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Zhang M, Wang J, Huo R, Liang Q, Liu J. Association between air pollution and skin cutaneous melanoma: A Mendelian randomization study. Medicine (Baltimore) 2024; 103:e38050. [PMID: 38701275 PMCID: PMC11062689 DOI: 10.1097/md.0000000000038050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
There has been a consistent and notable increase in the global prevalence of skin cutaneous melanoma (SKCM). Although genetic factors are closely associated with the occurrence and development of melanoma, the potential influence of environmental factors cannot be overlooked. The existing literature lacks a definitive consensus on the correlation between air pollution and the incidence rate of SKCM. This study seeks to investigate the causal relationship between air pollution, specifically focusing on particulate matter (PM) 2.5, PM2.5-10, PM10, and nitrogen oxides, and the risk of SKCM. A 2-sample Mendelian randomization (MR) method was applied, utilizing extensive publicly accessible genome-wide association studies summary datasets within European populations. The primary analytical method employed was the inverse variance weighted method. Supplementary methods, including the weighted median model, MR-Egger, simple model, and weighted model, were chosen to ensure robust analysis. Heterogeneity assessment was conducted using Cochran's Q test. To identify potential pleiotropy, both MR-Egger regression and the MR-PRESSO global test were employed. Additionally, a sensitivity analysis was performed using the leave-one-out method. The analysis revealed no statistically significant association between air pollution and SKCM risk, with specific findings as follows: PM2.5 (P = .485), PM2.5-10 (P = .535), PM10 (P = .136), and nitrogen oxides (P = .745). While some results exhibited heterogeneity, all findings demonstrated an absence of pleiotropy. This study did not find substantive evidence supporting a causal relationship between air pollution and the risk of SKCM within European populations. The comprehensive MR analysis, encompassing various pollutants, suggests that environmental factors such as air pollution may not be significant contributors to the development of SKCM.
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Affiliation(s)
- Min Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Jianfeng Wang
- Department of Gastrointestinal Surgery, 970 Hospital of the PLA Joint Logistic Support Force, Yantai, Shandong, P.R. China
| | - Rentao Huo
- The Fourth People’s Hospital of Jinan, Jinan, Shandong, P.R. China
| | - Qian Liang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jian Liu
- Department of Otolaryngology-Head and Neck Surgery, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, P.R. China
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2
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Xu Z, Huang J, Shi W, Qi Y, Yuan F, Lin B. Identification of an anoikis-related gene signature and characterization of immune infiltration in skin cutaneous melanoma. Medicine (Baltimore) 2024; 103:e37900. [PMID: 38669429 PMCID: PMC11049774 DOI: 10.1097/md.0000000000037900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Anoikis is considered strongly associated with a biological procession of tumors. Herein, we utilized anoikis-related genes (ARGs) to predict the prognosis and immunotherapeutic efficacy for skin cutaneous melanoma (SKCM). RNA-seq data were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. After dividing patients into novel subtypes based on the expression of prognostic ARGs, K-M survival was conducted to compare the survival status. Subsequently, differentially expressed ARGs were identified and the predictive model was established. The predictive effects were validated using the areas under the curve about the receiver operating characteristic. Moreover, tumor mutation burden, the enriched functional pathway, immune cells and functions, and the immunotherapeutic response were also analyzed and compared. The distribution of model genes at cell level was visualized by the single-cell seq with tumor immune single-cell hub database. Patients of The Cancer Genome Atlas-SKCM cohort were divided into 2 clusters, the cluster 1 performed a better prognosis. Cluster 2 was more enriched in metabolism-related pathways whereas cluster 1 was more associated with immune pathways. A predictive risk model was established with 6 ARGs, showing the areas under the curves of 1-year, 3-year, and 5-year ROC were 0.715, 0,720, and 0.731, respectively. Moreover, risk score was negatively associated with tumor mutation burden and immune-related pathways enrichment. In addition, patients with high-risk scores performed immunosuppressive status but the decreasing scores enhanced immune cell infiltration, immune function activation, and immunotherapeutic response. In this study, we established a novel signature in predicting prognosis and immunotherapy. It can be considered reliable to formulate the complex treatment for SKCM patients.
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Affiliation(s)
- Ziqian Xu
- Department of Dermatology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Juntao Huang
- Department of Otolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
| | - Weimin Shi
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Qi
- Department of Dermatology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Feng Yuan
- Department of Dermatology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Bingjiang Lin
- Department of Dermatology, The First Affiliated Hospital of Ningbo University, Ningbo, China
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Zhang Z, Zhu H, Hua H. Inhibiting IL11RA to mitigate hepatic metastasis in skin cutaneous melanoma: Comprehensive insights from in vitro and in vivo investigations. Skin Res Technol 2024; 30:e13618. [PMID: 38468436 PMCID: PMC10928329 DOI: 10.1111/srt.13618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 03/13/2024]
Abstract
OBJECTIVE This study aimed to investigate the role of Interleukin-11 receptor alpha (IL11RA) in skin cutaneous melanoma (SKCM) metastasis to the liver. METHODS Human SKCM cell lines (A375, A375-MA2, SK-MEL-28, RPMI-7951) and primary dermal fibroblasts (HDFa) were utilized to assess IL11RA expression. IL11RA siRNA was transfected into RPMI-7951 and A375-MA2 cells for Wound healing and Transwell invasion assays. Il11ra knockout (KO) mice and wild-type (WT) mice were injected with B16-F10 cells into the spleen to evaluate hepatic melanoma metastasis. Correlation between IL11RA and MMP family genes was explored using online databases, including LinkedOmics, TIMER (Tumor Immune Estimation Resource), and GEPIA (Gene Expression Profiling Interactive Analysis). RT-qPCR and Western blotting were performed for expression analysis of Mmp2 and Mmp9 in liver tissues of mice. The impact of IL11RA on the STAT3 pathway was investigated in vitro and in vivo. RESULTS Elevated expression of IL11RA was observed in SKCM cell lines compared to normal cells. IL11RA downregulation significantly inhibited migratory and invasive capabilities of A375-MA2 and RPMI-7951 in vitro. Il11ra gene knockout in mice demonstrated a substantial reduction in hepatic melanoma metastasis. Correlation analyses revealed associations between IL11RA and MMP2/MMP8. Il11ra gene knockout significantly decreased Mmp2 expression while increasing Mmp8 in liver tissues. IL11RA correlated positively with STAT3, and its inhibition led to a suppressed STAT3 pathway in SKCM cells and mouse liver tissue. CONCLUSION IL11RA plays a crucial role in SKCM metastasis, affecting migratory and invasive abilities. Targeting IL11RA may offer a promising avenue for therapeutic interventions in cutaneous melanoma progression.
