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Guo X, Yu X, Zhang Y, Luo H, Huang R, Zeng Y, Duan C, Chen C. A Novel Glycolysis-Related Signature for Predicting the Prognosis and Immune Infiltration of Uveal Melanoma. Ophthalmic Res 2023; 66:692-705. [PMID: 36858025 DOI: 10.1159/000529818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/14/2023] [Indexed: 03/03/2023]
Abstract
INTRODUCTION As the most common aggressive intraocular cancer in adults, uveal melanoma (UVM) threatens the survival and vision of many people. Glycolysis is a novel hallmark of cancer, but the role of glycolysis-related genes in UVM prognosis remains unknown. The purpose of the study was to establish a glycolysis-related gene signature (GRGS) to predict UVM prognosis. METHODS Raw data were obtained from TCGA-UVM and GSE22138 datasets. The GRGS was established by univariate, LASSO, and multivariate Cox regression analyses. Kaplan-Meier survival and time-dependent receiver operating characteristic curves were used to evaluate the predictive ability of the GRGS. The relationships of the GRGS with infiltrating immune cell levels and mutations were analyzed with CIBERSORT and maftools. RESULTS A novel GRGS (risk score = 0.690861*ISG20 + 0.070991*MET - 0.227520*SDC2 + 0.690223*FBP1 + 0.048008*CLN6 - 0.128520*SDC3) was developed for predicting UVM prognosis. The GRGS had robust predictive stability in UVM. Enrichment annotation suggested that the high-risk group had stronger adaptive immune responses and that the low-risk group had more innate immune cell infiltration. Moreover, BAP1 mutation was related to high risk, and SF3B1 mutation was related to low risk. CONCLUSIONS This study developed and validated a novel GRGS to predict UVM prognosis and immune infiltration. The signature revealed an association between glycolysis-related genes and the tumor microenvironment, providing new insights into the role of glycolysis in UVM.
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Affiliation(s)
- Xiaoyu Guo
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China,
| | - Xin Yu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuying Zhang
- Oral Histopathology Department, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei_MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Huijuan Luo
- Department of Ophthalmology, The People's Hospital of Yidu, Yichang, China
| | - Rong Huang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuyang Zeng
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chaoye Duan
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Changzheng Chen
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
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Wang W, Wang S. The prognostic value of immune-related genes AZGP1, SLCO5A1, and CTF1 in Uveal melanoma. Front Oncol 2022; 12:918230. [PMID: 36052234 PMCID: PMC9425775 DOI: 10.3389/fonc.2022.918230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
Objective Uveal melanoma (UM) is an aggressive malignancy with a poor prognosis and no available effective treatment. Therefore, exploring a potential prognostic marker for UM could provide new possibilities for early detection, recurrence, and treatment. Methods In this study, we used “ConsensusClusterPlus” to classify patients with UM into subgroups, screened for significant differences in immune prognostic factors between subgroups, selected three genes using LASSO (Least absolute shrinkage and selection operator) regression to construct a risk model, and performed tumor immune cell infiltration analysis on the risk model. infiltration analysis, and then verified the heterogeneous role of the 3 core genes in other cancers by pan-cancer analysis and validate its expression by RT-qPCR in normal and tumor cells. Results We consistently categorized 80 UM patients into two subgroups after the immunogenetic set, where the UM1 subgroup had a better prognosis than the UM2 subgroup, and used 3 immune-related genes AZGP1, SLCO5A1, and CTF1 to derive risk scores as independent prognostic markers and predictors of UM clinicopathological features. We found significant differences in overall survival (OS) between low- and high-risk groups, and prognostic models were negatively correlated with B cell and myeloid dendritic cell and positively correlated with CD8+ T cell AZGP1 and CTF1 were significantly upregulated in UM cells compared with normal UM cells. Conclusion Immunogens are significantly associated with the prognosis of UM, and further classification based on genetic characteristics may help to develop immunotherapeutic strategies and provide new approaches to develop customized treatment strategies for patients.
