| Genomic and immunogenomic analysis of three prognostic signature genes in LUAD | |
| Feng, Hai-Ming1; Zhao, Ye2; Yan, Wei-Jian1; Li, Bin1 | |
| 2023-12-01 | |
| Source Publication | BMC Bioinformatics Impact Factor & Quartile |
| Volume | 24Issue:1 |
| Abstract | Background: Searching for immunotherapy-related markers is an important research content to screen for target populations suitable for immunotherapy. Prognosis-related genes in early stage lung cancer may also affect the tumor immune microenvironment, which in turn affects immunotherapy. Results: We analyzed the differential genes affecting lung cancer patients receiving immunotherapy through the Cancer Treatment Response gene signature DataBase (CTR-DB), and set a threshold to obtain a total of 176 differential genes between response and non-response to immunotherapy. Functional enrichment analysis found that these differential genes were mainly involved in immune regulation-related pathways. The early-stage lung adenocarcinoma (LUAD) prognostic model was constructed through the cancer genome atlas (TCGA) database, and three target genes (MMP12, NFE2, HOXC8) were screened to calculate the risk score of early-stage LUAD. The receiver operating characteristic (ROC) curve indicated that the model had good prognostic value, and the validation set (GSE50081, GSE11969 and GSE42127) from the gene expression omnibus (GEO) analysis indicated that the model had good stability, and the risk score was correlated with immune infiltrations to varying degrees. Multi-type survival analysis and immune infiltration analysis revealed that the transcriptome, methylation and the copy number variation (CNV) levels of the three genes were correlated with patient prognosis and some tumor microenvironment (TME) components. Drug sensitivity analysis found that the three genes may affect some anti-tumor drugs. The mRNA expression of immune checkpoint-related genes showed significant differences between the high and low group of the three genes, and there may be a mutual regulatory network between immune checkpoint-related genes and target genes. Tumor immune dysfunction and exclusion (TIDE) analysis found that three genes were associated with immunotherapy response and maybe the potential predictors to immunotherapy, consistent with the CTR-DB database analysis. Conclusions: From the perspective of data mining, this study suggests that MMP12, NFE2, and HOXC8 may be involved in tumor immune regulation and affect immunotherapy. They are expected to become markers of immunotherapy and are worthy of further experimental research. © 2023, The Author(s). |
| Keyword | Alkylation Biological organs Data mining Database systems Diagnosis Diseases Gene expression Risk assessment Sensitivity analysis Gene signatures Genomics Immunotherapy Lung adenocarcinoma Prognostic analysis Risk score Signature database Target genes Treatment response Tumor microenvironments |
| Publisher | BioMed Central Ltd |
| DOI | 10.1186/s12859-023-05137-y |
| Indexed By | EI |
| Language | 英语 |
| EI Accession Number | 20230413419965 |
| EI Keywords | Tumors |
| EI Classification Number | 461.2 Biological Materials and Tissue Engineering ; 461.6 Medicine and Pharmacology ; 461.9 Biology ; 723.2 Data Processing and Image Processing ; 723.3 Database Systems ; 802.2 Chemical Reactions ; 914.1 Accidents and Accident Prevention ; 921 Mathematics |
| Original Document Type | Journal article (JA) |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | https://ir.lzu.edu.cn/handle/262010/498479 |
| Collection | 兰州大学 第二临床医学院 |
| Corresponding Author | Li, Bin |
| Affiliation | 1.Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, 82 Cuiyingmen, Chengguan District, Gansu, Lanzhou; 730030, China; 2.Department of Radiotherapy, Gansu Provincial People’s Hospital, Lanzhou City; 730030, China |
| First Author Affilication | Second Clinical School |
| Corresponding Author Affilication | Second Clinical School |
| Recommended Citation GB/T 7714 | Feng, Hai-Ming,Zhao, Ye,Yan, Wei-Jian,et al. Genomic and immunogenomic analysis of three prognostic signature genes in LUAD[J]. BMC Bioinformatics,2023,24(1). |
| APA | Feng, Hai-Ming,Zhao, Ye,Yan, Wei-Jian,&Li, Bin.(2023).Genomic and immunogenomic analysis of three prognostic signature genes in LUAD.BMC Bioinformatics,24(1). |
| MLA | Feng, Hai-Ming,et al."Genomic and immunogenomic analysis of three prognostic signature genes in LUAD".BMC Bioinformatics 24.1(2023). |
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| Feng-2023-Genomic an（9051KB） | 期刊论文 | 出版稿 | 限制开放 | CC BY-NC-SA | View Application Full Text |