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Affiliation(s)
- Zhen‐Guo Zhang
- Plastic and Reconstructive SurgeryLishui People’ s HospitalLishuiZhejiangChina
| | - Hong‐Mei Zhu
- General practiceXin Bi Community Health CenterLishuiZhejiangChina
| | - Huai‐Kang Hua
- Plastic and Reconstructive SurgeryLishui People’ s HospitalLishuiZhejiangChina
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Wang Y, Zou L, Song M, Zong J, Wang S, Meng L, Jia Z, Zhao L, Han X, Lu M. Establishment of skin cutaneous melanoma prognosis model based on vascular mimicry risk score. Medicine (Baltimore) 2024; 103:e36679. [PMID: 38363903 PMCID: PMC10869071 DOI: 10.1097/md.0000000000036679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 11/24/2023] [Indexed: 02/18/2024] Open
Abstract
Studies have indicated that Vascular mimicry (VM) could contribute to the unfavorable prognosis of skin cutaneous melanoma (SKCM). Thus, the objective of this study was to identify therapeutic targets associated with VM in SKCM and develop a novel prognostic model. Gene expression data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) were utilized to identify differentially expressed genes (DEGs). By intersecting these DEGs with VM genes, we acquired VM-related DEGs specific to SKCM, and then identified prognostic-related VM genes. A VM risk score system was established based on these prognosis-associated VM genes, and patients were then categorized into high- and low-score groups using the median score. Subsequently, differences in clinical characteristics, gene set enrichment analysis (GSEA), and other analyses were further presented between the 2 groups of patients. Finally, a novel prognostic model for SKCM was established using the VM score and clinical characteristics. 26 VM-related DEGs were identified in SKCM, among the identified DEGs associated with VM in SKCM, 5 genes were found to be prognostic-related. The VM risk score system, comprised of these genes, is an independent prognostic risk factor. There were significant differences between the 2 patient groups in terms of age, pathological stage, and T stage. VM risk scores are associated with epithelial biological processes, angiogenesis, regulation of the SKCM immune microenvironment, and sensitivity to targeted drugs. The novel prognostic model demonstrates excellent predictive ability. Our study identified VM-related prognostic markers and therapeutic targets for SKCM, providing novel insights for clinical diagnosis and treatment.
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Affiliation(s)
- Yubo Wang
- Dalian Medical University, Dalian, China
- Department of Trauma and Tissue Repair Surgery, Dalian Municipal Central Hospital, Dalian, China
| | - Linxuan Zou
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Mingzhi Song
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Junwei Zong
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shouyu Wang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Lei Meng
- The First Affiliated Hospital of Nanhua Medical University, Hengyang, China
| | - Zhuqiang Jia
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Naqu People’s Hospital, Tibet, China
| | - Lin Zhao
- Department of Quality Management, Dalian Municipal Central Hospital, Dalian, China
| | - Xin Han
- Naqu People’s Hospital, Tibet, China
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ming Lu
- Department of Trauma and Tissue Repair Surgery, Dalian Municipal Central Hospital, Dalian, China
- Department of Trauma and Tissue Repair Surgery, Dalian Municipal Central Hospital of Dalian Medical University, Dalian, China
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Arroyo Villora S, Castellanos Silva P, Zenz T, Kwon JS, Schlaudraff N, Nitaj D, Meckbach C, Dammann R, Richter AM. Biomarker RIPK3 Is Silenced by Hypermethylation in Melanoma and Epigenetic Editing Reestablishes Its Tumor Suppressor Function. Genes (Basel) 2024; 15:175. [PMID: 38397165 PMCID: PMC10888250 DOI: 10.3390/genes15020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
For several decades, cancers have demonstrably been one of the most frequent causes of death worldwide. In addition to genetic causes, cancer can also be caused by epigenetic gene modifications. Frequently, tumor suppressor genes are epigenetically inactivated due to hypermethylation of their CpG islands, actively contributing to tumorigenesis. Since CpG islands are usually localized near promoters, hypermethylation of the promoter can have a major impact on gene expression. In this study, the potential tumor suppressor gene Receptor Interacting Serine/Threonine Protein Kinase 3 (RIPK3) was examined for an epigenetic regulation and its gene inactivation in melanomas. A hypermethylation of the RIPK3 CpG island was detected by bisulfite pyrosequencing and was accompanied by a correlated loss of its expression. In addition, an increasing RIPK3 methylation rate was observed with increasing tumor stage of melanomas. For further epigenetic characterization of RIPK3, epigenetic modulation was performed using a modified CRISPR/dCas9 (CRISPRa activation) system targeting its DNA hypermethylation. We observed a reduced fitness of melanoma cells by (re-)expression and demethylation of the RIPK3 gene using the epigenetic editing-based method. The tumor suppressive function of RIPK3 was evident by phenotypic determination using fluorescence microscopy, flow cytometry and wound healing assay. Our data highlight the function of RIPK3 as an epigenetically regulated tumor suppressor in melanoma, allowing it to be classified as a biomarker.
