1
|
Ma Z, Wang Y, Yu Y, Fu F, Zhang Y. Exploring diverse programmed cell-death patterns to develop a novel gene signature for predicting the prognosis of lung adenocarcinoma patients. J Thorac Dis 2024; 16:911-923. [PMID: 38505063 PMCID: PMC10944735 DOI: 10.21037/jtd-23-1275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/15/2023] [Indexed: 03/21/2024]
Abstract
Background Programmed cell death (PCD) plays a critical role in tumor progression and malignancy, and exploring its relationship with lung adenocarcinoma (LUAD)'s survival outcomes is important for personalized diagnosis and treatment. This study aimed to identify survival-related genes and construct an effective prognostic indicator for LUAD based on 12 forms of PCD. Methods A total of 1,933 candidate genes related to PCD were collected from published studies and public data center. A prognostic gene signature, called the cell death index (CDI), was established based on RNA-Seq and immunohistochemistry (IHC). IHC staining on tissue microarray was applied for the validation of protein level. Moreover, GSE42127, GSE72094 were used as validation datasets. Results The CDI based on expression level of nine genes (CCNB2, HMGA1, CACNA2D2, BUB1B, BTG2, KIF14, PTGDS, SERPINB5, BRCA1) was highly predictive for overall survival (OS) of LUAD in our cohort [36-month area under the curve (AUC): 0.750, 60-month AUC: 0.809]. The CDI was further validated in independent cohorts (GSE72094, 36-month AUC: 0.717, 60-month AUC: 0.737; GSE42127, 12-month AUC: 0.829, 60-month AUC: 0.663). And the CDI was found to be an independent prognostic factor after adjusting for other clinical characteristics. Furthermore, the high-CDI group was associated with upregulated tumor immune infiltration compared to the low-CDI group. Conclusions This study identified a 9-gene signature (CDI) based on PCD-related genes that accurately predicted the prognosis of LUAD patients. The CDI could serve as a valuable prognostic indicator and guide personalized therapeutic strategies for LUAD.
Collapse
Affiliation(s)
- Zhanming Ma
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yaxin Yu
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fangqiu Fu
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yang Zhang
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| |
Collapse
|
2
|
Ge Z, Song D. A five ferroptosis-related genes risk score for prognostic prediction of osteosarcoma. Medicine (Baltimore) 2022; 101:e32083. [PMID: 36550843 PMCID: PMC9771194 DOI: 10.1097/md.0000000000032083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Osteosarcoma (OS) is the most common bone cancer in adolescents, and has a high propensity to metastasize. Ferroptosis is a unique modality of cell death, driving the metastasis of cancer cells. Identifying ferroptosis-related genes (FRGs) as prognostic factors will be critical to predict the outcomes of OS. This study aimed to explore the prognostic value of FRGs in OS and build a prognostic model to indirectly improve OS patients' outcomes. METHODS OS data were downloaded from the TARGET database and 2 Gene Expression Omnibus datasets. Univariate Cox regression was conducted to assess FRGs. A risk score model basing on 5 FRGs was constructed via LASSO-Cox regression. Multivariate Cox regression analysis was used to determine the independent prognostic factors. The Nomogram model was built using independent prognostic factors. The relationship between the risk score and the immune cell infiltration was estimated by CIBERSORT, and the correlation between the risk score and immune checkpoints was also analyzed. RESULTS Based on the prognosis-related FRGs, we built a regression model: Risk score = (-0.01382853 × ACSL4) - (0.05371778 × HMOX1) - (0.02434655 × GPX4) - (0.16432810 × PRNP) - (0.15567120 × ATG7). OS patients with high risk score tended to suffer from poor prognosis, validated in 2 Gene Expression Omnibus datasets. The Nomogram model showed the combination of the risk score and the tumour-node-metastasis stage improved predictive effectiveness. The risk score was also related to immune cell infiltration and immune checkpoint expression. CONCLUSION The risk score model based on 5 FRGs was a reliable prognostic predictive indicator for OS patients.
Collapse
Affiliation(s)
- Zhanyong Ge
- Department of Orthopaedic, Tianjin Jinnan Hospital, Tianjin, P.R. China
| | - Delei Song
- Department of West Hospital Orthopaedic Trauma, ZiBo Central Hospital, Zibo, P.R. China
- * Correspondence: Delei Song, Department of West Hospital Orthopaedic Trauma, ZiBo Central Hospital, No. 54 Gongqingtuan West Road, Zhangdian District, Zibo, Shandong 255020, P.R. China (e-mail: )
| |
Collapse
|
3
|
Affiliation(s)
- Robert Walters
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, 1 Discovery Drive (Room 238), Rensselaer, New York 12144 USA
| | - Shaker A. Mousa
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, 1 Discovery Drive (Room 238), Rensselaer, New York 12144 USA
| |
Collapse
|