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Qin Z, Luo K, Liu Y, Liao S, He J, He M, Xie T, Jiang X, Li B, Liu H, Huang Q, Tang H, Feng W, Zhan X. ATG16L1 is a Potential Prognostic Biomarker and Immune Signature for Osteosarcoma: A Study Based on Bulk RNA and Single-Cell RNA-Sequencing. Int J Gen Med 2022; 15:1033-1045. [PMID: 35140506 PMCID: PMC8818976 DOI: 10.2147/ijgm.s341879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background Osteosarcoma is a common solid malignancy of the bone in children and adolescents, and its metastasis and recurrence are the principal causes of poor treatment outcomes. Methods Autophagy-related genes were used to cluster osteosarcoma patients by consensus clustering analysis using the GSE21257 database. Differentially expressed genes (DEGs) were identified by limma package. Multiple-gene risk signature was constructed using least absolute shrinkage and selection operator (LASSO) analysis and Cox regression analyses. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to determine gene expression levels. Then, single-cell RNA-sequencing dataset GSE152048 were used to identify the correlation between the DEGs and effector molecules expressed in specific tumor-infiltrating immune cells. Results Two clusters were identified in the consensus clustering analysis, which were confirmed by principal component analysis. Limma analysis revealed that 15 genes were related, and 9 genes were screened using protein-protein interaction network and LASSO regression analysis. Cox regression analyses identified 5 genes. Combined with survival analysis, only the autophagy related 16 like 1 gene (ATG16L1) was significant. The results of qRT-PCR showed low expression levels of ATG16L1 in tumor cells group. Immune infiltration analysis revealed significantly lower expression of CD8+ T cells in the high ATG16L1 gene expression group. ScRNA-seq revealed that in the ATG16L1+CD8+ T cell group, the expression of GZMB was lower, whereas the expression of ITGA1 was higher. These results showed that ATG16L1 is an immune-related gene, which is associated with poor prognosis in patients with osteosarcoma. Conclusion ATG16L1 is a potential prognostic biomarker and immune signature and may be a therapeutic target for osteosarcoma.
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Affiliation(s)
- Zhaojie Qin
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
- Department of Orthopedic, The People’s Hospital of Hechi, Hechi, 547600, Guangxi, People’s Republic of China
| | - Kai Luo
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Yun Liu
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Shijie Liao
- Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Juliang He
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, People’s Republic of China
| | - Mingwei He
- Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Tianyu Xie
- Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Xiaohong Jiang
- Department of Orthopedic, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Boxiang Li
- Department of Orthopedic, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Huijiang Liu
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
- Department of Orthopedics, The First People’s Hospital of Nanning, Nanning, 530021, Guangxi, People’s Republic of China
| | - Qian Huang
- Department of Orthopedics, The First People’s Hospital of Nanning, Nanning, 530021, Guangxi, People’s Republic of China
| | - Haijun Tang
- Department of Orthopedic, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
| | - Wenyu Feng
- Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
- Correspondence: Xinli Zhan, Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China, Tel +86 771-5350189, Fax +867715350001, Email ; Wenyu Feng, Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China, Tel +86 18277185646, Fax +867715350001, Email
| | - Xinli Zhan
- Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China
- Correspondence: Xinli Zhan, Department of Spinal Bone Disease, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China, Tel +86 771-5350189, Fax +867715350001, Email ; Wenyu Feng, Department of Trauma Orthopedic and Hand Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People’s Republic of China, Tel +86 18277185646, Fax +867715350001, Email
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