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Affiliation(s)
- Sarah Arroyo Villora
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | | | - Tamara Zenz
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Ji Sun Kwon
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
- Department of Mathematics, Natural Sciences and Computer Science, University of Applied Sciences Mittelhessen, 35390 Giessen, Germany
| | - Nico Schlaudraff
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Dafina Nitaj
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Cornelia Meckbach
- Department of Mathematics, Natural Sciences and Computer Science, University of Applied Sciences Mittelhessen, 35390 Giessen, Germany
| | - Reinhard Dammann
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Antje M. Richter
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
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Wang X, Yang X, Zhang Y, Guo A, Luo S, Xiao M, Xue L, Zhang G, Wang H. Fatty Acid Metabolism-Related lncRNAs are Potential Biomarkers for Predicting Prognoses and Immune Responses in Patients with Skin Cutaneous Melanoma. Clin Cosmet Investig Dermatol 2023; 16:3595-3614. [PMID: 38116144 PMCID: PMC10729836 DOI: 10.2147/ccid.s417805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Introduction Skin cutaneous melanoma is becoming more dangerous since it has a poor prognosis and is resistant to treatment. Previous research has shown that lncRNAs and fatty acid metabolism are essential for numerous biological activities. There are no studies on the relationship between fatty acid metabolism-Related lncRNAs and skin cutaneous melanoma. Methods and Results In order to better understand the prognosis and survival of SKCM patients, we investigated the significance of lncRNAs related to fatty acid metabolism. In this work, we looked at the fatty acid metabolism genes and lncRNAs expression patterns. On the basis of lncRNAs associated with fatty acid metabolism, a nomogram and a prognosis prediction model were created. Based on the profile of lncRNAs associated with fatty acid metabolism, functional and pharmacological sensitivity investigations were also carried out. We also looked at the connection between immunotherapy and the immune response. The findings demonstrated that a risk score model based on 11 essential lncRNAs for fatty acid metabolism may discriminate between the clinical condition of SKCM and more accurately predict prognosis and survival. We conducted quantitative reverse transcription polymerase-chain reaction (RT-PCR) to verify the model. Conclusion These important lncRNAs further showed a strong association with the tumor immune system, and these important lncRNAs also showed a connection between SKCM and chemotherapeutic treatment sensitivity. Our research strives to provide fresh viewpoints and innovative approaches to the treatment and administration of SKCM.
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Affiliation(s)
- Xing Wang
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Department of Dermatovenereology, Baotou Central Hospital, Baotou City, Inner Mongolia, People’s Republic of China
| | - Xiaojing Yang
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Department of Dermatovenereology, the First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, People’s Republic of China
| | - Yiming Zhang
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Afei Guo
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Suju Luo
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Meng Xiao
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Lu Xue
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Guohui Zhang
- Department of Dermatovenereology, Baotou Central Hospital, Baotou City, Inner Mongolia, People’s Republic of China
| | - Huiping Wang
- Department of Dermatovenereology, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
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Cai Z, Duan Y, Li W, Liu Z, Gong Z, Hong S, He X, Xuanyuan X, Chen Y, Bi X, Wang W. FANCI serve as a prognostic biomarker correlated with immune infiltrates in skin cutaneous melanoma. Front Immunol 2023; 14:1295831. [PMID: 38077326 PMCID: PMC10703153 DOI: 10.3389/fimmu.2023.1295831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Background As a member of tumor, Skin cutaneous melanoma (SKCM) poses a serious threat to people's health because of its strong malignancy. Unfortunately, effective treatment methods for SKCM remain lacking. FANCI plays a vital role in the occurrence and metastasis of various tumor types. However, its regulatory role in SKCM is unclear. The purpose of this study was to explore the association of FANCI with SKCM. Methods This study investigated the expression of FANCI in GSE46517, GSE15605, and GSE114445 from the Gene Expression Omnibus database and The Cancer Genome Atlas (TCGA)-SKCM datasets using the package "limma" or "DESeq2" in R environment and also investigated the prognostic significance of FANCI by utilizing the GEPIA database. Additionally, our research made use of real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining to verify FANCI expression between SKCM and normal tissues and developed the knockdown of FANCI in A375 and A875 cells to further analyze the function of FANCI. Finally, this study analyzed the correlation of FANCI and tumor-infiltrating immune cells by CIBERSORT, ESTIMATE, and ssGSEA algorithms. Results The FANCI level was increasing in SKCM tissues from GSE46517, GSE15605, GSE114445, and TCGA-SKCM. However, high FANCI expression correlated with poor overall survival. The RT-qPCR and IHC confirmed the accuracy of bioinformatics. Knocking down FANCI suppresses A375 and A875 cell proliferation, migration, and invasion. FANCI could be involved in the immunological milieu of SKCM by regulating immune responses and infiltrating numerous immune cells, particularly neutrophils, CD8+ T cells, and B cells. Furthermore, patients with SKCM who have a high FANCI expression level are reported to exhibit immunosuppression, whereas those with a low FANCI expression level are more likely to experience positive outcomes from immunotherapy. Conclusions The increased FANCI expression in SKCM can be a prognostic biomarker. Knockdown FANCI can reduce the occurrence and progression of SKCM. The FANCI expression provides a foundation for predicting the immune status and treatment of SKCM.
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Affiliation(s)
- Zhenguo Cai
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yanjuan Duan
- Department of Dermatology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wen Li
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhuohang Liu
- Department of Neurology, Minhang Hospital, Fudan University/Central Hospital of Minhang District, Shanghai, China
| | - Zijun Gong
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sheng Hong
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xu He
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xinyang Xuanyuan
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Youdong Chen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinling Bi
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Wuqing Wang
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Song L, Wang S, Zhang X, Song N, Lu Y, Qin C. Bridging the gap between clear cell renal cell carcinoma and cutaneous melanoma: the role of SCARB1 in dysregulated cholesterol metabolism. Aging (Albany NY) 2023; 15:10370-10388. [PMID: 37801479 PMCID: PMC10599744 DOI: 10.18632/aging.205083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/22/2023] [Indexed: 10/08/2023]
Abstract
OBJECTIVE The metabolism of cholesterol has been found to be closely related to the proliferation, invasion, and metastasis of tumors. The purpose of this study was to investigate the correlation between cholesterol metabolic genes and the prognosis of clear cell renal cell carcinoma (ccRCC). METHODS Gene expression profiles and clinical information of individuals diagnosed with prevalent malignant tumors were obtained from the TCGA database. For survival analysis, Kaplan-Meier curves were used. Consensus clustering was utilized to identify distinct molecular clusters. LASSO regression analysis was utilized to construct a novel prognostic signature. Differential analysis was used to analyze the differences in gene expression and various evaluation indicators between different subgroups. RT-qPCR and Immunohistochemistry were performed to examine the gene expression. Small interfering RNA transfection, CCK-8, and clone formation assays were conducted to verify the function of the target gene in ccRCC cell lines. RESULTS Based on genes involved in cholesterol metabolism related to survival, two molecular ccRCC subtypes were identified with distinct clinical, immune, and biological features. A molecular signature which would be utilized to evaluate the prognosis and the immune status of the tumor microenvironment of ccRCC patients was also established. The SCARB1-mediated cholesterol-dependent metabolism occurred both in ccRCC and skin cutaneous melanoma. CONCLUSION A gene signature related to cholesterol metabolism was developed and validated to forecast the prognosis of ccRCC, demonstrating a correlation with immune infiltration. Cholesterol metabolic genes such as SCARB1, were expected to contribute to the diagnosis and precision treatment of both ccRCC and skin cutaneous melanoma.
