IET Systems Biology最新文献

{"title":"A tumour-associated macrophage-based signature for deciphering prognosis and immunotherapy response in prostate cancer","authors":"Jian Wang,&nbsp;Tao Guo,&nbsp;Yuanyuan Mi,&nbsp;Xiangyu Meng,&nbsp;Shuang Xu,&nbsp;Feng Dai,&nbsp;Chengwen Sun,&nbsp;Yi Huang,&nbsp;Jun Wang,&nbsp;Lijie Zhu,&nbsp;Jianquan Hou,&nbsp;Sheng Wu","doi":"10.1049/syb2.12097","DOIUrl":"10.1049/syb2.12097","url":null,"abstract":"<p>For the multistage progression of prostate cancer (PCa) and resistance to immunotherapy, tumour-associated macrophage is an essential contributor. Although immunotherapy is an important and promising treatment modality for cancer, most patients with PCa are not responsive towards it. In addition to exploring new therapeutic targets, it is imperative to identify highly immunotherapy-sensitive individuals. This research aimed to establish a signature risk model, which derived from the macrophage, to assess immunotherapeutic responses and predict prognosis. Data from the UCSC-XENA, GEO and TISCH databases were extracted for analysis. Based on both single-cell datasets and bulk transcriptome profiles, a macrophage-related score (MRS) consisting of the 10-gene panel was constructed using the gene set variation analysis. MRS was highly correlated with hypoxia, angiogenesis, and epithelial-mesenchymal transition, suggesting its potential as a risk indicator. Moreover, poor immunotherapy responses and worse prognostic performance were observed in the high-MRS group of various immunotherapy cohorts. Additionally, APOE, one of the constituent genes of the MRS, affected the polarisation of macrophages. In particular, the reduced level of M2 macrophage and tumour progression suppression were observed in PCa xenografts which implanted in Apolipoprotein E-knockout mice. The constructed MRS has the potential as a robust prognostic prediction tool, and can aid in the treatment selection of PCa, especially immunotherapy options.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 5","pages":"155-171"},"PeriodicalIF":1.9,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12097","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141977112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and analysis of epithelial-mesenchymal transition-related key long non-coding RNAs in hypospadias","authors":"Hongjie Gao,&nbsp;Chen Ding,&nbsp;Mengmeng Chang,&nbsp;Zhiyi Lu,&nbsp;Ding Li,&nbsp;Dan Bi,&nbsp;Fengyin Sun","doi":"10.1049/syb2.12096","DOIUrl":"10.1049/syb2.12096","url":null,"abstract":"<p>EMT dysfunction is a dominant mechanisms of hypospadias. Thus, identification of EMT-related lncRNAs based on transcriptome sequencing data of hypospadias might provide novel molecular markers and therapeutic targets for hypospadias. First, the microarray data related to hypospadias were downloaded from Gene Expression Omnibus (GEO). Besides, the differentially expressed lncRNAs and messenger RNAs (mRNAs) related to EMT were screened to construct lncRNA-mRNA co-expression interaction pairs. In addition, the microRNA (miRNA) prediction analysis was performed through bioinformatics methods to construct a ceRNA network. Moreover, function prediction and function enrichment and pathway analyses were also performed. Finally, the core EMT-related lncRNAs were verified based on mRNA expression changes and cell functions. A total of 6 EMT-related lncRNAs were identified and 123 mRNA-lncRNA co-expression interaction pairs were screened in this study. Additionally, a ceRNA regulatory network comprising 17 mRNAs, 4 lncRNAs, and 28 miRNAs was constructed based on the prediction of hypospadias-related miRNAs. The validation results of the dataset GSE121712 revealed that only BEX1 was positively correlated with the expression of the lncRNA GNAS-AS1 (r = 0.874, <i>P</i> &lt; 0.01), both of which had high expression. The cell experiment results demonstrated that interfering with the expression of GNAS-AS1 significantly promoted the proliferation, migration, and EMT of cells. Importantly, it was confirmed that GNAS-AS1 can serve as a ceRNA and play an important role in the EMT of hypospadias. Hence, it may be considered as a potential target in the treatment of this disease.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 4","pages":"143-154"},"PeriodicalIF":1.9,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12096","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revealing the potential role of hub metabolism-related genes and their correlation with immune cells in acute ischemic stroke","authors":"Xianjing Zhang,&nbsp;Tengxiao Xu,&nbsp;Chen Wang,&nbsp;Yueyue Lin,&nbsp;Weimi Hu,&nbsp;Maokui Yue,&nbsp;Hao Li","doi":"10.1049/syb2.12095","DOIUrl":"10.1049/syb2.12095","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Objectives</h3>\u0000 \u0000 <p>Acute ischemic stroke (AIS) is caused by cerebral ischemia due to thrombosis in the blood vessel. The purpose of this study is to identify key genes related to metabolism to aid in the mechanism research and management of AIS.