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Zhao R, Jiang Y, Zhang J, Huang Y, Xiong C, Zhao Z, Huang T, Liu W, Zhou N, Li Z, Luo X, Tang Y. Development and validation of a novel necroptosis-related gene signature for predicting prognosis and therapeutic response in Ewing sarcoma. Front Med (Lausanne) 2023; 10:1239487. [PMID: 37663658 PMCID: PMC10470467 DOI: 10.3389/fmed.2023.1239487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
Ewing sarcoma (ES) is the second most common malignant bone tumor in children and has a poor prognosis due to early metastasis and easy recurrence. Necroptosis is a newly discovered cell death method, and its critical role in tumor immunity and therapy has attracted widespread attention. Thus, the emergence of necroptosis may provide bright prospects for the treatment of ES and deserves our further study. Here, based on the random forest algorithm, we identified 6 key necroptosis-related genes (NRGs) and used them to construct an NRG signature with excellent predictive performance. Subsequent analysis showed that NRGs were closely associated with ES tumor immunity, and the signature was also good at predicting immunotherapy and chemotherapy response. Next, a comprehensive analysis of key genes showed that RIPK1, JAK1, and CHMP7 were potential therapeutic targets. The Cancer Dependency Map (DepMap) results showed that CHMP7 is associated with ES cell growth, and the Gene Set Cancer Analysis (GSCALite) results revealed that the JAK1 mutation frequency was the highest. The expression of 3 genes was all negatively correlated with methylation and positively with copy number variation (CNV). Finally, an accurate nomogram was constructed with this signature and clinical traits. In short, this study constructed an accurate prognostic signature and identified 3 novel therapeutic targets against ES.
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Affiliation(s)
- Runhan Zhao
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Yu Jiang
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Jun Zhang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Yanran Huang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Chuang Xiong
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Zenghui Zhao
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Tianji Huang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Wei Liu
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Nian Zhou
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Zefang Li
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Orthopedics, Qianjiang Central Hospital of Chongqing, Chongqing, China
| | - Xiaoji Luo
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Yongli Tang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Zhao J, Guan K, Xing J. Construction and evaluation of an aging-associated genes-based model for pancreatic adenocarcinoma prognosis and therapies. Int J Immunopathol Pharmacol 2023; 37:3946320231172072. [PMID: 37072128 PMCID: PMC10127222 DOI: 10.1177/03946320231172072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Objectives: Pancreatic adenocarcinoma (PAAD) is a highly malignant tumor. Despite extensive research, the precise role of aging-related genes in the initiation, microenvironment regulation, and progression of PAAD remains unclear.Methods: Patients with PAAD were selected from the International Cancer Genome Consortium (ICGC), and The Cancer Genome Atlas (TCGA) cohorts and the cell senescence-associated genes were obtained from CellAge. ConsensusClusterPlus was utilized for cluster identification. The least absolute shrinkage and selection operator (LASSO) Cox regression analysis was performed to construct a prognosis prediction model.Results: We identified three clusters (C1, C2, and C3) based on aging-associated gene profiles. The C1 cluster had a shorter overall survival time, advanced clinical grades, lower immune ESTIMATE score, and tumor immune dysfunction and exclusion (TIDE) score than the C3 subgroup. Moreover, signaling pathways for cell cycle activation were enriched in the C1 cluster. We also identified eight hub genes and constructed a risk model. The high cellular senescence-related signature (CSRS) score subtype exhibited poor prognosis, advanced clinical grades, M2 macrophage infiltration, higher immune checkpoint gene expression, and lower immunotherapeutic benefits.Conclusion: Our risk score model shows high prediction accuracy and survival prediction ability in individual clinical prognosis and pre-immunotherapy evaluation.