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Affiliation(s)
- Lebin Song
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shuai Wang
- Department of Urology, The State Key Lab of Reproductive, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xi Zhang
- Department of Urology, The State Key Lab of Reproductive, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ninghong Song
- Department of Urology, The State Key Lab of Reproductive, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yan Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Chao Qin
- Department of Urology, The State Key Lab of Reproductive, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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Huang Y, Lin A, Gu T, Hou S, Yao J, Luo P, Zhang J. CACNA1C mutation as a prognosis predictor of immune checkpoint inhibitor in skin cutaneous melanoma. Immunotherapy 2023; 15:1275-1291. [PMID: 37584225 DOI: 10.2217/imt-2022-0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Abstract
Aims: There is an urgent need for appropriate biomarkers that can precisely and reliably predict immunotherapy efficacy, as immunotherapy responses can differ in skin cutaneous melanoma (SKCM) patients. Methods: In this study, univariate regression models and survival analysis were used to examine the link between calcium voltage-gated channel subunit alpha 1C (CACNA1C) mutation status and immunotherapy outcome in SKCM patients receiving immunotherapy. Mutational landscape, immunogenicity, tumor microenvironment and pathway-enrichment analyses were also performed. Results: The CACNA1C mutation group had a better prognosis, higher immunogenicity, lower endothelial cell infiltration, significant enrichment of antitumor immune response pathways and significant downregulation of protumor pathways. Conclusion: CACNA1C mutation status is anticipated to be a biomarker for predicting melanoma immunotherapy effectiveness.
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Affiliation(s)
- Yushan Huang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Tianqi Gu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Shuang Hou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Jiarong Yao
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
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Wang F, Cheng F, Zheng F. Bioinformatic-based genetic characterizations of neural regulation in skin cutaneous melanoma. Front Oncol 2023; 13:1166373. [PMID: 37404751 PMCID: PMC10315675 DOI: 10.3389/fonc.2023.1166373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/31/2023] [Indexed: 07/06/2023] Open
Abstract
Background Recent discoveries uncovered the complex cancer-nerve interactions in several cancer types including skin cutaneous melanoma (SKCM). However, the genetic characterization of neural regulation in SKCM is unclear. Methods Transcriptomic expression data were collected from the TCGA and GTEx portal, and the differences in cancer-nerve crosstalk-associated gene expressions between normal skin and SKCM tissues were analyzed. The cBioPortal dataset was utilized to implement the gene mutation analysis. PPI analysis was performed using the STRING database. Functional enrichment analysis was analyzed by the R package clusterProfiler. K-M plotter, univariate, multivariate, and LASSO regression were used for prognostic analysis and verification. The GEPIA dataset was performed to analyze the association of gene expression with SKCM clinical stage. ssGSEA and GSCA datasets were used for immune cell infiltration analysis. GSEA was used to elucidate the significant function and pathway differences. Results A total of 66 cancer-nerve crosstalk-associated genes were identified, 60 of which were up- or downregulated in SKCM and KEGG analysis suggested that they are mainly enriched in the calcium signaling pathway, Ras signaling pathway, PI3K-Akt signaling pathway, and so on. A gene prognostic model including eight genes (GRIN3A, CCR2, CHRNA4, CSF1, NTN1, ADRB1, CHRNB4, and CHRNG) was built and verified by independent cohorts GSE59455 and GSE19234. A nomogram was constructed containing clinical characteristics and the above eight genes, and the AUCs of the 1-, 3-, and 5-year ROC were 0.850, 0.811, and 0.792, respectively. Expression of CCR2, GRIN3A, and CSF1 was associated with SKCM clinical stages. There existed broad and strong correlations of the prognostic gene set with immune infiltration and immune checkpoint genes. CHRNA4 and CHRNG were independent poor prognostic genes, and multiple metabolic pathways were enriched in high CHRNA4 expression cells. Conclusion Comprehensive bioinformatics analysis of cancer-nerve crosstalk-associated genes in SKCM was performed, and an effective prognostic model was constructed based on clinical characteristics and eight genes (GRIN3A, CCR2, CHRNA4, CSF1, NTN1, ADRB1, CHRNB4, and CHRNG), which were widely related to clinical stages and immunological features. Our work may be helpful for further investigation in the molecular mechanisms correlated with neural regulation in SKCM, and in searching new therapeutic targets.
