1
|
Zhan Z, Lin K, Wang T. Construction of oxidative phosphorylation-related prognostic risk score model in uveal melanoma. BMC Ophthalmol 2024; 24:204. [PMID: 38698303 PMCID: PMC11067154 DOI: 10.1186/s12886-024-03441-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/09/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Uveal melanoma (UVM) is a malignant intraocular tumor in adults. Targeting genes related to oxidative phosphorylation (OXPHOS) may play a role in anti-tumor therapy. However, the clinical significance of oxidative phosphorylation in UVM is unclear. METHOD The 134 OXPHOS-related genes were obtained from the KEGG pathway, the TCGA UVM dataset contained 80 samples, served as the training set, while GSE22138 and GSE39717 was used as the validation set. LASSO regression was carried out to identify OXPHOS-related prognostic genes. The coefficients obtained from Cox multivariate regression analysis were used to calculate a risk score, which facilitated the construction of a prognostic model. Kaplan-Meier survival analysis, logrank test and ROC curve using the time "timeROC" package were conducted. The immune cell frequency in low- and high-risk group was analyzed through Cibersort tool. The specific genomic alterations were analyzed by "maftools" R package. The differential expressed genes between low- or high-risk group were analyzed and performed Gene Ontology (GO) and GSEA. Finally, we verified the function of CYC1 in UVM by gene silencing in vitro. RESULTS A total of 9 OXPHOS-related prognostic genes were identified, including NDUFB1, NDUFB8, ATP12A, NDUFA3, CYC1, COX6B1, ATP6V1G2, ATP4B and NDUFB4. The UVM prognostic risk model was constructed based on the 9 OXPHOS-related prognostic genes. The prognosis of patients in the high-risk group was poorer than low-risk group. Besides, the ROC curve demonstrated that the area under the curve of the model for predicting the 1 to 5-year survival rate of UVM patients were all more than 0.88. External validation in GSE22138 and GSE39717 dataset revealed that these 9 genes could also be utilized to evaluate and predict the overall survival of patients with UVM. The risk score levels related to immune cell frequency and specific genomic alterations. The DEGs between the low- and high- risk group were enriched in tumor OXPHOS and immune related pathway. In vitro experiments, CYC1 silencing significantly inhibited UVM cell proliferation and invasion, induced cell apoptosis. CONCLUSION In sum, a prognostic risk score model based on oxidative phosphorylation-related genes in UVM was developed to enhance understanding of the disease. This prognostic risk score model may help to find potential therapeutic targets for UVM patients. CYC1 acts as an oncogene role in UVM.
Collapse
Affiliation(s)
- Zhiyun Zhan
- Ophthalmology Department, First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang District, 350004, Fuzhou, Fujian, China
| | - Kun Lin
- Department of Neurosurgery, Shengli Clinical Medical College of Fujian Medical University, 516 Jinrong South Road, 350001, Fuzhou, China
| | - Tingting Wang
- Ophthalmology Department, First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang District, 350004, Fuzhou, Fujian, China.
| |
Collapse
|
2
|
Zhao M, Yu Y, Song Z. Identification and validation of a costimulatory molecule-related signature to predict the prognosis for uveal melanoma patients. Sci Rep 2024; 14:9146. [PMID: 38644411 PMCID: PMC11033288 DOI: 10.1038/s41598-024-59827-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 04/16/2024] [Indexed: 04/23/2024] Open
Abstract
Uveal melanoma (UVM) is the most common primary tumor in adult human eyes. Costimulatory molecules (CMs) are important in maintaining T cell biological functions and regulating immune responses. To investigate the role of CMs in UVM and exploit prognostic signature by bioinformatics analysis. This study aimed to identify and validate a CMs associated signature and investigate its role in the progression and prognosis of UVM. The expression profile data of training cohort and validation cohort were downloaded from The Cancer Genome Atlas (TCGA) dataset and the Gene Expression Omnibus (GEO) dataset. 60 CM genes were identified, and 34 genes were associated with prognosis by univariate Cox regression. A prognostic signature was established with six CM genes. Further, high- and low-risk groups were divided by the median, and Kaplan-Meier (K-M) curves indicated that high-risk patients presented a poorer prognosis. We analyzed the correlation of gender, age, stage, and risk score on prognosis by univariate and multivariate regression analysis. We found that risk score was the only risk factor for prognosis. Through the integration of the tumor immune microenvironment (TIME), it was found that the high-risk group presented more immune cell infiltration and expression of immune checkpoints and obtained higher immune scores. Enrichment analysis of the biological functions of the two groups revealed that the differential parts were mainly related to cell-cell adhesion, regulation of T-cell activation, and cytokine-cytokine receptor interaction. No differences in tumor mutation burden (TMB) were found between the two groups. GNA11 and BAP1 have higher mutation frequencies in high-risk patients. Finally, based on the Genomics of Drug Sensitivity in Cancer 2 (GDSC2) dataset, drug sensitivity analysis found that high-risk patients may be potential beneficiaries of the treatment of crizotinib or temozolomide. Taken together, our CM-related prognostic signature is a reliable biomarker that may provide ideas for future treatments for the disease.