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Affiliation(s)
- Junjie Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Chin
| | - Kelei Guan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Chin
| | - Jiyuan Xing
- Infectious Diseases Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Jia M, Liu C, Liu Y, Bao Z, Jiang Y, Sun X. Discovery and Validation of a SIT1-Related Prognostic Signature Associated with Immune Infiltration in Cutaneous Melanoma. J Pers Med 2022; 13:jpm13010013. [PMID: 36675674 PMCID: PMC9866779 DOI: 10.3390/jpm13010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Signaling threshold regulating transmembrane adaptor 1 (SIT1) encodes a disulfide-linked homodimeric lymphocyte-specific glycoprotein involved in immune cell activation. However, the relationship between SIT1 and the prognosis of skin cutaneous melanoma (SKCM) and tumor-infiltrating lymphocytes remains elusive. Here, we first compared the differences in SIT1 expression levels between SKCM tissues and adjacent normal tissues. Next, we found that the immune cell infiltration levels and signature pattern of immune infiltration were positively associated with the SIT1 gene mRNA levels. TCGA_SKCM RNA-seq data unveiled that the SIT1 upregulated several immune-associated signaling pathways in GSEA analysis. The high expression of SIT1 was closely related to improved survival in patients with SKCM. A pathway enrichment analysis of SIT1-associated immunomodulators indicated the involvement of the NF-κB signaling pathways. Based on SIT1-associated immunomodulators, we built a 13-gene signature by LASSO Cox regression which served as an independent prognostic factor for the survival of melanoma patients. By using the signature risk score, we achieved a good prediction result for the immunotherapy response and survival of SKCM patients. Our findings provided evidence for SIT1's implication in tumor immunity and survival of SKCM patients. The nominated immune signature is a promising predictive model for prognosis and immunotherapy sensitivity in SKCM patients.
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Affiliation(s)
- Ming Jia
- Department of Cancer Center, The Secondary Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - Chengfei Liu
- Department of Cancer Center, The Secondary Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - Yuean Liu
- Department of Pharmacy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Zhengqiang Bao
- Department of Cancer Center, The Secondary Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - Yuhua Jiang
- Department of Cancer Center, The Secondary Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
- Correspondence: (Y.J.); (X.S.)
| | - Xifeng Sun
- Department of Emergency Medicine, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan 250012, China
- Correspondence: (Y.J.); (X.S.)
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Zi Q, Cui H, Liang W, Chi Q. Machine learning algorithm and deep neural networks identified a novel subtype in hepatocellular carcinoma. Cancer Biomark 2022; 35:305-320. [DOI: 10.3233/cbm-220147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors. Due to the lack of specific characteristics in the early stage of the disease, patients are usually diagnosed in the advanced stage of disease progression. OBJECTIVE: This study used machine learning algorithms to identify key genes in the progression of hepatocellular carcinoma and constructed a prediction model to predict the survival risk of HCC patients. METHODS: The transcriptome data and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The differential expression analysis and COX proportional-hazards model participated in the identification of survival-related genes. K-Means, Random forests, and LASSO regression are involved in identifying novel subtypes of HCC and screening key genes. The prediction model was constructed by deep neural networks (DNN), and Gene Set Enrichment Analysis (GSEA) reveals the metabolic pathways where key genes are located. RESULTS: Two subtypes were identified with significantly different survival rates (p< 0.0001, AUC = 0.720) and 17 key genes associated with the subtypes. The accuracy rate of the deep neural network prediction model is greater than 93.3%. The GSEA analysis found that the survival-related genes were significantly enriched in hallmark gene sets in the MSigDB database. CONCLUSIONS: In this study, we used machine learning algorithms to screen out 17 genes related to the survival risk of HCC patients, and trained a DNN model based on them to predict the survival risk of HCC patients. The genes that make up the model are all key genes that affect the formation and development of cancer.