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Affiliation(s)
- Fengdi Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fanjun Cheng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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11
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Lesicka M, Nedoszytko B, Reszka E. Disruptions of Circadian Genes in Cutaneous Melanoma-An In Silico Analysis of Transcriptome Databases. Int J Mol Sci 2023; 24:10140. [PMID: 37373286 DOI: 10.3390/ijms241210140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Circadian genes are a set of genes that regulate the body's internal clock and influence various physiological processes, including sleep-wake cycles, metabolism and immune function. Skin cutaneous melanoma (SKCM) is a type of skin cancer that arises from the pigment-producing cells in the skin and is the most deadly form of skin cancer. This study has investigated the relevance of circadian gene expression and immune infiltrations in the outcomes of cutaneous melanoma patients. In the present study, in silico methods based on the GEPIa, TIMER 2.0 and cBioPortal databases were performed, so as to investigate the transcript level and prognostic value of 24 circadian genes in SKCM and their relationship with the immune infiltration level. The in silico analysis showed that significantly more than half of the investigated circadian genes have an altered transcript pattern in cutaneous melanoma compared to normal skin. The mRNA levels of TIMELES and BHLHE41 were upregulated, whereas those of NFIL3, BMAL1, HLF, TEF, RORA, RORC, NR1D1, PER1, PER2, PER3, CRY2 and BHLHE40 were downregulated. The presented research shows that SKCM patients with at least one alteration of their circadian genes have decreased overall survival. Additionally, majority of the circadian genes are significantly corelated with the immune cells' infiltration level. The strongest correlation was found for neutrophils and was followed by circadian genes: NR1D2 r = 0.52 p < 0.0001, BMAL1 r = 0.509 p < 0.0001; CLOCK r = 0.45 p < 0.0001; CSNKA1A1 r = 0.45 p < 0.0001; RORA r = 0.44 p < 0.0001. The infiltration level of immune cells in skin tumors has been associated with patient prognosis and treatment response. Circadian regulation of immune cell infiltration may further contribute to these prognostic and predictive markers. Examining the correlation between circadian rhythm and immune cell infiltration can provide valuable insights into disease progression and guide personalized treatment decisions.
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Affiliation(s)
- Monika Lesicka
- Department of Translational Research, Nofer Institute of Occupational Medicine, 91-349 Lodz, Poland
| | - Bogusław Nedoszytko
- Department of Dermatology, Venerology and Allergology Medical University of Gdansk, 80-211 Gdansk, Poland
- Molecular Laboratory, Invicta Fertility and Reproductive Centre, Polna 64, 81-740 Sopot, Poland
| | - Edyta Reszka
- Department of Translational Research, Nofer Institute of Occupational Medicine, 91-349 Lodz, Poland
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Yang L, Cao ZJ, Zhang Y, Zhou JK, Tian J. Disulfidptosis-related classification patterns and tumor microenvironment characterization in skin cutaneous melanoma. Melanoma Manag 2023; 10:MMT65. [PMID: 38230203 PMCID: PMC10789442 DOI: 10.2217/mmt-2023-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024] Open
Abstract
Aim To identify distinct disulfidptosis-molecular subtypes and develop a novel prognostic signature. Methods/materials We integrated into this study multiple SKCM transcriptomic datasets from the Cancer Genome Atlas database and Gene Expression Omnibus dataset. The consensus clustering algorithm was applied to categorize SKCM patients into different DRG subtypes. Results Three distinct DRG subtypes were identified, which were correlated to different clinical outcomes and signaling pathways. Then, a disulfidptosis-relaed signature and nomogram were constructed, which could accurately predict the individual OS of patients with SKCM. The high-risk group was less sensitive to immunotherapy than the low-risk group. Conclusion The signature can assist healthcare professionals in making more accurate and individualized treatment choices for patients with SKCM.
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Affiliation(s)
- Li Yang
- Department of Dermatology, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Zi-jian Cao
- Department of Dermatology, The 63600 Hospital of PLA, Lanzhou, 732750, China
| | - Yuan Zhang
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Jin-ke Zhou
- Department of Dermatology, The 63600 Hospital of PLA, Lanzhou, 732750, China
| | - Jun Tian
- Department of Dermatology, Shaanxi Provincial People's Hospital, Xi'an 710068, China
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Wu M, Wang Z, Zhang J. Analysis on tumor immune microenvironment and construction of a prognosis model for immune-related skin cutaneous melanoma. Zhong Nan Da Xue Xue Bao Yi Xue Ban 2023; 48:671-681. [PMID: 37539569 PMCID: PMC10930407 DOI: 10.11817/j.issn.1672-7347.2023.230069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Indexed: 08/05/2023]
Abstract
OBJECTIVES Malignant melanoma is a highly malignant and heterogeneous skin cancer. Although immunotherapy has improved survival rates, the inhibitory effect of tumor microenvironment has weakened its efficacy. To improve survival and treatment strategies, we need to develop immune-related prognostic models. Based on the analysis of the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Sequence Read Archive (SRA) database, this study aims to establish an immune-related prognosis prediction model, and to evaluate the tumor immune microenvironment by risk score to guide immunotherapy. METHODS Skin cutaneous melanoma (SKCM) transcriptome sequencing data and corresponding clinical information were obtained from the TCGA database, differentially expressed genes were analyzed, and prognostic models were developed using univariate Cox regression, the LASSO method, and stepwise regression. Differentially expressed genes in prognostic models confirmed by real-time reverse transcription PCR (real-time RT-PCR) and Western blotting. Survival analysis was performed by using the Kaplan-Meier method, and the effect of the model was evaluated by time-dependent receiver operating characteristic curve as well as multivariate Cox regression, and the prognostic model was validated by 2 GEO melanoma datasets. Furthermore, correlations between risk score and immune cell infiltration, Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) score, immune checkpoint mRNA expression levels, tumor immune cycle, or tumor immune micro-environmental pathways were analyzed. Finally, we performed association analysis for risk score and the efficacy of immunotherapy. RESULTS We identified 4 genes that were differentially expressed in TCGA-SKCM datasets, which were mainly associated with the tumor immune microenvironment. A prognostic model was also established based on 4 genes. Among 4 genes, the mRNA and protein levels of killer cell lectin like receptor D1 (KLRD1), leukemia inhibitory factor (LIF), and cellular retinoic acid binding protein 2 (CRABP2) genes in melanoma tissues differed significantly from those in normal skin (all P<0.01). The prognostic model was a good predictor of prognosis for patients with SKCM. The patients with high-risk scores had significantly shorter overall survival than those with low-risk scores, and consistent results were achieved in the training cohort and multiple validation cohorts (P<0.001). The risk score was strongly associated with immune cell infiltration, ESTIMATE score, immune checkpoint mRNA expression levels, tumor immune cycle, and tumor immune microenvironmental pathways (P<0.001). The correlation analysis showed that patients with the high-risk scores were in an inhibitory immune microenvironment based on the prognostic model (P<0.01). CONCLUSIONS The immune-related SKCM prognostic model constructed in this study can effectively predict the prognosis of SKCM patients. Considering its close correlation to the tumor immune microenvironment, the model has some reference value for clinical immunotherapy of SKCM.