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Affiliation(s)
- Wanpeng Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Sha Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- *Correspondence: Sha Wang,
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Development and validation of an immune and stromal prognostic signature in uveal melanoma to guide clinical therapy. Aging (Albany NY) 2020; 12:20254-20267. [PMID: 33100273 PMCID: PMC7655180 DOI: 10.18632/aging.103779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022]
Abstract
The tumor microenvironment is known to play an important role in uveal melanoma. Reliable prognostic signatures are needed to aid high risk patients and improve prognosis. Uveal melanoma tissues from three public datasets were analyzed. RNA sequence data of uveal melanoma and corresponding clinical features were obtained from The Cancer Genome Atlas database. Immune and stromal scores were calculated by applying the "ESTIMATE" algorithm. The samples were divided into high and low immune or stromal score groups. We constructed prognostic models by using the 'lasso' package and tested them for 500 iterations. The cell signature was validated in another GSE44295 and GSE84976 datasets. We found that the median survival time of the low immune/stromal score group is longer than that of the high-score group. Thirteen immune cells and one stromal cell were concerned significant in predicting poor overall survival rate. Finally, a four-cell model was identified. Further validation revealed that the low-risk group has a significantly better survival than the high-risk group in another two datasets (P < 0.05). Moreover, the high-risk group is more sensitive to immunotherapy and chemotherapy. Summarizing, the proposed immune cells signature is a promising biomarker for estimating overall survival in uveal melanoma.
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Tura A, Thieme C, Brosig A, Merz H, Ranjbar M, Vardanyan S, Zuo H, Maassen T, Kakkassery V, Grisanti S. Lower Levels of Adiponectin and Its Receptor Adipor1 in the Uveal Melanomas With Monosomy-3. Invest Ophthalmol Vis Sci 2020; 61:12. [PMID: 32396633 PMCID: PMC7405622 DOI: 10.1167/iovs.61.5.12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Purpose Adiponectin is an insulin-sensitizing and anticarcinogenic hormone that is encoded by a gene on chromosome 3. Here, we analyzed the expression of adiponectin and its receptor Adipor1 in primary uveal melanoma (UM) with regard to the monosomy-3 status and clinical factors, as well as the physiological response of UM cells to adiponectin. Methods Immunohistochemistry was performed on the primary UM of 34 patients. Circulating melanoma cells (CMC) were isolated by immunomagnetic enrichment. Monosomy-3 was evaluated by Immuno-FISH. Gene expression was analyzed using the RNAseq data of The Cancer Genome Atlas study. Cultures of choroidal melanocytes and UM were established from the samples of two patients. The proliferative potential of the UM cell lines Mel-270 and OMM-2.5 was determined by immunocytochemistry, immunoblotting, cell cycle analysis, nucleolar staining, and adenosine triphosphate (ATP) levels. Results UM with monosomy-3 exhibited a lower immunoreactivity for adiponectin and Adipor1, which was associated with monosomy-3-positive CMC and the development of extraocular growth or metastases. Both proteins were more abundant in the irradiated tumors and present in the cultured cells. Gene expression profile indicated the impairment of adiponectin-mediated signaling in the monosomy-3 tumors. Adiponectin induced a significant decline in the ATP levels, Ki-67 expression, cells in the G2/M phase, and nucleolar integrity in UM cultures. Conclusions Adiponectin deficiency appears to enhance the metastatic potential of the UM cells with monosomy-3 and the termination of tumor dormancy. Counteracting insulin resistance and improving the serum adiponectin levels might therefore be a valuable approach to prevent or delay the UM metastases.
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Wan Q, Sang X, Jin L, Wang Z. Alternative Splicing Events as Indicators for the Prognosis of Uveal Melanoma. Genes (Basel) 2020; 11:genes11020227. [PMID: 32098099 PMCID: PMC7074237 DOI: 10.3390/genes11020227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Growing evidence has revealed that abnormal alternative splicing (AS) events are closely related to carcinogenic processes. However, the comprehensive study on the prognostic value of splicing events involved in uveal melanoma (UM) is still lacking. Therefore, splicing data of 80 UM patients were obtained from the Cancer Genome Atlas (TCGA) SpliceSeq and RNA sequence data of UM and patient clinical features were downloaded from the Cancer Genome Atlas (TCGA) database to identify survival related splicing events in UM. As a result, a total of 37996 AS events of 17911 genes in UM were detected, among which 5299 AS events of 3529 genes were significantly associated with UM patients’ survival. Functional enrichment analysis revealed that this survival related splicing genes are corelated with mRNA catabolic process and ribosome pathway. Based on survival related splicing events, seven types of prognostic markers and the final overall prognostic signature could independently predict the overall survival of UM patients. Finally, an 11 spliced gene was identified in the final signature. On the basis of these 11 genes, we constructed a Support Vector Machine (SVM) classifier and evaluated it with leave-one-out cross-validation. The results showed that the 11 genes could determine short- and long-term survival with a predicted accuracy of 97.5%. Besides, the splicing factors and alternative splicing events correlation network was constructed to serve as therapeutic targets for UM treatment. Thus, our study depicts a comprehensive landscape of alternative splicing events in the prognosis of UM. The correlation network and associated pathways would provide additional potential targets for therapy and prognosis.
