美洲柏树和玫瑰苦参乙醇提取物对氯化铝诱导的阿尔茨海默病大鼠的神经保护作用
Medicine in Omics Pub Date : 2025-06-26 DOI: 10.1016/j.meomic.2025.100044
Olayinka Fisayo Onifade , Oluwasayo Peter Abodunrin , Esther Omolara Oyeneye , Ebubechukwu Goodness Chigozie , Abdusalam Gbemisola Arafa , Benjamen Olujide Okunlola
{"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 ,&nbsp;Oluwasayo Peter Abodunrin ,&nbsp;Esther Omolara Oyeneye ,&nbsp;Ebubechukwu Goodness Chigozie ,&nbsp;Abdusalam Gbemisola Arafa ,&nbsp;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}
引用次数: 0
Omics-based evaluation of m6A modification patterns in uveal melanoma and their prognostic implications 葡萄膜黑色素瘤中m6A修饰模式的组学评估及其预后意义
Medicine in Omics Pub Date : 2025-03-01 DOI: 10.1016/j.meomic.2025.100041
Xiaohui Shi , Xiao Zhu , Dongpei Li
{"title":"Omics-based evaluation of m6A modification patterns in uveal melanoma and their prognostic implications","authors":"Xiaohui Shi ,&nbsp;Xiao Zhu ,&nbsp;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}
引用次数: 0
Uncovering prognostic markers and therapeutic targets in acute myeloid leukemia: Insights from differential gene expression and Mendelian randomization analysis 揭示急性髓系白血病的预后标志物和治疗靶点:来自差异基因表达和孟德尔随机化分析的见解
Medicine in Omics Pub Date : 2025-03-01 DOI: 10.1016/j.meomic.2025.100042
Yaqi Huang , Xiao Zhu , Dongpei Li
{"title":"Uncovering prognostic markers and therapeutic targets in acute myeloid leukemia: Insights from differential gene expression and Mendelian randomization analysis","authors":"Yaqi Huang ,&nbsp;Xiao Zhu ,&nbsp;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}
引用次数: 0
Functional prediction and assignment of Clostridium botulinum type A1 operome: A quest for prioritizing drug targets A1 型肉毒杆菌操作体的功能预测和分配:寻找优先药物靶点
Medicine in Omics Pub Date : 2024-07-23 DOI: 10.1016/j.meomic.2024.100040
B. Roja, S. Saranya, R. Prathiviraj, P. Chellapandi
{"title":"Functional prediction and assignment of Clostridium botulinum type A1 operome: A quest for prioritizing drug targets","authors":"B. Roja,&nbsp;S. Saranya,&nbsp;R. Prathiviraj,&nbsp;P. Chellapandi","doi":"10.1016/j.meomic.2024.100040","DOIUrl":"10.1016/j.meomic.2024.100040","url":null,"abstract":"<div><p><em>Clostridium botulinum</em> strain Hall produces potent botulinum neurotoxin type A1, which causes food-borne, infant, and wound botulism in humans. Antibiotics and botulinum antitoxins can control growth and prevent botulinum toxicity. However, limited information on a protein with an unknown function hinders the discovery of new drug targets for this disease. In this study, a combined bioinformatics approach with literature support was applied to predict, assign, and validate operome functions. Our functional annotation scheme was based on sequence motifs, conserved domains, structures, protein folds, and evolutionary relationships. Approximately 14.62 % of the operome exhibited sequence similarity to known proteins, with 6.65 % predicted functions for 293 proteins, including 121 proteins exclusive to <em>C. botulinum</em>. Structural analysis revealed a significant presence of the Rossmann fold (26 %) and miscellaneous folds (43 %) among the operome. Transporters (&gt;85) and transcriptional regulators (&gt;45) were prevalent, underscoring their importance in <em>C. botulinum</em> adaptive strategies. The newly identified operome contributed to the diverse cellular and metabolic processes of this organism. The function of its operome was involved in amino acid metabolism and botulinum neurotoxin biosynthesis. In this study, we identified and characterized 13 new virulence proteins from the operome to determine their structure–function relationships. These new metabolic and virulence proteins allow the organism to colonize and interact with the human gastrointestinal tract. This study provides a quest for new drugs and targets for treating the underlying diseases of <em>C. botulinum</em> in humans.</p></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"12 ","pages":"Article 100040"},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590124924000099/pdfft?md5=3b712395b442155b1c8d4d1c892889a7&pid=1-s2.0-S2590124924000099-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141843471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Systems medicine framework for repurposable drug combinations for COVID-19 comorbidities 针对 COVID-19 合并症的可再利用药物组合的系统医学框架
Medicine in Omics Pub Date : 2024-05-22 DOI: 10.1016/j.meomic.2024.100038
S. Saranya, L. Thamanna, P. Chellapandi