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Affiliation(s)
- Meng Wu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008.
- Department of Dermatology, Hunan Provincial People's Hospital, Changsha 410002.
| | - Zheng Wang
- School of Computer Science, Hunan First Normal University, Changsha 410205. w8614@ hotmail.com
| | - Jianglin Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008.
- Department of Dermatology, Shenzhen People's Hospital, Shenzhen Guangdong 518020, China.
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Liu Y, Zhang H, Mao Y, Shi Y, Wang X, Shi S, Hu D, Liu S. Bulk and single-cell RNA-sequencing analyses along with abundant machine learning methods identify a novel monocyte signature in SKCM. Front Immunol 2023; 14:1094042. [PMID: 37304304 PMCID: PMC10248046 DOI: 10.3389/fimmu.2023.1094042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
Background Global patterns of immune cell communications in the immune microenvironment of skin cutaneous melanoma (SKCM) haven't been well understood. Here we recognized signaling roles of immune cell populations and main contributive signals. We explored how multiple immune cells and signal paths coordinate with each other and established a prognosis signature based on the key specific biomarkers with cellular communication. Methods The single-cell RNA sequencing (scRNA-seq) dataset was downloaded from the Gene Expression Omnibus (GEO) database, in which various immune cells were extracted and re-annotated according to cell markers defined in the original study to identify their specific signs. We computed immune-cell communication networks by calculating the linking number or summarizing the communication probability to visualize the cross-talk tendency in different immune cells. Combining abundant analyses of communication networks and identifications of communication modes, all networks were quantitatively characterized and compared. Based on the bulk RNA sequencing data, we trained specific markers of hub communication cells through integration programs of machine learning to develop new immune-related prognostic combinations. Results An eight-gene monocyte-related signature (MRS) has been built, confirmed as an independent risk factor for disease-specific survival (DSS). MRS has great predictive values in progression free survival (PFS) and possesses better accuracy than traditional clinical variables and molecular features. The low-risk group has better immune functions, infiltrated with more lymphocytes and M1 macrophages, with higher expressions of HLA, immune checkpoints, chemokines and costimulatory molecules. The pathway analysis based on seven databases confirms the biological uniqueness of the two risk groups. Additionally, the regulon activity profiles of 18 transcription factors highlight possible differential regulatory patterns between the two risk groups, suggesting epigenetic event-driven transcriptional networks may be an important distinction. MRS has been identified as a powerful tool to benefit SKCM patients. Moreover, the IFITM3 gene has been identified as the key gene, validated to express highly at the protein level via the immunohistochemical assay in SKCM. Conclusion MRS is accurate and specific in evaluating SKCM patients' clinical outcomes. IFITM3 is a potential biomarker. Moreover, they are promising to improve the prognosis of SKCM patients.
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Affiliation(s)
- Yuyao Liu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Haoxue Zhang
- Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, Anhui, China
| | - Yan Mao
- Department of Dermatology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yangyang Shi
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xu Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Shaomin Shi
- Department of Dermatology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Delin Hu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Shengxiu Liu
- Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, Anhui, China
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15
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Zhang L, Shi Z, Zhang F, Chen B, Qiu W, Cai L, Lin X. Ubiquitination-related biomarkers in metastatic melanoma patients and their roles in tumor microenvironment. Front Oncol 2023; 13:1170190. [PMID: 37274231 PMCID: PMC10235493 DOI: 10.3389/fonc.2023.1170190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023] Open
Abstract
Background Skin cutaneous melanoma (SKCM) is the deadliest type of cutaneous malignancy. Ubiquitination is a process of protein sorting and degradation that exhibits multiple functions in the progression of various tumors. This study aimed to characterize a set of genes for ubiquitination in SKCM. Methods The expression patterns of ubiquitin-associated genes (URGs) and the corresponding clinical information in SKCM tissues were comprehensively analyzed based on The Cancer Genome Atlas (TCGA) database. We performed univariate and multivariate Cox proportional regression models to characterize the risk scores and identify four critical genes related to prognostic ubiquitination (HCLS1, CORO1A, NCF1 and CCRL2), which were used to construct the prognostic signatures. We also studied the effects of HCLS1, CORO1A and CCRL2 on tumor metastasis-related indicators at the cellular level through in vitro experiments. Results SKCM patients in the low-risk group showing a longer survival than those in the high-risk group. Characteristic risk scores correlated with several clinicopathological variables and reflected the infiltration of multiple immune cells. In addition, the knockdown of CLS1, CORO1A and CCRL2 affected cellular malignant biological behavior through the EMT signaling pathway. Conclusion This study provides a novel and prospective strategy to improve the clinical survival of SKCM patients.
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Wu L, Li S, Xu J, Shen C, Qian Q. AGAP2-AS1/BRD7/c-Myc signaling axis promotes skin cutaneous melanoma progression. Am J Transl Res 2023; 15:350-362. [PMID: 36777828 PMCID: PMC9908487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/19/2022] [Indexed: 02/14/2023]
Abstract
OBJECTIVE To examine the effects and mechanisms of AGAP2 Antisense RNA 1 (AGAP2-AS1) in progression of skin cutaneous melanoma (SKCM). METHODS AGAP2-AS1 expression and SKCM survival outcomes were assessed using bioinformatics analysis. In vitro and in vivo assays, including cell proliferation, colony formation, migration, and tumor formation assays, were performed to detect AGAP2-AS1 oncogenic effects in SKCM. RNA pull-down, RNA immunoprecipitation (RIP), and co-immunoprecipitation were used to evaluate the mechanism of AGAP2-AS1 in SKCM progression. RESULTS AGAP2-AS1 was upregulated in human SKCM tissues and cells and predicted a worse prognosis. AGAP2-AS1 silencing in two SKCM cell lines inhibited cell proliferation, as well as colony formation and migration both in vitro and in vivo. The RNA pull-down assay and RIP analysis results indicated that AGAP2-AS1 interacted with bromodomain containing 7 (BRD7). AGAP2-AS1 knockdown attenuated the BRD7 and c-Myc interaction, which reduced c-Myc expression. The altered phenotypes found in AGAP2-AS1- and BRD7-deficient cells were rescued by overexpression of c-Myc. CONCLUSIONS AGAP2-AS1 participated in oncogenesis in SKCM via the BRD7/c-Myc signaling pathway. These results suggest a molecular mechanism for AGAP2-AS1 in the carcinogenesis of SKCM.