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Materials and Methods</h3>\u0000 \u0000 <p>Gene expression data were downloaded from the Gene Expression Omnibus database. Weighted gene co-expression network analysis, Gene Ontology and kyoto encyclopedia of genes and genomes analysis were used to identify metabolism-related genes that may be involved in the regulation of AIS. A protein protein interaction network was mapped using Cytoscape based on the STRING database. Subsequently, hub metabolism-related genes were identified based on Cytoscape-CytoNCA and Cytoscape-MCODE plug-ins. Least absolute shrinkage and selection operator algorithm and differential expression analysis. In addition, drug prediction, molecular docking, ceRNA network construction, and correlation analysis with immune cell infiltration were performed to explore their potential molecular mechanisms of action in AIS. Finally, the expression of hub gene was verified by real-time PCR.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Metabolism-related genes FBL, HEATR1, HSPA8, MTMR4, NDUFC1, NDUFS8 and SNU13 were identified. The AUC values of FBL, HEATR1, HSPA8, MTMR4, NDUFS8 and SNU13 were all greater than 0.8, suggesting that they had good diagnostic accuracy. Correlation analysis found that their expression levels were also related to the infiltration levels of multiple immune cells, such as Activated.CD8.T.cell and Activated.dendritic.cell. It was found that only HSPA8 was successfully matched to drugs with literature support, and these drugs were acetaminophen, bupivacaine, dexamethasone, gentamicin, tretinoin and cisplatin. Moreover, it was also identified that the ENSG000000218510-hsa-miR-330-3p-HEATR1 axis may be involved in regulating AIS.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The identification of FBL, HEATR1, HSPA8, MTMR4, NDUFC1, NDUFS8 and SNU13 provides a new research direction for exploring the molecular mechanisms of AIS, which can help in clinical management and diagnosis.</p>\u0000 </section>\u0000 </div>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 4","pages":"129-142"},"PeriodicalIF":1.9,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12095","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141293868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene signatures of endoplasmic reticulum stress and mitophagy for prognostic risk prediction in lung adenocarcinoma","authors":"Xiong Lin,&nbsp;Miaoling Yang,&nbsp;Yuanling Huang,&nbsp;Xiaoli Huang,&nbsp;Huibo Shi,&nbsp;Binbin Chen,&nbsp;Jianle Kang,&nbsp;Sunkui Ke","doi":"10.1049/syb2.12092","DOIUrl":"10.1049/syb2.12092","url":null,"abstract":"<p>Genes associated with endoplasmic reticulum stress (ERS) and mitophagy can be conducive to predicting solid tumour prognosis. The authors aimed to develop a prognosis prediction model for these genes in lung adenocarcinoma (LUAD). Relevant gene expression and clinical information were collected from public databases including Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). A total of 265 differentially expressed genes was finally selected (71 up-regulated and 194 downregulated) in the LUAD dataset. Among these, 15 candidate ERS and mitophagy genes (<i>ATG12, CSNK2A1, MAP1LC3A, MAP1LC3B, MFN2, PGAM5, PINK1, RPS2</i>7A<i>, SQSTM1, SRC, UBA52, UBB, UBC, ULK1</i>, and <i>VDAC1</i>) might be critical to LUAD based on the expression analysis after crossing with the ERS and mitochondrial autophagy genes. The prediction model demonstrated the ability to effectively predict the 5-, 3-, and 1-year prognoses of LUAD patients in both GEO and TCGA databases. Moreover, high VDAC1 expression was associated with poor overall survival in LUAD (<i>p</i> &lt; 0.001), suggesting it might be a critical gene for LUAD prognosis prediction. Overall, the prognosis model based on ERS and mitophagy genes in LUAD can be useful for evaluating the prognosis of patients with LUAD, and VDAC1 may serve as a promising biomarker for LUAD prognosis.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 3","pages":"103-117"},"PeriodicalIF":2.3,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12092","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adjusting laser power to control the heat generated by nanoparticles at the site of a patient's cells","authors":"Seyed Ehsan Razavi,&nbsp;Hamed Khodadadi,&nbsp;Masoud Goharimanesh","doi":"10.1049/syb2.12093","DOIUrl":"10.1049/syb2.12093","url":null,"abstract":"<p>Cancer treatment often involves heat therapy, commonly administered alongside chemotherapy and radiation therapy. The authors address the challenges posed by heat treatment methods and introduce effective control techniques. These approaches enable the precise adjustment of laser radiation over time, ensuring the tumour's core temperature attains an acceptable level with a well-defined transient response. In these control strategies, the input is the actual tumour temperature compared to the desired value, while the output governs laser radiation power. Efficient control methods are explored for regulating tumour temperature in the presence of nanoparticles and laser radiation, validated through simulations on a relevant physiological model. Initially, a Proportional-Integral-Derivative (PID) controller serves as the foundational compensator. The PID controller parameters are optimised using a combination of trial and error and the Imperialist Competitive Algorithm (ICA). ICA, known for its swift convergence and reduced computational complexity, proves instrumental in parameter determination. Furthermore, an intelligent controller based on an artificial neural network is integrated with the PID controller and compared against alternative methods. Simulation results underscore the efficacy of the combined neural network-PID controller in achieving precise temperature control. This comprehensive study illuminates promising avenues for enhancing heat therapy's effectiveness in cancer treatment.