{"title":"Systems medicine framework for repurposable drug combinations for COVID-19 comorbidities","authors":"S. Saranya,&nbsp;L. Thamanna,&nbsp;P. Chellapandi","doi":"10.1016/j.meomic.2024.100038","DOIUrl":"10.1016/j.meomic.2024.100038","url":null,"abstract":"<div><p>Currently, vaccines have shown efficacy against new SARS-CoV-2 variants. This study aimed to develop a systems medicine framework that can predict and validate drug combinations that can be repurposed for treating COVID-19 and its comorbidities, specifically type 2 diabetes and hypertension. This study found that gut microbes could potentially influence the action of drugs, innate immune response, intestinal dysfunction, and susceptibility to the virus in individuals with these comorbidities. It was also discovered that the spike protein of the virus interacts with 57 human genes, many of which are linked to food-borne bacteria. An analysis of disease enrichment showed that arthritis and hypertension were frequently observed as comorbidities in patients infected with SARS-CoV-2. Several drugs, including Fluvoxamine, Donepezil, and Ifenprodil, have been identified as potentially repurposable drugs for treating COVID-19 in individuals with hypertension. Moreover, nitazoxanide and tocilizumab (antivirals), bacitracin (antibacterial), and gliclazide (antidiabetics) were also identified as potential repurposable drugs. Tocilizumab and gliclazide are effective drug combinations for treating COVID-19 in individuals with type 2 diabetes. A combination of tocilizumab and lidocaine has also been suggested for treating COVID-19 in individuals infected with food-borne bacteria.</p></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"11 ","pages":"Article 100038"},"PeriodicalIF":0.0,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590124924000075/pdfft?md5=c548377f45b6d4562ed5e05c6f4c1cc5&pid=1-s2.0-S2590124924000075-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141142783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The omics technologies and liquid biopsies: Advantages, limitations, applications omics技术和液体活检:优势、局限性和应用
Medicine in Omics Pub Date : 2024-05-21 DOI: 10.1016/j.meomic.2024.100039
Daniele Magro, Marika Venezia, Carmela Rita Balistreri
{"title":"The omics technologies and liquid biopsies: Advantages, limitations, applications","authors":"Daniele Magro,&nbsp;Marika Venezia,&nbsp;Carmela Rita Balistreri","doi":"10.1016/j.meomic.2024.100039","DOIUrl":"10.1016/j.meomic.2024.100039","url":null,"abstract":"<div><p>In the recent years, the development of so-called omics technologies has greatly contributed to the discovery of new biomarkers and targets, spanning different areas from diagnosis to therapy, and helping to accelerate the progress of precision and personalized medicine. In addition to classic omics, including genomics, transcriptomics, proteomics, and metabolomics, newer-generation omics technologies and related platforms, such as microbiomics and nutrigenomics, are emerging. At the same time, the use of liquid biopsies is becoming established as optimal biological samples, consisting in biological fluids (i.e. blood, saliva, and urine), that are easy to collect, and whose components (cells, nucleic acids, exosome) can be analysed using throughput techniques. In addition, it is becoming attractive, because it consents the extrapolation of big data via multi-omics technologies. Here, we report a brief description and discussion of such technologies, highlighting applications and possible limitations.</p></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"11 ","pages":"Article 100039"},"PeriodicalIF":0.0,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590124924000087/pdfft?md5=f30f9d627c62fdbe645f3283504dd6d2&pid=1-s2.0-S2590124924000087-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141135404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Early-stage biomarkers identification by integrated genomic analysis in hepatocellular carcinoma 通过综合基因组分析鉴定肝细胞癌早期生物标记物
Medicine in Omics Pub Date : 2024-05-01 DOI: 10.1016/j.meomic.2024.100037