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Affiliation(s)
- Lei Wu
- Department of Dermatology, First Affiliated Hospital of Soochow UniversitySuzhou 215006, Jiangsu, China
| | - Shenyi Li
- Department of Obstetrics and Gynecology, Affiliated Hospital of Jiangnan UniversityWuxi 214062, Jiangsu, China
| | - Jinfu Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical UniversityNanjing 211166, Jiangsu, China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical UniversityNanjing 211166, Jiangsu, China,State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, Jiangsu, China
| | - Qihong Qian
- Department of Dermatology, First Affiliated Hospital of Soochow UniversitySuzhou 215006, Jiangsu, China
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He J, Huang W, Li X, Wang J, Nie Y, Li G, Wang X, Cao H, Chen X, Wang X. A new ferroptosis-related genetic mutation risk model predicts the prognosis of skin cutaneous melanoma. Front Genet 2023; 13:988909. [PMID: 36685905 PMCID: PMC9849373 DOI: 10.3389/fgene.2022.988909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Ferroptosis is an iron-dependent cell death mode and closely linked to various cancers, including skin cutaneous melanoma (SKCM). Although attempts have been made to construct ferroptosis-related gene (FRG) signatures for predicting the prognosis of SKCM, the prognostic impact of ferroptosis-related genetic mutations in SKCM remains lacking. This study aims to develop a prediction model to explain the relationship between ferroptosis-related genetic mutations and clinical outcomes of SKCM patients and to explore the potential value of ferroptosis in SKCM treatment. Methods: FRGs which significantly correlated with the prognosis of SKCM were firstly screened based on their single-nucleotide variant (SNV) status by univariate Cox regression analysis. Subsequently, the least absolute shrinkage and selection operator (LASSO) and Cox regressions were performed to construct a new ferroptosis-related genetic mutation risk (FerrGR) model for predicting the prognosis of SKCM. We then illustrate the survival and receiver operating characteristic (ROC) curves to evaluate the predictive power of the FerrGR model. Moreover, independent prognostic factors, genomic and clinical characteristics, immunotherapy, immune infiltration, and sensitive drugs were compared between high-and low-FerrGR groups. Results: The FerrGR model was developed with a good performance on survival and ROC analysis. It was a robust independent prognostic indicator and followed a nomogram constructed to predict prognostic outcomes for SKCM patients. Besides, FerrGR combined with tumor mutational burden (TMB) or MSI (microsatellite instability) was considered as a combined biomarker for immunotherapy response. The high FerrGR group patients were associated with an inhibitory immune microenvironment. Furthermore, potential drugs target to high FerrGR samples were predicted. Conclusion: The FerrGR model is valuable to predict prognosis and immunotherapy in SKCM patients. It offers a novel therapeutic option for SKCM.
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Affiliation(s)
- Jia He
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou, China,Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China
| | - Wenting Huang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Xinxin Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Jingru Wang
- Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China
| | - Yaxing Nie
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Guiqiang Li
- Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China
| | - Xiaoxiang Wang
- Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China
| | - Huili Cao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Xiaodong Chen
- Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China,*Correspondence: Xusheng Wang, ; Xiaodong Chen,
| | - Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou, China,*Correspondence: Xusheng Wang, ; Xiaodong Chen,
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Shen X, Shang L, Han J, Zhang Y, Niu W, Liu H, Shi H. Immune-related gene signature associates with immune landscape and predicts prognosis accurately in patients with skin cutaneous melanoma. Front Genet 2023; 13:1095867. [PMID: 36685954 PMCID: PMC9845246 DOI: 10.3389/fgene.2022.1095867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/02/2022] [Indexed: 01/06/2023] Open
Abstract
Skin cutaneous melanoma (SKCM) is the skin cancer that causes the highest number of deaths worldwide. There is growing evidence that the tumour immune microenvironment is associated with cancer prognosis, however, there is little research on the role of immune status in melanoma prognosis. In this study, data on patients with Skin cutaneous melanoma were downloaded from the GEO, TCGA, and GTEx databases. Genes associated with the immune pathway were screened from published papers and lncRNAs associated with them were identified. We performed immune microenvironment and functional enrichment analyses. The analysis was followed by applying univariate/multivariate Cox regression algorithms to finally identify three lncRNAs associated with the immune pathway for the construction of prognostic prediction models (CXCL10, RXRG, and SCG2). This stepwise downscaling method, which finally screens out prognostic factors and key genes and then uses them to build a risk model, has excellent predictive power. According to analyses of the model's reliability, it was able to differentiate the prognostic value and continued existence of Skin cutaneous melanoma patient populations more effectively. This study is an analysis of the immune pathway that leads lncRNAs in Skin cutaneous melanoma in an effort to open up new treatment avenues for Skin cutaneous melanoma.