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 4","pages":"119-128"},"PeriodicalIF":1.9,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12093","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141094226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA methylation plays important roles in lifestyle transition of Arthrobotrys oligospora","authors":"Jiajia Shi,&nbsp;Jiaxin Liu,&nbsp;Heng Li,&nbsp;Yao Tang,&nbsp;Shuqun Liu,&nbsp;Zhirong Sun,&nbsp;Zefen Yu,&nbsp;Xinglai Ji","doi":"10.1049/syb2.12094","DOIUrl":"10.1049/syb2.12094","url":null,"abstract":"<p>Trap formation is the key indicator of carnivorous lifestyle transition of nematode-trapping fungi (NTF). Here, the DNA methylation profile was explored during trap induction of <i>Arthrobotrys oligospora</i>, a typical NTF that captures nematodes by developing adhesive networks. Whole-genome bisulfite sequencing identified 871 methylation sites and 1979 differentially methylated regions (DMRs). This first-of-its-kind investigation unveiled the widespread presence of methylation systems in NTF, and suggested potential regulation of ribosomal RNAs through DNA methylation. Functional analysis indicated DNA methylation's involvement in complex gene regulations during trap induction, impacting multiple biological processes like response to stimulus, transporter activity, cell reproduction and molecular function regulator. These findings provide a glimpse into the important roles of DNA methylation in trap induction and offer new insights for understanding the molecular mechanisms driving carnivorous lifestyle transition of NTF.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 3","pages":"92-102"},"PeriodicalIF":2.3,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12094","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated bioinformatics analysis identified leucine rich repeat containing 15 and secreted phosphoprotein 1 as hub genes for calcific aortic valve disease and osteoarthritis","authors":"Shuji Gong,&nbsp;Kun Xiang,&nbsp;Le Chen,&nbsp;Huanwei Zhuang,&nbsp;Yaning Song,&nbsp;Jinlan Chen","doi":"10.1049/syb2.12091","DOIUrl":"10.1049/syb2.12091","url":null,"abstract":"<p>Calcific aortic valve disease (CAVD) and osteoarthritis (OA) are common diseases in the ageing population and share similar pathogenesis, especially in inflammation. This study aims to discover potential diagnostic and therapeutic targets in patients with CAVD and OA. Three CAVD datasets and one OA dataset were obtained from the Gene Expression Omnibus database. We used bioinformatics methods to search for key genes and immune infiltration, and established a ceRNA network. Immunohistochemical staining was performed to verify the expression of candidate genes in human and mice aortic valve tissues. Two key genes obtained, leucine rich repeat containing 15 (LRRC15) and secreted phosphoprotein 1 (SPP1), were further screened using machine learning and verified in human and mice aortic valve tissues. Compared to normal tissues, the infiltration of immune cells in CAVD tissues was significantly higher, and the expressions of LRRC15 and SPP1 were positively correlated with immune cells infiltration. Moreover, the ceRNA network showed extensive regulatory interactions based on LRRC15 and SPP1. The authors’ findings identified LRRC15 and SPP1 as hub genes in immunological mechanisms during CAVD and OA initiation and progression, as well as potential targets for drug development.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 3","pages":"77-91"},"PeriodicalIF":2.3,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12091","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140750892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Excavation of gene markers associated with pancreatic ductal adenocarcinoma based on interrelationships of gene expression","authors":"Zhao-Yue Zhang,&nbsp;Zi-Jie Sun,&nbsp;Dong Gao,&nbsp;Yu-Duo Hao,&nbsp;Hao Lin,&nbsp;Fen Liu","doi":"10.1049/syb2.12090","DOIUrl":"10.1049/syb2.12090","url":null,"abstract":"<p>Pancreatic ductal adenocarcinoma (PDAC) accounts for 95% of all pancreatic cancer cases, posing grave challenges to its diagnosis and treatment. Timely diagnosis is pivotal for improving patient survival, necessitating the discovery of precise biomarkers. An innovative approach was introduced to identify gene markers for precision PDAC detection. The core idea of our method is to discover gene pairs that display consistent opposite relative expression and differential co-expression patterns between PDAC and normal samples. Reversal gene pair analysis and differential partial correlation analysis were performed to determine reversal differential partial correlation (RDC) gene pairs. Using incremental feature selection, the authors refined the selected gene set and constructed a machine-learning model for PDAC recognition. As a result, the approach identified 10 RDC gene pairs. And the model could achieve a remarkable accuracy of 96.1% during cross-validation, surpassing gene expression-based models. The experiment on independent validation data confirmed the model's performance. Enrichment analysis revealed the involvement of these genes in essential biological processes and shed light on their potential roles in PDAC pathogenesis. Overall, the findings highlight the potential of these 10 RDC gene pairs as effective diagnostic markers for early PDAC detection, bringing hope for improving patient prognosis and survival.