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Affiliation(s)
- Quan Zi
- Department of Engineering Structure and Mechanics, Wuhan University of Technology, Wuhan, Hubei, China
| | - Hanwei Cui
- Department of Science and Education, Shenzhen Samii Medical Center, Shenzhen, Guangdong, China
| | - Wei Liang
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Qingjia Chi
- Department of Engineering Structure and Mechanics, Wuhan University of Technology, Wuhan, Hubei, China
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Characterization of Aging-Related Genes to Predict Prognosis and Evaluate the Tumor Immune Microenvironment in Malignant Melanoma. JOURNAL OF ONCOLOGY 2022; 2022:1271378. [PMID: 35368886 PMCID: PMC8970875 DOI: 10.1155/2022/1271378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/25/2022] [Indexed: 12/18/2022]
Abstract
Objective. Malignant melanoma (MM) is one of the most malignant types of skin cancer and its incidence and mortality rates are increasing worldwide. Aging is well recognized as a significant risk factor for cancer. However, few studies have analyzed in depth the association between aging-related genes (AGs) and malignant melanoma prognosis with tumor immune microenvironment. Methods. Here, we downloaded 471 MM patients from The Cancer Genome Atlas (TCGA) with RNA sequence and clinicopathological data. 58 AGs from the TCGA dataset were examined using Cox regression and the LASSO assay. As a result, a gene signature for aging-related genes was created. The time-dependent ROC curve and Kaplan–Meier analysis were calculated to determine its predictive capability. Moreover, we created a nomogram for the clinicopathologic variables and the AGs gene signature to determine overall survival (OS). We also explored the association between three immune checkpoints, immune cell infiltration, and the aging-related gene signature. Results. We established an aging risk model to identify and predict the immune microenvironment in malignant melanoma. Then we developed and validated a prognosis risk model using three AGs (CSNK1E, C1QA, and SOD-2) in the GSE65904 dataset. The aging signature was positively associated with clinical and molecular characteristics and can be used as a prognostic factor for malignant melanoma. The low aging risk score was associated with a poor prognosis and indicated an immunosuppressive microenvironment. Conclusions. To summarize, we established and validated a model of aging risk based on three aging-related genes that acted as an independent prognostic predictor of overall survival. Besides, it also characterized the immune response in the malignant melanoma microenvironment and could provide a potential indicator of individualized immunotherapy in malignant melanoma.
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Liu J, Xu J, Luo B, Tang J, Hou Z, Zhu Z, Zhu L, Yao G, Li C. Immune Landscape and an RBM38-Associated Immune Prognostic Model with Laboratory Verification in Malignant Melanoma. Cancers (Basel) 2022; 14:cancers14061590. [PMID: 35326741 PMCID: PMC8946480 DOI: 10.3390/cancers14061590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The primary treatment of malignant melanoma is a classical regimen of surgery combined with chemotherapy, targeted drugs, and immunotherapy. The purpose of this study was to explore the immune response mechanism of RNA binding protein RBM38 in the development of melanoma with the screening of effective immunodiagnostic models and targeted therapy. We found that RBM38, as an oncogene, promotes the proliferation, invasion, and migration of melanoma cells and is associated with immune infiltration and pathways. Our investigation presented the prognostic significance of RBM38-associated immune signature. In addition, this model may provide a potential strategy for improving the survival and immunotherapy of melanoma patients. Abstract Background: Current studies have revealed that RNA-binding protein RBM38 is closely related to tumor development, while its role in malignant melanoma remains unclear. Therefore, this research aimed to investigate the function of RBM38 in melanoma and the prognosis of the disease. Methods: Functional experiments (CCK-8 assay, cell colony formation, transwell cell migration/invasion experiment, wound healing assay, nude mouse tumor formation, and immunohistochemical analysis) were applied to evaluate the role of RBM38 in malignant melanoma. Immune-associated differentially expressed genes (DEGs) on RBM38 related immune pathways were comprehensively analyzed based on RNA sequencing results. Results: We found that high expression of RBM38 promoted melanoma cell proliferation, invasion, and migration, and RBM38 was associated with immune infiltration. Then, a five-gene (A2M, NAMPT, LIF, EBI3, and ERAP1) model of RBM38-associated immune DEGs was constructed and validated. Our signature showed superior prognosis capacity compared with other melanoma prognostic signatures. Moreover, the risk score of our signature was connected with the infiltration of immune cells, immune-regulatory proteins, and immunophenoscore in melanoma. Conclusions: We constructed an immune prognosis model using RBM38-related immune DEGs that may help evaluate melanoma patient prognosis and immunotherapy modalities.