Collapse
Affiliation(s)
- Minyao Zhao
- Department of Ophthalmology, Shanghai Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yue Yu
- Department of Ophthalmology, Shanghai Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhengyu Song
- Department of Ophthalmology, Shanghai Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| |
Collapse
|
3
|
Barbagallo C, Stella M, Broggi G, Russo A, Caltabiano R, Ragusa M. Genetics and RNA Regulation of Uveal Melanoma. Cancers (Basel) 2023; 15:775. [PMID: 36765733 PMCID: PMC9913768 DOI: 10.3390/cancers15030775] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Uveal melanoma (UM) is the most common intraocular malignant tumor and the most frequent melanoma not affecting the skin. While the rate of UM occurrence is relatively low, about 50% of patients develop metastasis, primarily to the liver, with lethal outcome despite medical treatment. Notwithstanding that UM etiopathogenesis is still under investigation, a set of known mutations and chromosomal aberrations are associated with its pathogenesis and have a relevant prognostic value. The most frequently mutated genes are BAP1, EIF1AX, GNA11, GNAQ, and SF3B1, with mutually exclusive mutations occurring in GNAQ and GNA11, and almost mutually exclusive ones in BAP1 and SF3B1, and BAP1 and EIF1AX. Among chromosomal aberrations, monosomy of chromosome 3 is the most frequent, followed by gain of chromosome 8q, and full or partial loss of chromosomes 1 and 6. In addition, epigenetic mechanisms regulated by non-coding RNAs (ncRNA), namely microRNAs and long non-coding RNAs, have also been investigated. Several papers investigating the role of ncRNAs in UM have reported that their dysregulated expression affects cancer-related processes in both in vitro and in vivo models. This review will summarize current findings about genetic mutations, chromosomal aberrations, and ncRNA dysregulation establishing UM biology.
Collapse
Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Andrea Russo
- Department of Ophthalmology, University of Catania, 95123 Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| |
Collapse
|
4
|
Lu J, Tan J, Yu X. A prognostic model based on tumor microenvironment-related lncRNAs predicts therapy response in pancreatic cancer. Funct Integr Genomics 2023; 23:32. [PMID: 36625842 DOI: 10.1007/s10142-023-00964-x] [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: 10/08/2022] [Revised: 12/21/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023]
Abstract
Pancreatic cancer is an aggressive malignant tumor with high mortality and a low survival rate. The immune and stromal cells that infiltrate in the tumor microenvironment (TME) significantly impact immunotherapy and drug responses. Therefore, we identify the TME-related lncRNAs to develop a prognostic model for predicting the therapy efficacy in pancreatic cancer patients. Firstly, we identified differentially expressed genes (DEGs) for weighted gene co-expression network analysis (WGCNA) to identify the TME-related module eigengenes. According to the module eigengenes, the TME-related prognostic lncRNAs were screened through the univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox analyses to construct a prognostic risk score (RS) model. Next, the predictive power of this model was evaluated by the time-dependent receiver operating characteristic (ROC) curve and Kaplan-Meier analyses. In addition, functional enrichment, immune cell infiltration, and somatic mutation analyses were performed. Finally, tumor immune dysfunction and exclusion (TIDE) score and drug sensitivity analyses were applied to predict therapy response. In this study, 11 TME-related prognostic lncRNAs were identified to develop the prognostic RS model. According to the RS, the low-risk patients had a better prognosis, lower rates of somatic mutation, lower TIDE scores, and higher sensitivity to gemcitabine and paclitaxel compared to high-risk patients. The findings above suggested that low-risk patients may benefit more from immunotherapy, and high-risk patients may benefit more from chemotherapy. Within this study, we established a prognostic RS model based on 11 TME-related lncRNAs, which may help improve clinical decision-making.
Collapse
Affiliation(s)
- Jianzhong Lu
- School of Sciences, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Jinhua Tan
- School of Sciences, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Xiaoqing Yu
- School of Sciences, Shanghai Institute of Technology, Shanghai, 201418, China.
| |
Collapse
|
5
|
Li AA, Li F, Lan M, Zhang Y, Xie D, Yan MY. A novel endoplasmic reticulum stress-related lncRNA prognostic risk model for cutaneous melanoma. J Cancer Res Clin Oncol 2022; 148:3227-3241. [PMID: 35687183 DOI: 10.1007/s00432-022-04086-y] [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: 04/06/2022] [Accepted: 05/20/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Endoplasmic reticulum stress (ERS) and long non-coding RNAs (lncRNAs) are important in melanoma development and progression. This study aimed to explore the prognostic value of ERS-associated lncRNA profiles in cutaneous melanoma (CM). METHODS The Cancer Genome Atlas (TCGA) provides the raw data of CM. GSEA website was used to obtain ERS-related genes, and mRNA and LncRNA co-expression network were used to obtain ERS-related lncRNAs. A Lasso regression analysis was used to identify a prognostic risk model for the composition of ERS-related lncRNAs. Patients were divided into high- and low-risk groups based on the model's risk score. The researchers then compared the two groups' survival rates, immune infiltration, chemotherapeutic drug sensitivity, and immune checkpoint gene expression. RESULTS Thirty-nine ERS-related lncRNAs were discovered to be prognostic. A prognostic risk model made up of ten ERS-related lncRNAs was discovered. Patients in the low-risk group had a better prognosis than those in the high-risk group. An examination of tumor microenvironment revealed that risk scores correlated with immune cell infiltration in eight cases. Dacarbazine, paclitaxel, and cisplatin, three chemotherapy drugs, were more sensitive in the low-risk group than in the high-risk group. CONCLUSION This study identified a risk model of ten ERS-related lncRNAs that have significant prognostic value in CM and could help guide clinical treatment.