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 6","pages":"261-270"},"PeriodicalIF":1.9,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140289489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of disulfidptosis- and cuproptosis-related LncRNAs in modulating the immune microenvironment and chemosensitivity in colon adenocarcinoma","authors":"Qiang Fan,&nbsp;Guang-Bo Wu,&nbsp;Min Chen,&nbsp;Lei Zheng,&nbsp;Hong-Jie Li,&nbsp;Lv-Zhu Xiang,&nbsp;Meng Luo","doi":"10.1049/syb2.12089","DOIUrl":"10.1049/syb2.12089","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>The main objective was to establish a prognostic model utilising long non-coding RNAs associated with disulfidptosis and cuproptosis. The data for RNA-Sequence and clinicopathological information of Colon adenocarcinoma (COAD) were acquired from The Cancer Genome Atlas. A prognostic model was constructed using Cox regression and the Least Absolute Shrinkage and Selection Operator method. The model's predictive ability was assessed through principal component analysis, Kaplan–Meier analysis, nomogram etc. The ability of identifying the rates of overall survival, infiltration of immune cells, and chemosensitivity was also explored. In vitro experiments were conducted for the validation of differential expression and function of lncRNAs. A disulfidptosis and cuproptosis-related lncRNA prognostic model was constructed. The prognostic model exhibits excellent independent predictive capability for patient outcomes. Based on the authors’ model, the high-risk group exhibited higher tumour mutation burdened worse survival. Besides, differences in immune cell infiltration and responsiveness to chemotherapeutic medications exist among patients with different risk scores. Furthermore, aberrant expressions in certain lncRNAs have been validated in HCT116 cells. In particular, FENDRR and SNHG7 could affect the proliferation and migration of colorectal cancer cells. Our study developed a novel prognostic signature, providing valuable insights into prognosis, immune infiltration, and chemosensitivity in COAD patients.</p>\u0000 </section>\u0000 </div>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 2","pages":"55-75"},"PeriodicalIF":2.3,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12089","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140066164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anoikis-related genes as potential prognostic biomarkers in gastric cancer: A multilevel integrative analysis and predictive therapeutic value","authors":"Yongjian Lin,&nbsp;Jinlu Liu","doi":"10.1049/syb2.12088","DOIUrl":"10.1049/syb2.12088","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Gastric cancer (GC) is a frequent malignancy of the gastrointestinal tract. Exploring the potential anoikis mechanisms and pathways might facilitate GC research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Purpose</h3>\u0000 \u0000 <p>The authors aim to determine the significance of anoikis-related genes (ARGs) in GC prognosis and explore the regulatory mechanisms in epigenetics.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>After describing the genetic and transcriptional alterations of ARGs, we searched differentially expressed genes (DEGs) from the cancer genome atlas and gene expression omnibus databases to identify major cancer marker pathways. The non-negative matrix factorisation algorithm, Lasso, and Cox regression analysis were used to construct a risk model, and we validated and assessed the nomogram. Based on multiple levels and online platforms, this research evaluated the regulatory relationship of ARGs with GC.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Overexpression of ARGs is associated with poor prognosis, which modulates immune signalling and promotes anti-anoikis. The consistency of the DEGs clustering with weighted gene co-expression network analysis results and the nomogram containing 10 variable genes improved the clinical applicability of ARGs. In anti-anoikis mode, cytology, histology, and epigenetics could facilitate the analysis of immunophenotypes, tumour immune microenvironment (TIME), and treatment prognosis.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>A novel anoikis-related prognostic model for GC is constructed, and the significance of anoikis-related prognostic genes in the TIME and the metabolic pathways of tumours is initially explored.</p>\u0000 </section>\u0000 </div>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 2","pages":"41-54"},"PeriodicalIF":2.3,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139913983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}