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Affiliation(s)
- Jinfang Liu
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Jun Xu
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Soochow 213000, China;
| | - Binlin Luo
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Jian Tang
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Zuoqiong Hou
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Zhechen Zhu
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Lingjun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China;
| | - Gang Yao
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
- Correspondence: (G.Y.); (C.L.)
| | - Chujun Li
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
- Correspondence: (G.Y.); (C.L.)
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Multi-Level Analysis and Identification of Tumor Mutational Burden Genes across Cancer Types. Genes (Basel) 2022; 13:genes13020365. [PMID: 35205408 PMCID: PMC8872466 DOI: 10.3390/genes13020365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
Tumor mutational burden (TMB) is considered a potential biomarker for predicting the response and effect of immune checkpoint inhibitors (ICIs). However, there are still inconsistent standards of gene panels using next-generation sequencing and poor correlation between the TMB genes, immune cell infiltrating, and prognosis. We applied text-mining technology to construct specific TMB-associated gene panels cross various cancer types. As a case exploration, Pearson’s correlation between TMB genes and immune cell infiltrating was further analyzed in colorectal cancer. We then performed LASSO Cox regression to construct a prognosis predictive model and calculated the risk score of each sample for receiver operating characteristic (ROC) analysis. The results showed that the assessment of TMB gene panels performed well with fewer than 500 genes, highly mutated genes, and the inclusion of synonymous mutations and immune regulatory and drug-target genes. Moreover, the analysis of TMB differentially expressed genes (DEGs) suggested that JAKMIP1 was strongly correlated with the gene expression level of CD8+ T cell markers in colorectal cancer. Additionally, the prognosis predictive model based on 19 TMB DEGs reached AUCs of 0.836, 0.818, and 0.787 in 1-, 3-, and 5-year OS models, respectively (C-index: 0.810). In summary, the gene panel performed well and TMB DEGs showed great potential value in immune cell infiltration and in predicting survival.
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Liu J, Zhou Z, Ma L, Li C, Lin Y, Yu T, Wei JF, Zhu L, Yao G. Effects of RNA methylation N6-methyladenosine regulators on malignant progression and prognosis of melanoma. Cancer Cell Int 2021; 21:453. [PMID: 34446007 PMCID: PMC8393813 DOI: 10.1186/s12935-021-02163-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022] Open
Abstract
Background Melanoma is an extremely aggressive type of skin cancer and experiencing a expeditiously rising mortality in a current year. Exploring new potential prognostic biomarkers and therapeutic targets of melanoma are urgently needed. The ambition of this research was to identify genetic markers and assess prognostic performance of N6-methyladenosine (m6A) regulators in melanoma. Methods Gene expression data and corresponding clinical informations of melanoma patients as well as sequence data of normal controls are collected from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. Quantitative real-time PCR (qRT-PCR) analysis was carried out to detect the RNA expression of IGF2BP3 in A375 cell line, melanoma tissues, and normal tissues. Western blot, cell proliferation, and migration assays were performed to assess the ability of IGF2BP3 in A375 cell line. Results Differently expressed m6A regulators between tumor samples and normal samples were analyzed. A three-gene prognostic signature including IGF2BP3, RBM15B, and METTL16 was constructed, and the risk score of this signature was identified to be an independent prognostic indicator for melanoma. In addition, IGF2BP3 was verified to promote melanoma cell proliferation and migration in vitro and associate with lymph node metastasis in clinical samples. Moreover, risk score and the expression of IGF2BP3 were positively associated with the infiltrating immune cells and these hub genes made excellent potential drug targets in melanoma. Conclusion We identified the genetic changes in m6A regulatory genes and constructed a three-gene risk signature with distinct prognostic value in melanoma. This research provided new insights into the epigenetic understanding of m6A regulators and novel therapeutic strategies in melanoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02163-9.