Collapse
Affiliation(s)
- An-An Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Fan Li
- Ji'an College, Ji'an, Jiangxi, People's Republic of China
| | - Min Lan
- Department of Orthopedic Surgery, Jiangxi Provincial People's Hospital, Nanchang, Jiangxi, People's Republic of China
| | - Yu Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Dong Xie
- Department of Dermatology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Mei-Ying Yan
- Medical Imaging Center, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Road, Donghu District, Nanchang, 330006, Jiangxi, People's Republic of China.
| |
Collapse
|
6
|
Li W, Yang G, Dong H, Zhu J, Liu T. A prognostic signature based on cuprotosis-related long non-coding RNAs predicts the prognosis and sensitivity to chemotherapy in patients with colorectal cancer. Front Med (Lausanne) 2022; 9:1055785. [PMCID: PMC9709405 DOI: 10.3389/fmed.2022.1055785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022] Open
Abstract
Cuprotosis, a newly proposed mechanism of cell death, can trigger acute oxidative stress that leads to cell death by mediating protein lipidation in the tricarboxylic acid cycle. However, cuprotosis-related long non-coding RNAs (CRLNCs) and their relationship with prognosis and the immunological landscape of colorectal cancer (CRC) are unclear. We have developed a lncRNA signature to predict survival time, immune infiltration, and sensitivity to chemotherapy. CRLNCs were screened using the Cor function of the R software and the differentially expressed lncRNAs were collected with the limma package. Differentially expressed long non-coding RNAs (lncRNAs) associated with prognosis were selected using univariate regression analysis. A prognostic signature was developed using the least absolute shrinkage and selection operator (LASSO) and multivariate regression analysis. Patients with CRC were divided into two groups based on the risk score. The low-risk group had a more favorable prognosis, higher expression of immune checkpoints, and a higher level of immune cell infiltration compared with the high-risk group. Furthermore, there was a close association between the risk score and the clinical stage, tumor mutational burden, cancer stem cell index, and microsatellite instability. We also assessed chemotherapy response in the two risk groups. Our study analyzed the role of CRLNCs in CRC and provided novel targets and strategies for CRC chemotherapy and immunotherapy.
Collapse
Affiliation(s)
- Wei Li
- Department of Colorectal and Anal Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Guiyun Yang
- Department of Operating Room, The Second Hospital of Jilin University, Changchun, China
| | - Hao Dong
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Jiajing Zhu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, China
- *Correspondence: Jiajing Zhu,
| | - Tongjun Liu
- Department of Colorectal and Anal Surgery, The Second Hospital of Jilin University, Changchun, China
- Tongjun Liu,
| |
Collapse
|
7
|
Identification of Immune-Related lncRNAs for Predicting Prognosis and Immune Landscape Characteristics of Uveal Melanoma. JOURNAL OF ONCOLOGY 2022; 2022:7680657. [DOI: 10.1155/2022/7680657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/18/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022]
Abstract
Immune-related genes and long noncoding RNAs (lncRNAs) have a significant impact on the prognostic value and immunotherapeutic response of uveal melanoma (UM). Therefore, we tried to develop a prognostic model on the basis of irlncRNAs for predicting prognosis and response on immunotherapy of UM patients. We identified 1,664 immune-related genes and 2,216 immune-related lncRNAs (irlncRNAs) and structured a prognostic model with 3 prognostic irlncRNAs by co-expression analysis, univariable Cox, LASSO, and multivariate Cox regression analyses. The Kaplan–Meier analysis indicated that patients in the high-risk group had a shorter survival time than patients in the low-risk group. The ROC curves demonstrated the high sensitivity and specificity of the signature for survival prediction, and the one-, three-, and five-year AUC values, respectively, were 0.974, 0.929, and 0.941 in the entire set. Cox regression analysis, C-index, DCA, PCA analysis, and nomogram were also applied to assess the validity and accuracy of the risk model. The GO and KEGG enrichment analyses indicated that this signature is significantly related to immune-related pathways and molecules. Finally, we investigated the immunological characteristics and immunotherapy of the model and identified various novel potential compounds in the model for UM. In summary, we constructed a new model on the basis of irlncRNAs that can accurately predict prognosis and response on immunotherapy of UM patients, which may provide valuable clinical applications in antitumor immunotherapy.
Collapse
|