An autophagy-related four-lncRNA signature helps to predict progression-free survival of neuroblastoma patients
BackgroundThis study aimed to identify autophagy-related long non-coding RNAs (lncRNAs) associated with progression of neuroblastoma (NB), and to build an autophagy-related lncRNA signature that helps to predict progression-free survival (PFS) of NB.MethodsThree independent gene expression datasets...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Oncology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2022.1014845/full |
| _version_ | 1797987761897078784 |
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| author | Jing Wang Xinyao Meng Ke Chen Jiexiong Feng |
| author_facet | Jing Wang Xinyao Meng Ke Chen Jiexiong Feng |
| author_sort | Jing Wang |
| collection | DOAJ |
| description | BackgroundThis study aimed to identify autophagy-related long non-coding RNAs (lncRNAs) associated with progression of neuroblastoma (NB), and to build an autophagy-related lncRNA signature that helps to predict progression-free survival (PFS) of NB.MethodsThree independent gene expression datasets were utilized in this study. Autophagy-related genes (ARG) associated with PFS of NB patients were firstly identified by univariate Cox survival analysis. lncRNAs correlated with those PFS-related ARGs were then identified. The least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analyses were performed to select out those lncRNAs with the best prognostic value for PFS. The Receiver Operating Characteristic (ROC) and Area Under Curve (AUC) analyses were performed to assess the prediction accuracy.ResultsFour autophagy-related lncRNAs (AL356599.1, AC022075.1, AC020928.1 and LINC02076) were found to be with the best prognostic value and integrated into a four-lncRNA risk signature for predicting PFS of NB patients. The four-lncRNA signature significantly stratify NB patients into two risk groups, with high-risk group has significantly poorer PFS than the low-risk group. The prognostic role of the lncRNA signature was independent with other clinical risk factors. The ROC curves revealed that the lncRNA signature has a good performance in predicting PFS (AUC > 0.70). A nomogram based on COG (Children’s Oncology Group) risk and the lncRNA risk score was constructed, showing good prediction accuracy (C-index = 0.700). The prognostic ability of the nomogram was better than that of COG risk alone (AUC = 0.790 versus AUC = 0.748). GSEA analyses revealed that multiple autophagy-related gene sets are significantly enriched in the low-risk group.ConclusionsWe identified an autophagy-related four-lncRNA signature that could help to predict the PFS of NB patients. Autophagy-related gene sets are significantly enriched in low-risk group, suggesting tumor suppressive roles of autophagy in NB. |
| first_indexed | 2024-04-11T07:53:19Z |
| format | Article |
| id | doaj.art-01d8481c24e143f68f660e8163e7f4aa |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-04-11T07:53:19Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj.art-01d8481c24e143f68f660e8163e7f4aa2022-12-22T04:36:00ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2022-12-011210.3389/fonc.2022.10148451014845An autophagy-related four-lncRNA signature helps to predict progression-free survival of neuroblastoma patientsJing WangXinyao MengKe ChenJiexiong FengBackgroundThis study aimed to identify autophagy-related long non-coding RNAs (lncRNAs) associated with progression of neuroblastoma (NB), and to build an autophagy-related lncRNA signature that helps to predict progression-free survival (PFS) of NB.MethodsThree independent gene expression datasets were utilized in this study. Autophagy-related genes (ARG) associated with PFS of NB patients were firstly identified by univariate Cox survival analysis. lncRNAs correlated with those PFS-related ARGs were then identified. The least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analyses were performed to select out those lncRNAs with the best prognostic value for PFS. The Receiver Operating Characteristic (ROC) and Area Under Curve (AUC) analyses were performed to assess the prediction accuracy.ResultsFour autophagy-related lncRNAs (AL356599.1, AC022075.1, AC020928.1 and LINC02076) were found to be with the best prognostic value and integrated into a four-lncRNA risk signature for predicting PFS of NB patients. The four-lncRNA signature significantly stratify NB patients into two risk groups, with high-risk group has significantly poorer PFS than the low-risk group. The prognostic role of the lncRNA signature was independent with other clinical risk factors. The ROC curves revealed that the lncRNA signature has a good performance in predicting PFS (AUC > 0.70). A nomogram based on COG (Children’s Oncology Group) risk and the lncRNA risk score was constructed, showing good prediction accuracy (C-index = 0.700). The prognostic ability of the nomogram was better than that of COG risk alone (AUC = 0.790 versus AUC = 0.748). GSEA analyses revealed that multiple autophagy-related gene sets are significantly enriched in the low-risk group.ConclusionsWe identified an autophagy-related four-lncRNA signature that could help to predict the PFS of NB patients. Autophagy-related gene sets are significantly enriched in low-risk group, suggesting tumor suppressive roles of autophagy in NB.https://www.frontiersin.org/articles/10.3389/fonc.2022.1014845/fullautophagyneuroblastomaprogression-free survivalprognosislong non-coding RNA |
| spellingShingle | Jing Wang Xinyao Meng Ke Chen Jiexiong Feng An autophagy-related four-lncRNA signature helps to predict progression-free survival of neuroblastoma patients Frontiers in Oncology autophagy neuroblastoma progression-free survival prognosis long non-coding RNA |
| title | An autophagy-related four-lncRNA signature helps to predict progression-free survival of neuroblastoma patients |
| title_full | An autophagy-related four-lncRNA signature helps to predict progression-free survival of neuroblastoma patients |
| title_fullStr | An autophagy-related four-lncRNA signature helps to predict progression-free survival of neuroblastoma patients |
| title_full_unstemmed | An autophagy-related four-lncRNA signature helps to predict progression-free survival of neuroblastoma patients |
| title_short | An autophagy-related four-lncRNA signature helps to predict progression-free survival of neuroblastoma patients |
| title_sort | autophagy related four lncrna signature helps to predict progression free survival of neuroblastoma patients |
| topic | autophagy neuroblastoma progression-free survival prognosis long non-coding RNA |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2022.1014845/full |
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