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Li X, Kang J, Yue J, Xu D, Liao C, Zhang H, Zhao J, Liu Q, Jiao J, Wang L, Li G. Identification and validation of immunogenic cell death-related score in uveal melanoma to improve prediction of prognosis and response to immunotherapy. Aging (Albany NY) 2023; 15:3442-3464. [PMID: 37142279 PMCID: PMC10449274 DOI: 10.18632/aging.204680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Immunogenic cell death (ICD) could activate innate and adaptive immune response. In this work, we aimed to develop an ICD-related signature in uveal melanoma (UVM) patients and facilitate assessment of their prognosis and immunotherapy. METHODS A set of machine learning methods, including non-negative matrix factorization (NMF) method and least absolute shrinkage and selection operator (LASSO) logistic regression model, and bioinformatics analytic tools were integrated to construct an ICD-related risk score (ICDscore). CIBERSORT and ESTIMATE algorithms were used to evaluate the infiltration of immune cells. The Genomics of Drug Sensitivity in Cancer (GDSC), cellMiner and tumor immune dysfunction and exclusion (TIDE) databases were used for therapy sensitivity analyses. The predictive performance between ICDscore with other mRNA signatures was also compared. RESULTS The ICDscore could predict the prognosis of UVM patients in both the training and four validating cohorts. The ICDscore outperformed 19 previously published signatures. Patients with high ICDscore exhibited a substantial increase in immune cell infiltration and expression of immune checkpoint inhibitor-related genes, leading to a higher response rate to immunotherapy. Furthermore, the downregulation of poly (ADP-ribose) polymerase family member 8 (PARP8), a critical gene involved in the development of the ICDscore, resulted in decreased cell proliferation and slower migration of UVM cells. CONCLUSION In conclusion, we developed a robust and powerful ICD-related signature for evaluating the prognosis and benefits of immunotherapy that could serve as a promising tool to guide decision-making and surveillance for UVM patients.
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Affiliation(s)
- Xiaoyan Li
- Department of Central Laboratory, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi, China
- Department of Blood Transfusion, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi, China
| | - Jing Kang
- Department of Clinical Laboratory, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jing Yue
- Department of Clinical Laboratory, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Dawei Xu
- Department of Blood Transfusion, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi, China
| | - Chunhua Liao
- Department of Physiotherapy and Rehabilitation, The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Huina Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jin Zhao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Qiongwen Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinke Jiao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Lin Wang
- Department of Geriatrics, Xijing Hospital, The Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Shaanxi Normal University, Xi’an, Shaanxi, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
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Yin Y, Du W, Li F. The construction of a hypoxia-based signature identified CA12 as a risk gene affecting uveal melanoma cell malignant phenotypes and immune checkpoint expression. Front Oncol 2022; 12:1008770. [PMID: 36226072 PMCID: PMC9548707 DOI: 10.3389/fonc.2022.1008770] [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: 08/01/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
Uveal melanoma (UM) is a deadly intraocular neoplasm in the adult population and harbors limited therapeutic effects from the current treatment. Here, we aimed to investigate the role of hypoxia in UM progress. We adopted the Cancer Genome Atlas data set as a training cohort and Gene Expression Omnibus data sets as validating cohorts. We first used consensus clustering to identify hypoxia-related subtypes, and the C1 subtype predicted an unfavorable prognosis and exhibited high infiltration of immunocytes and globally elevated immune checkpoint expression. Besides this, the patients with the C1 subtype were predicted to respond to the PD-1 treatment. By the least absolute shrinkage and selection operator algorithm, we constructed a hypoxia risk score based on the hypoxia genes and identified 10 genes. The risk score predicted patient survival with high performance, and the high-risk group also harbored high immunocyte infiltration and immune checkpoint expression. Furthermore, we confirmed that the risk genes were upregulated under hypoxia, and knockdown of CA12 inhibited the epithelial–mesenchymal transition process, clone formation ability, and G1/S phase transformation of the UM cells. The CD276 was also downregulated when CA12 knockdown was performed. These results validate the prognostic role of the hypoxia signature in UM and demonstrate that CA12 is a critical factor for UM cell progression as well as a target to improve immunotherapeutic effects. We believe our study contributes to the understanding of hypoxia’s roles in UM and provides a novel target that will benefit future therapeutic strategy development.
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Affiliation(s)
- Yan Yin
- Department of Ophthalmology, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Wei Du
- Department of Ophthalmology, The Shandong Second Rehabilitation Hospital, Taian, China
| | - Fei Li
- Department of Medicine, Shandong First Medical University, Taian, China
- *Correspondence: Fei Li,
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