Identification and verification of a prognostic autophagy-related gene signature in hepatocellular carcinoma
Abstract This study aimed to investigate the potential of autophagy-related genes (ATGs) as a prognostic signature for HCC and explore their relationships with immune cells and immune checkpoint molecules. A total of 483 samples were collected from the GEO database (n = 115) and The Cancer Genome At...
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| Format: | Article |
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Nature Portfolio
2024-02-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-53565-4 |
| _version_ | 1797274706676547584 |
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| author | Zhen Ma Mali Chen XiaoLong Liu Hongbin Cui |
| author_facet | Zhen Ma Mali Chen XiaoLong Liu Hongbin Cui |
| author_sort | Zhen Ma |
| collection | DOAJ |
| description | Abstract This study aimed to investigate the potential of autophagy-related genes (ATGs) as a prognostic signature for HCC and explore their relationships with immune cells and immune checkpoint molecules. A total of 483 samples were collected from the GEO database (n = 115) and The Cancer Genome Atlas (TCGA) database (n = 368). The GEO dataset was used as the training set, while the TCGA dataset was used for validation. The list of ATGs was obtained from the human autophagy database (HADB). Using Cox regression and LASSO regression methods, a prognostic signature based on ATGs was established. The independent use of this prognostic signature was tested through subgroup analysis. Additionally, the predictive value of this signature for immune-related profiles was explored. Following selection through univariate Cox regression analysis and iterative LASSO Cox analysis, a total of 11 ATGs were used in the GEO dataset to establish a prognostic signature that stratified patients into high- and low-risk groups based on survival. The robustness of this prognostic signature was validated using an external dataset. This signature remained a prognostic factor even in subgroups with different clinical features. Analysis of immune profiles revealed that patients in the high-risk group exhibited immunosuppressive states characterized by lower immune scores and ESTIMATE scores, greater tumour purity, and increased expression of immune checkpoint molecules. Furthermore, this signature was found to be correlated with the infiltration of different immune cell subpopulations. The results suggest that the ATG-based signature can be utilized to evaluate the prognosis of HCC patients and predict the immune status within the tumour microenvironment (TME). However, it is important to note that this study represents a preliminary attempt to use ATGs as prognostic indicators for HCC, and further validation is necessary to determine the predictive power of this signature. |
| first_indexed | 2024-03-07T15:02:07Z |
| format | Article |
| id | doaj.art-29f44a211f984bfaa1ff0498439627ee |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-07T15:02:07Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj.art-29f44a211f984bfaa1ff0498439627ee2024-03-05T19:04:27ZengNature PortfolioScientific Reports2045-23222024-02-0114111410.1038/s41598-024-53565-4Identification and verification of a prognostic autophagy-related gene signature in hepatocellular carcinomaZhen Ma0Mali Chen1XiaoLong Liu2Hongbin Cui3The Second Clinical Medical School, Lanzhou UniversityDepartment of Obstetrics, Gansu Provincial Maternity and Child-Care HospitalThe Second Hospital of Lanzhou UniversityThe Second Hospital of Lanzhou UniversityAbstract This study aimed to investigate the potential of autophagy-related genes (ATGs) as a prognostic signature for HCC and explore their relationships with immune cells and immune checkpoint molecules. A total of 483 samples were collected from the GEO database (n = 115) and The Cancer Genome Atlas (TCGA) database (n = 368). The GEO dataset was used as the training set, while the TCGA dataset was used for validation. The list of ATGs was obtained from the human autophagy database (HADB). Using Cox regression and LASSO regression methods, a prognostic signature based on ATGs was established. The independent use of this prognostic signature was tested through subgroup analysis. Additionally, the predictive value of this signature for immune-related profiles was explored. Following selection through univariate Cox regression analysis and iterative LASSO Cox analysis, a total of 11 ATGs were used in the GEO dataset to establish a prognostic signature that stratified patients into high- and low-risk groups based on survival. The robustness of this prognostic signature was validated using an external dataset. This signature remained a prognostic factor even in subgroups with different clinical features. Analysis of immune profiles revealed that patients in the high-risk group exhibited immunosuppressive states characterized by lower immune scores and ESTIMATE scores, greater tumour purity, and increased expression of immune checkpoint molecules. Furthermore, this signature was found to be correlated with the infiltration of different immune cell subpopulations. The results suggest that the ATG-based signature can be utilized to evaluate the prognosis of HCC patients and predict the immune status within the tumour microenvironment (TME). However, it is important to note that this study represents a preliminary attempt to use ATGs as prognostic indicators for HCC, and further validation is necessary to determine the predictive power of this signature.https://doi.org/10.1038/s41598-024-53565-4Autophagy-related genesHCCImmunityImmune checkpointPrognosis |
| spellingShingle | Zhen Ma Mali Chen XiaoLong Liu Hongbin Cui Identification and verification of a prognostic autophagy-related gene signature in hepatocellular carcinoma Scientific Reports Autophagy-related genes HCC Immunity Immune checkpoint Prognosis |
| title | Identification and verification of a prognostic autophagy-related gene signature in hepatocellular carcinoma |
| title_full | Identification and verification of a prognostic autophagy-related gene signature in hepatocellular carcinoma |
| title_fullStr | Identification and verification of a prognostic autophagy-related gene signature in hepatocellular carcinoma |
| title_full_unstemmed | Identification and verification of a prognostic autophagy-related gene signature in hepatocellular carcinoma |
| title_short | Identification and verification of a prognostic autophagy-related gene signature in hepatocellular carcinoma |
| title_sort | identification and verification of a prognostic autophagy related gene signature in hepatocellular carcinoma |
| topic | Autophagy-related genes HCC Immunity Immune checkpoint Prognosis |
| url | https://doi.org/10.1038/s41598-024-53565-4 |
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