A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinoma
Abstract Background Colon cancer is the foremost reason of cancer-related mortality worldwide. Colon adenocarcinoma constitutes 90% of colon cancer, and most patients with colon adenocarcinoma (COAD) are identified until advanced stage. With the emergence of an increasing number of novel pathogenic...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-10-01
|
| Series: | BMC Medical Informatics and Decision Making |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12911-022-02020-3 |
| _version_ | 1797985958739574784 |
|---|---|
| author | Hongli Gao Fei Xing |
| author_facet | Hongli Gao Fei Xing |
| author_sort | Hongli Gao |
| collection | DOAJ |
| description | Abstract Background Colon cancer is the foremost reason of cancer-related mortality worldwide. Colon adenocarcinoma constitutes 90% of colon cancer, and most patients with colon adenocarcinoma (COAD) are identified until advanced stage. With the emergence of an increasing number of novel pathogenic mechanisms and treatments, the role of mitochondria in the development of cancer, has been studied and reported with increasing frequency. Methods We systematically analyzed the effect of mitochondria-related genes in COAD utilizing RNA sequencing dataset from The Cancer Genome Atlas database and 1613 mitochondrial function-related genes from MitoMiner database. Our approach consisted of differentially expressed gene, gene set enrichment analysis, gene ontology terminology, Kyoto Encyclopedia of Genes and Genomes, independent prognostic analysis, univariate and multivariate analysis, Kaplan–Meier survival analysis, immune microenvironment correlation analysis, and Cox regression analysis. Results Consequently, 8 genes were identified to construct 8 mitochondrial-related gene model by applying Cox regression analysis, CDC25C, KCNJ11, NOL3, P4HA1, QSOX2, Trap1, DNAJC28, and ATCAY. Meanwhile, we assessed the connection between this model and clinical parameters or immune microenvironment. Risk score was an independent predictor for COAD patients’ survival with an AUC of 0.687, 0.752 and 0.762 at 1-, 3- and 5-year in nomogram, respectively. The group with the highest risk score had the lowest survival rate and the worst clinical stages. Additionally, its predictive capacity was validated in GSE39582 cohort. Conclusion In summary, we established a prognostic pattern of mitochondrial-related genes, which can predict overall survival in COAD, which may enable a more optimized approach for the clinical treatment and scientific study of COAD. This gene signature model has the potential to improve prognosis and treatment for COAD patients in the future, and to be widely implemented in clinical settings. The utilization of this mitochondrial-related gene signature model may be benefit in the treatments and medical decision-making of COAD. |
| first_indexed | 2024-04-11T07:26:18Z |
| format | Article |
| id | doaj.art-44b25fd98a874be3b2baf0a62e608089 |
| institution | Directory Open Access Journal |
| issn | 1472-6947 |
| language | English |
| last_indexed | 2024-04-11T07:26:18Z |
| publishDate | 2022-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Informatics and Decision Making |
| spelling | doaj.art-44b25fd98a874be3b2baf0a62e6080892022-12-22T04:37:04ZengBMCBMC Medical Informatics and Decision Making1472-69472022-10-0122111810.1186/s12911-022-02020-3A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinomaHongli Gao0Fei Xing1Department of Oncology, Shengjing Hospital of China Medical UniversityDepartment of Oncology, Shengjing Hospital of China Medical UniversityAbstract Background Colon cancer is the foremost reason of cancer-related mortality worldwide. Colon adenocarcinoma constitutes 90% of colon cancer, and most patients with colon adenocarcinoma (COAD) are identified until advanced stage. With the emergence of an increasing number of novel pathogenic mechanisms and treatments, the role of mitochondria in the development of cancer, has been studied and reported with increasing frequency. Methods We systematically analyzed the effect of mitochondria-related genes in COAD utilizing RNA sequencing dataset from The Cancer Genome Atlas database and 1613 mitochondrial function-related genes from MitoMiner database. Our approach consisted of differentially expressed gene, gene set enrichment analysis, gene ontology terminology, Kyoto Encyclopedia of Genes and Genomes, independent prognostic analysis, univariate and multivariate analysis, Kaplan–Meier survival analysis, immune microenvironment correlation analysis, and Cox regression analysis. Results Consequently, 8 genes were identified to construct 8 mitochondrial-related gene model by applying Cox regression analysis, CDC25C, KCNJ11, NOL3, P4HA1, QSOX2, Trap1, DNAJC28, and ATCAY. Meanwhile, we assessed the connection between this model and clinical parameters or immune microenvironment. Risk score was an independent predictor for COAD patients’ survival with an AUC of 0.687, 0.752 and 0.762 at 1-, 3- and 5-year in nomogram, respectively. The group with the highest risk score had the lowest survival rate and the worst clinical stages. Additionally, its predictive capacity was validated in GSE39582 cohort. Conclusion In summary, we established a prognostic pattern of mitochondrial-related genes, which can predict overall survival in COAD, which may enable a more optimized approach for the clinical treatment and scientific study of COAD. This gene signature model has the potential to improve prognosis and treatment for COAD patients in the future, and to be widely implemented in clinical settings. The utilization of this mitochondrial-related gene signature model may be benefit in the treatments and medical decision-making of COAD.https://doi.org/10.1186/s12911-022-02020-3Colon adenocarcinoma (COAD)Mitochondrial-related genesRisk scoreOverall survival (OS)SignatureImmune checkpoint |
| spellingShingle | Hongli Gao Fei Xing A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinoma BMC Medical Informatics and Decision Making Colon adenocarcinoma (COAD) Mitochondrial-related genes Risk score Overall survival (OS) Signature Immune checkpoint |
| title | A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinoma |
| title_full | A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinoma |
| title_fullStr | A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinoma |
| title_full_unstemmed | A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinoma |
| title_short | A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinoma |
| title_sort | novel signature model based on mitochondrial related genes for predicting survival of colon adenocarcinoma |
| topic | Colon adenocarcinoma (COAD) Mitochondrial-related genes Risk score Overall survival (OS) Signature Immune checkpoint |
| url | https://doi.org/10.1186/s12911-022-02020-3 |
| work_keys_str_mv | AT hongligao anovelsignaturemodelbasedonmitochondrialrelatedgenesforpredictingsurvivalofcolonadenocarcinoma AT feixing anovelsignaturemodelbasedonmitochondrialrelatedgenesforpredictingsurvivalofcolonadenocarcinoma AT hongligao novelsignaturemodelbasedonmitochondrialrelatedgenesforpredictingsurvivalofcolonadenocarcinoma AT feixing novelsignaturemodelbasedonmitochondrialrelatedgenesforpredictingsurvivalofcolonadenocarcinoma |