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Affiliation(s)
- Jinfang Liu
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Zijian Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Ling Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Chujun Li
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yu Lin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Ting Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Lingjun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Gang Yao
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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Oncogenic activity and cellular functionality of melanoma associated antigen A3. Biochem Pharmacol 2021; 192:114700. [PMID: 34303709 DOI: 10.1016/j.bcp.2021.114700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/27/2022]
Abstract
Cancer testis antigen Melanoma associated antigen A3 (MAGE-A3) has been subject of research for many years. Being expressed in various tumor types and influencing proliferation, metastasis, and tumor pathogenicity, MAGE-A3 is an attractive target for cancer therapy, particularly because in healthy tissues, MAGE-A3 is only expressed in testes and placenta. MAGE-A3 acts as a cellular master regulator by stimulating E3 ubiquitin ligase tripartite motif-containing protein 28 (TRIM28), resulting in regulation of various cellular targets. These include tumor suppressor protein p53 and cellular energy sensor AMP-activated protein kinase (AMPK). The restricted expression of MAGE-A3 in tumor cells makes MAGE-A3 an attractive target for vaccine-based immune therapy. However, although phase I and phase II clinical trials involving MAGE-A3-specific immunotherapeutic interventions were promising, large phase III studies failed. This article gives an overview about the role of MAGE-A3 as a cellular master switch and discusses approaches to improve MAGE-A3-based immunotherapies.
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Yuan Y, Zhu Z, Lan Y, Duan S, Zhu Z, Zhang X, Li G, Qu H, Feng Y, Cai H, Song Z. Development and Validation of a CD8+ T Cell Infiltration-Related Signature for Melanoma Patients. Front Immunol 2021; 12:659444. [PMID: 34040608 PMCID: PMC8141567 DOI: 10.3389/fimmu.2021.659444] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
Aim Immunotherapy shows efficacy in only a subset of melanoma patients. Here, we intended to construct a risk score model to predict melanoma patients’ sensitivity to immunotherapy. Methods Integration analyses were performed on melanoma patients from high-dimensional public datasets. The CD8+ T cell infiltration related genes (TIRGs) were selected via TIMER and CIBERSORT algorithm. LASSO Cox regression was performed to screen for the crucial TIRGs. Single sample gene set enrichment analysis (ssGSEA) and ESTIMATE algorithm were used to evaluate the immune activity. The prognostic value of the risk score was determined by univariate and multivariate Cox regression analysis. Results 184 candidate TIRGs were identified in melanoma patients. Based on the candidate TIRGs, melanoma patients were classified into three clusters which were characterized by different immune activity. Six signature genes were further screened out of 184 TIRGs and a representative risk score for patient survival was constructed based on these six signature genes. The risk score served as an indicator for the level of CD8+ T cell infiltration and acted as an independent prognostic factor for the survival of melanoma patients. By using the risk score, we achieved a good predicting result for the response of cancer patients to immunotherapy. Moreover, pan-cancer analysis revealed the risk score could be used in a wide range of non-hematologic tumors. Conclusions Our results showed the potential of using signature gene-based risk score as an indicator to predict melanoma patients’ sensitivity to immunotherapy.