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Chattopadhyay C, Oba J, Roszik J, Marszalek JR, Chen K, Qi Y, Eterovic K, Robertson AG, Burks JK, McCannel TA, Grimm EA, Woodman SE. Elevated Endogenous SDHA Drives Pathological Metabolism in Highly Metastatic Uveal Melanoma. Invest Ophthalmol Vis Sci 2019; 60:4187-4195. [PMID: 31596927 PMCID: PMC6785781 DOI: 10.1167/iovs.19-28082] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Purpose Metastatic uveal melanoma (UM) has a very poor prognosis and no effective therapy. Despite remarkable advances in treatment of cutaneous melanoma, UM remains recalcitrant to chemotherapy, small-molecule kinase inhibitors, and immune-based therapy. Methods We assessed two sets of oxidative phosphorylation (OxPhos) genes within 9858 tumors across 31 cancer types. An OxPhos inhibitor was used to characterize differential metabolic programming of highly metastatic monosomy 3 (M3) UM. Seahorse analysis and global metabolomics profiling were done to identify metabolic vulnerabilities. Analyses of UM TCGA data set were performed to determine expressions of key OxPhos effectors in M3 and non-M3 UM. We used targeted knockdown of succinate dehydrogenase A (SDHA) to determine the role of SDHA in M3 UM in conferring resistance to OxPhos inhibition. Results We identified UM to have among the highest median OxPhos levels and showed that M3 UM exhibits a distinct metabolic profile. M3 UM shows markedly low succinate levels and has highly increased levels of SDHA, the enzyme that couples the tricarboxylic acid cycle with OxPhos by oxidizing (lowering) succinate. We showed that SDHA-high M3 UM have elevated expression of key OxPhos molecules, exhibit abundant mitochondrial reserve respiratory capacity, and are resistant to OxPhos antagonism, which can be reversed by SDHA knockdown. Conclusions Our study has identified a critical metabolic program within poor prognostic M3 UM. In addition to the heightened mitochondrial functional capacity due to elevated SDHA, M3 UM SDHA-high mediate resistance to therapy that is reversible with targeted treatment.
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Affiliation(s)
| | - Junna Oba
- Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, Texas, United States
| | - Jason Roszik
- Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, Texas, United States
- Genomic Medicine, UT MD Anderson Cancer Center, Houston, Texas, United States
| | - Joseph R Marszalek
- Institute of Applied Cancer Science & Center for Co-Clinical Trials, UT MD Anderson Cancer Center, Houston, Texas, United States
| | - Ken Chen
- Bioinformatics & Computational Biology, UT MD Anderson Cancer Center, Houston, Texas, United States
| | - Yuan Qi
- Bioinformatics & Computational Biology, UT MD Anderson Cancer Center, Houston, Texas, United States
| | - Karina Eterovic
- Bioinformatics & Computational Biology, UT MD Anderson Cancer Center, Houston, Texas, United States
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jared K Burks
- Leukemia, UT MD Anderson Cancer Center, Houston, Texas, United States
| | - Tara A McCannel
- Stein Eye and Doheny Eye Institutes, University of California Los Angeles, Los Angeles, California, United States
| | - Elizabeth A Grimm
- Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, Texas, United States
| | - Scott E Woodman
- Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, Texas, United States
- Systems Biology, UT MD Anderson Cancer Center, Houston, Texas, United States
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Cheng Y, Li Y, Huang X, Wei W, Qu Y. Expression of EZH2 in uveal melanomas patients and associations with prognosis. Oncotarget 2017; 8:76423-76431. [PMID: 29100322 PMCID: PMC5652716 DOI: 10.18632/oncotarget.19462] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 06/13/2017] [Indexed: 12/27/2022] Open
Abstract
Purpose To analyze the prognostic value and potential target for therapeutic intervention of enhancer of zeste homologue 2 (EZH2) in uveal melanomas (UM) patients. Method We analyzed EZH2 expression in 89 primary UM patients by immuno- histochemistry to observe the clinicopathological and prognostic value of EZH2. Results The high levels of mitoses count and Ki67 labeling index had significant correlation with overexpression EZH2 (R = 0.408, P. Conclusion Our critical finding is that overexpression EZH2 in UM can be served as predictive marker and is associated with adverse clinical outcomes. Further observation of EZH2 as a potential therapeutic target in UM is necessary.
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Affiliation(s)
- Ying Cheng
- Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Ying Li
- Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Xin Huang
- Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Wenbin Wei
- Beijing Tongren Hospital, Capital Medical University, Beijing Tongren Eye Center, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Yi Qu
- Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
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