{"title":"Early-stage biomarkers identification by integrated genomic analysis in hepatocellular carcinoma","authors":"","doi":"10.1016/j.meomic.2024.100037","DOIUrl":"10.1016/j.meomic.2024.100037","url":null,"abstract":"<div><p>Hepatocellular carcinoma (HCC), a type of liver cancer, ranks as the third-leading cause of death due to the lack of definite biomarkers for early-stage detection. HCC progression occurs by the dysregulation of several genes. Though several studies focus on biomarkers for HCC diagnosis, stage-specific marker identification remains elusive. Hence, the present study aims to identify early-stage biomarkers for the detection of HCC through integrated <em>in silico</em> analysis. The differential gene expression was performed using GEO2R for the datasets (GSE14520, GSE63898, GSE121248, GSE124535, GSE94660, and GSE6764) retrieved from Gene Expression Omnibus (GEO) of patients with cirrhotic liver or HCC. The common differentially expressed gene enrichment analysis was performed using Funrich for Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genomics (KEGG) gene mapping. The Protein-Protein Interaction (PPI) network was performed using the Search Tool for the Retrieval of Interacting Genes (STRING). The hub genes were identified using the CytoHubba plug-in of Cytoscape software. The identified genes were verified for their prognostic value using the Kaplan-Meier plotter and Immunohistochemistry micrographs obtained from the Human Protein Atlas database. An overall of 243 common differentially expressed genes (DEGs) were identified containing 171 upregulated and 72 downregulated genes. With the help of PPI network construction, ten hub genes were identified as <em>CDK1</em>, <em>AURKA</em>, <em>CCNB1</em>, <em>CCNB2</em>, <em>CENPF</em>, <em>CDC20</em>, <em>TOP2A</em>, <em>BUB1</em>, <em>RRM2</em>, and <em>HMMR,</em> which are dysregulated owing to HCC proliferation, tumorigenesis and poor prognosis in patients. These hub genes are suitable waypoints for the diagnosis and targeted therapy against early-stage HCC.</p></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"12 ","pages":"Article 100037"},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590124924000063/pdfft?md5=dd5f1eb29f5d713a6e648566cc4c6a5f&pid=1-s2.0-S2590124924000063-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141033788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Designing of multi-Epitope vaccine against spike glycoprotein of SARS-CoV-2 using immunoinformatics approach 利用免疫信息学方法设计针对 SARS-CoV-2 穗状糖蛋白的多表位疫苗
Medicine in Omics Pub Date : 2024-04-23 DOI: 10.1016/j.meomic.2024.100036
Deepak Kumar Jha , Niti Yashvardhini , Amit Kumar , Manjush Gaurav , Kumar Sayrav
{"title":"Designing of multi-Epitope vaccine against spike glycoprotein of SARS-CoV-2 using immunoinformatics approach","authors":"Deepak Kumar Jha ,&nbsp;Niti Yashvardhini ,&nbsp;Amit Kumar ,&nbsp;Manjush Gaurav ,&nbsp;Kumar Sayrav","doi":"10.1016/j.meomic.2024.100036","DOIUrl":"10.1016/j.meomic.2024.100036","url":null,"abstract":"<div><h3>Background</h3><p>COVID-19 caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome) has created an alarming situation worldwide. The surface (S) glycoprotein of novel coronavirus, encoded by the genome of SARS-CoV-2, plays an role in attachment, fusion as well as entry into the host cell. The spike glycoprotein plays vital role in not only infection but pathogenesis and adaptive immunity, and, therefore, the S glycoprotein is considered as the main target for the development of effective and durable vaccine against SARS-CoV-2. Present study aims to compare the SARS-CoV-2 spike sequence obtained from first Wuhan virus with those of Asian SARS-CoV-2 isolates.</p></div><div><h3>Result</h3><p>A total of 1165 mutations from 657 sequences of Asia submitted in the month of November 2020 to February 2021 were detected. Further, secondary structure prediction followed by protein modeling analysis was performed which revealed, these mutations, considerably altered the stability of Spike protein. Additionally, Physiochemical properties, toxicity, allergenicity and stability of spike glycoprotein were estimated to demonstrate the specificity of the epitope candidates. Subsequently, we identified a total of 34B-cell and 10 T-cell immune epitopes. Among the predicted epitopes, 26 B-cell and 9T-cell epitopes showed non-allergenic, non-toxic and highly antigenic properties.</p></div><div><h3>Conclusion</h3><p>Taken together, our study showed spike glycoprotein of SARS-CoV-2 can be a potentially good candidate for the development of vaccine to curb SARS-CoV-2 infections.</p></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"11 ","pages":"Article 100036"},"PeriodicalIF":0.0,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590124924000051/pdfft?md5=789563bd81cf8146de57a8c567f2aead&pid=1-s2.0-S2590124924000051-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140763248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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