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Affiliation(s)
- Yuan Yuan
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Zheng Zhu
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States
| | - Ying Lan
- School of Nursing, Yueyang Vocational and Technical College, Yueyang, China
| | - Saili Duan
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China.,Xiangya School of Medicine of Central South University, Changsha, China
| | - Ziqing Zhu
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China.,Xiangya School of Medicine of Central South University, Changsha, China
| | - Xi Zhang
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Hui Qu
- Department of Plastic Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan, China
| | - Yanhui Feng
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hui Cai
- Department of Orthopaedics, Loudi Central Hospital, Loudi, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
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Zhou JG, Liang B, Liu JG, Jin SH, He SS, Frey B, Gu N, Fietkau R, Hecht M, Ma H, Gaipl US. Identification of 15 lncRNAs Signature for Predicting Survival Benefit of Advanced Melanoma Patients Treated with Anti-PD-1 Monotherapy. Cells 2021; 10:cells10050977. [PMID: 33922038 PMCID: PMC8143567 DOI: 10.3390/cells10050977] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 02/07/2023] Open
Abstract
The blockade of programmed cell death protein 1 (PD-1) as monotherapy has been widely used in melanoma, but to identify melanoma patients with survival benefit from anti-PD-1 monotherapy is still a big challenge. There is an urgent need for prognostic signatures improving the prediction of immunotherapy responses of these patients. We analyzed transcriptomic data of pre-treatment tumor biopsies and clinical profiles in advanced melanoma patients receiving only anti-PD-1 monotherapy (nivolumab or pembrolizumab) from the PRJNA356761 and PRJEB23709 data sets as the training and validation cohort, respectively. Weighted gene co-expression network analysis was used to identify the key module, then least absolute shrinkage and selection operator was conducted to determine prognostic-related long noncoding RNAs (lncRNAs). Subsequently, the differentially expressed genes between different clusters were identified, and their function and pathway annotation were performed. In this investigation, 92 melanoma patients with complete survival information (51 from training cohort and 41 from validation cohort) were included in our analyses. We initiallyidentified the key module (skyblue) by weighted gene co-expression network analysis, and then identified a 15 predictive lncRNAs (AC010904.2, LINC01126, AC012360.1, AC024933.1, AL442128.2, AC022211.4, AC022211.2, AC127496.5, NARF-AS1, AP000919.3, AP005329.2, AC023983.1, AC023983.2, AC139100.1, and AC012615.4) signature in melanoma patients treated with anti-PD-1 monotherapy by least absolute shrinkage and selection operator in the training cohort. These results were then validated in the validation cohort. Finally, enrichment analysis showed that the functions of differentially expressed genes between two consensus clusters were mainly related to the immune process and treatment. In summary, the 15 lncRNAs signature is a novel effective predictor for prognosis in advanced melanoma patients treated with anti-PD-1 monotherapy.
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Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China; (J.-G.Z.); (S.-S.H.)
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Bo Liang
- Nanjing University of Chinese Medicine, Nanjing 210029, China;
| | - Jian-Guo Liu
- Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical University, Zunyi 563000, China; (J.-G.L.); (S.-H.J.)
| | - Su-Han Jin
- Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical University, Zunyi 563000, China; (J.-G.L.); (S.-H.J.)
| | - Si-Si He
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China; (J.-G.Z.); (S.-S.H.)
| | - Benjamin Frey
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Ning Gu
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210029, China;
| | - Rainer Fietkau
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Markus Hecht
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Hu Ma
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China; (J.-G.Z.); (S.-S.H.)
- Correspondence: (H.M.); (U.S.G.); Tel.: +49-(0)9131-85-44258 (U.S.G.); Fax: +49-(0)9131-85-39335 (U.S.G.)
| | - Udo S. Gaipl
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
- Correspondence: (H.M.); (U.S.G.); Tel.: +49-(0)9131-85-44258 (U.S.G.); Fax: +49-(0)9131-85-39335 (U.S.G.)
