Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies
Abstract Background Alimentary tract malignancies (ATM) caused nearly one-third of all tumor-related death. Cuproptosis is a newly identified cell death pattern. The role of cuproptosis-associated lncRNAs in ATM is unknown. Method Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-05-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05314-z |
| _version_ | 1797831878553632768 |
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| author | Yangyang Xie Xue Song Danwei Du Zhongkai Ni Hai Huang |
| author_facet | Yangyang Xie Xue Song Danwei Du Zhongkai Ni Hai Huang |
| author_sort | Yangyang Xie |
| collection | DOAJ |
| description | Abstract Background Alimentary tract malignancies (ATM) caused nearly one-third of all tumor-related death. Cuproptosis is a newly identified cell death pattern. The role of cuproptosis-associated lncRNAs in ATM is unknown. Method Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to identify prognostic lncRNAs by Cox regression and LASSO. Then a predictive nomogram was constructed based on seven prognostic lncRNAs. In addition, the prognostic potential of the seven-lncRNA signature was verified via survival analysis, the receiver operating characteristic (ROC) curve, calibration curve, and clinicopathologic characteristics correlation analysis. Furthermore, we explored the associations between the signature risk score and immune landscape, and somatic gene mutation. Results We identified 1211 cuproptosis-related lncRNAs and seven survival-related lncRNAs. Patients were categorized into high-risk and low-risk groups with significantly different prognoses. ROC and calibration curve confirmed the good prediction capability of the risk model and nomogram. Somatic mutations between the two groups were compared. We also found that patients in the two groups responded differently to immune checkpoint inhibitors and immunotherapy. Conclusion The proposed novel seven lncRNAs nomogram could predict prognosis and guide treatment of ATM. Further research was required to validate the nomogram. |
| first_indexed | 2024-04-09T13:58:46Z |
| format | Article |
| id | doaj.art-4b1c800a51884134b4c50d48bccc2ec4 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-09T13:58:46Z |
| publishDate | 2023-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-4b1c800a51884134b4c50d48bccc2ec42023-05-07T11:25:50ZengBMCBMC Bioinformatics1471-21052023-05-0124111810.1186/s12859-023-05314-zIdentification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignanciesYangyang Xie0Xue Song1Danwei Du2Zhongkai Ni3Hai Huang4Department of General Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical UniversityDepartment of Pneumology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical UniversityDepartment of General Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical UniversityDepartment of General Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical UniversityDepartment of General Surgery, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical UniversityAbstract Background Alimentary tract malignancies (ATM) caused nearly one-third of all tumor-related death. Cuproptosis is a newly identified cell death pattern. The role of cuproptosis-associated lncRNAs in ATM is unknown. Method Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to identify prognostic lncRNAs by Cox regression and LASSO. Then a predictive nomogram was constructed based on seven prognostic lncRNAs. In addition, the prognostic potential of the seven-lncRNA signature was verified via survival analysis, the receiver operating characteristic (ROC) curve, calibration curve, and clinicopathologic characteristics correlation analysis. Furthermore, we explored the associations between the signature risk score and immune landscape, and somatic gene mutation. Results We identified 1211 cuproptosis-related lncRNAs and seven survival-related lncRNAs. Patients were categorized into high-risk and low-risk groups with significantly different prognoses. ROC and calibration curve confirmed the good prediction capability of the risk model and nomogram. Somatic mutations between the two groups were compared. We also found that patients in the two groups responded differently to immune checkpoint inhibitors and immunotherapy. Conclusion The proposed novel seven lncRNAs nomogram could predict prognosis and guide treatment of ATM. Further research was required to validate the nomogram.https://doi.org/10.1186/s12859-023-05314-zCuproptosisLong non-coding RNAPrognosisImmune infiltrationAlimentary tract malignancies |
| spellingShingle | Yangyang Xie Xue Song Danwei Du Zhongkai Ni Hai Huang Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies BMC Bioinformatics Cuproptosis Long non-coding RNA Prognosis Immune infiltration Alimentary tract malignancies |
| title | Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies |
| title_full | Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies |
| title_fullStr | Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies |
| title_full_unstemmed | Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies |
| title_short | Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies |
| title_sort | identification of cuproptosis related lncrnas to predict prognosis and immune infiltration characteristics in alimentary tract malignancies |
| topic | Cuproptosis Long non-coding RNA Prognosis Immune infiltration Alimentary tract malignancies |
| url | https://doi.org/10.1186/s12859-023-05314-z |
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