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Zhang JA, Zhou XY, Huang D, Luan C, Gu H, Ju M, Chen K. Development of an Immune-Related Gene Signature for Prognosis in Melanoma. Front Oncol 2021; 10:602555. [PMID: 33585219 PMCID: PMC7874014 DOI: 10.3389/fonc.2020.602555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Melanoma remains a potentially deadly malignant tumor. The incidence of melanoma continues to rise. Immunotherapy has become a new treatment method and is widely used in a variety of tumors. Original melanoma data were downloaded from TCGA. ssGSEA was performed to classify them. GSVA software and the "hclust" package were used to analyze the data. The ESTIMATE algorithm screened DEGs. The edgeR package and Venn diagram identified valid immune-related genes. Univariate, LASSO and multivariate analyses were used to explore the hub genes. The "rms" package established the nomogram and calibrated the curve. Immune infiltration data were obtained from the TIMER database. Compared with that of samples in the high immune cell infiltration cluster, we found that the tumor purity of samples in the low immune cell infiltration cluster was higher. The immune score, ESTIMATE score and stromal score in the low immune cell infiltration cluster were lower. In the high immune cell infiltration cluster, the immune components were more abundant, while the tumor purity was lower. The expression levels of TIGIT, PDCD1, LAG3, HAVCR2, CTLA4 and the HLA family were also higher in the high immune cell infiltration cluster. Survival analysis showed that patients in the high immune cell infiltration cluster had shorter OS than patients in the low immune cell infiltration cluster. IGHV1-18, CXCL11, LTF, and HLA-DQB1 were identified as immune cell infiltration-related DEGs. The prognosis of melanoma was significantly negatively correlated with the infiltration of CD4+ T cells, CD8+ T cells, dendritic cells, neutrophils and macrophages. In this study, we identified immune-related melanoma core genes and relevant immune cell subtypes, which may be used in targeted therapy and immunotherapy of melanoma.
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Affiliation(s)
- Jia-An Zhang
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China
| | - Xu-Yue Zhou
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China
| | - Dan Huang
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China
| | - Chao Luan
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China
| | - Heng Gu
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China
| | - Mei Ju
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China
| | - Kun Chen
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, China
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Yu J, Xie M, Ge S, Chai P, Zhou Y, Ruan J. Hierarchical Clustering of Cutaneous Melanoma Based on Immunogenomic Profiling. Front Oncol 2020; 10:580029. [PMID: 33330057 PMCID: PMC7735560 DOI: 10.3389/fonc.2020.580029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022] Open
Abstract
Cutaneous melanoma is an aggressive malignancy with high heterogeneity. Several studies have been performed to identify cutaneous melanoma subtypes based on genomic profiling. However, few classifications based on assessments of immune-associated genes have limited clinical implications for cutaneous melanoma. Using 470 cutaneous melanoma samples from The Cancer Genome Atlas (TCGA), we calculated the enrichment levels of 29 immune-associated gene sets in each sample and hierarchically clustered them into Immunity High (Immunity_H, n=323, 68.7%), Immunity Medium (Immunity_M, n=135, 28.7%), and Immunity Low (Immunity_L, n=12, 2.6%) based on the ssGSEA score. The ESTIMATE algorithm was used to calculate stromal scores (range: -1,800.51-1,901.99), immune scores (range: -1,476.28-3,780.33), estimate scores (range: -2,618.28-5,098.14) and tumor purity (range: 0.216-0.976) and they were significantly correlated with immune subtypes (Kruskal-Wallis test, P < 0.001). The Immunity_H group tended to have higher expression levels of HLA and immune checkpoint genes (Kruskal-Wallis test, P < 0.05). The Immunity_H group had the highest level of naïve B cells, resting dendritic cells, M1 macrophages, resting NK cells, plasma cells, CD4 memory activated T cells, CD8 T cells, follicular helper T cells and regulatory T cells, and the Immunity_L group had better overall survival. The GO terms identified in the Immunity_H group were mainly immune related. In conclusion, immune signature-associated cutaneous melanoma subtypes play a role in cutaneous melanoma prognosis stratification. The construction of immune signature-associated cutaneous melanoma subtypes predicted possible patient outcomes and provided possible immunotherapy candidates.
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Affiliation(s)
| | | | | | - Peiwei Chai
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Yixiong Zhou
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jing Ruan
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
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