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Sun Y, Lei S, Luo X, Jiang C, Li Z. The value of cuproptosis-related differential genes in guiding prognosis and immune status in patients with skin cutaneous melanoma. Front Pharmacol 2023; 14:1129544. [PMID: 37138850 PMCID: PMC10149708 DOI: 10.3389/fphar.2023.1129544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Background: Skin cutaneous melanoma (SKCM) is one of the most common cutaneous malignancies, which incidence is increasing. Cuproptosis is a new type of programming cell death recently reported, which may affect the progression of SKCM. Method: The mRNA expression data of melanoma were obtained from the Gene Expression Omnibus and the Cancer Genome Atlas databases. We constructed a prognostic model according to the cuproptosis-related differential genes in SKCM. Finally, real-time quantitative PCR was performed to verify the expression of cuproptosis-related differential genes in patients with different stages of cutaneous melanoma. Results: We detected 767 cuproptosis-related differential genes based on 19 cuproptosis-related genes, and screened out 7 differential genes to construct a prognostic model, which including three high-risk differential genes (SNAI2, RAP1GAP, BCHE), and four low-risk differential genes (JSRP1, HAPLN3, HHEX, ERAP2). Kaplan-Meier analysis indicated that SKCM patients with low-risk differential genes signals had better prognosis. The Encyclopedia of Genomes results manifested that cuproptosis-related differential genes are not only involved in T cell receptor signaling channel, natural killer cell mediated cytotoxicity, but also chemokine signaling pathway and B cell receptor signaling pathway. In our risk scoring model, the receiver operating characteristic (ROC) values of the three-time nodes are 0.669 (1-year), 0.669 (3-year) and 0.685 (5-year), respectively. Moreover, the tumor burden mutational and immunology function, cell stemness characteristics and drug sensitivity have significant differences between low-risk group and high-risk group. The mRNA level of SNAI2, RAP1GAP and BCHE in stage Ⅲ+Ⅳ SKCM patients was significantly higher than that in stage Ⅰ+Ⅱ patients, while the level of JSRP1, HAPLN3, HHEX and ERAP2 in stage Ⅰ+Ⅱ SKCM patients was more remarkable higher than that in stage Ⅲ+Ⅳ SKCM patients. Conclusion: In summary, we suggest that cuproptosis can not only regulate the tumor immune microenvironment but also affect the prognosis of SKCM patients, and may offer a basic theory for SKCM patients survival studies and clinical decision-making with potentially therapeutic drugs.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Zhang X, Miao Y, Sun HW, Wang YX, Zhao WM, Pang AY, Wu XY, Shen CC, Chen XD. Integrated analysis from multi-center studies identities m7G-derived modification pattern and risk stratification system in skin cutaneous melanoma. Front Immunol 2022; 13:1034516. [PMID: 36532001 PMCID: PMC9751814 DOI: 10.3389/fimmu.2022.1034516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
The m7G modification has been proven to play an important role in RNA post-transcriptional modification and protein translation. However, the potential role of m7G modification patterns in assessing the prognosis of Skin cutaneous melanoma (SKCM) and tumor microenvironment (TME) has not been well studied. In this study, we investigated and finally identified 21 available m7G-related genes. We used hierarchical clustering (K-means) to classify 743 SKCM patients into three m7G-modified subtypes named m7G/gene cluster-A, B, C. We found that both m7G cluster B and gene cluster B exhibited higher prognosis and higher immune cell infiltration in TME compared to other subtypes. EIF4E3 and IFIT5, two m7G related genes, were both markedly elevated in Cluster B. Then, we constructed an m7G score system utilizing principal component analysis (PCA) in order to evaluate the patients' prognosis. High m7G score subtype was associated with better survival prognosis and active immune response. Overall, this article revealed that m7G modification patterns were involved in the development of the tumor microenvironment. Evaluating patients' m7G modification patterns will enhance our understanding of TME characteristics and help to guide personal treatment in clinics in the future.
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Affiliation(s)
- Xin Zhang
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Ying Miao
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Hao-Wen Sun
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Yi-Xiao Wang
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Wen-Min Zhao
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - A-Ying Pang
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xiao-Yan Wu
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Cong-Cong Shen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China,*Correspondence: Cong-Cong Shen, ; Xiao-Dong Chen,
| | - Xiao-Dong Chen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China,*Correspondence: Cong-Cong Shen, ; Xiao-Dong Chen,
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22
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Li AA, Zhang Y, Tong WL, Chen JW, Huang SH, Liu JM, Liu ZL. Identification of a Novel Pyroptosis-Related Gene Signature Indicative of Disease Prognosis and Treatment Response in Skin Cutaneous Melanoma. Int J Gen Med 2022; 15:6145-6163. [PMID: 35855761 PMCID: PMC9288220 DOI: 10.2147/ijgm.s367693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Pyroptosis plays an important role in the occurrence and progression of many tumors; however, the specific mechanisms involved remain unknown. Here, we construct a pyroptosis-related gene signature that can be used to predict survival prognosis of skin cutaneous melanoma (SKCM) and provide guidance for clinical treatment. Methods By integrating data from the two databases from the GTEx and TCGA, differentially expressed genes (DEGs) from normal tissues and skin cutaneous tumor tissues were identified. The main signaling pathways and function enrichment of these differential genes were determined. Univariate and multivariate COX regression analysis, and risk score analysis were used to construct a signature to assess its predictive value for overall survival. The mRNA expression of these five genes in melanoma cells was determined by quantitative polymerase chain reaction (qPCR). The pRRophetic algorithm was used to estimate the half-maximal inhibitory concentration (IC50) of chemotherapy drugs in SKCM patients. The expression of multiple immune checkpoint genes also was evaluated. Results Sixteen DEGs associated with pyroptosis in SKCM and normal skin tissues were identified. Of these, 12 pyroptosis-related DEGs were associated with the prognosis of SKCM. A five-gene signature (GSDMA, GSDMC, IL-18, NLRP6, and AIM2) model was constructed. Patients were divided into high-risk and low-risk groups using the risk scores. Of these, the high-risk group had a worse survival prognosis. There are significant differences in the predicted sensitivity of the high-risk and low-risk groups to chemotherapeutic drugs. In addition, compared with the high-risk group, the low-risk group showed higher expression of PD-1, PDL-1, CTLA-4, LAG-3, and VSIR. Conclusion In this study, we constructed a novel prognostic pyroptosis-related gene-signature for SKCM. These genes showed good predictive value for patient prognosis and could provide guidance for better treatment of SKCM patients.
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Affiliation(s)
- An-An Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Yu Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Wei-Lai Tong
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Jiang-Wei Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Shan-Hu Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Jia-Ming Liu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Zhi-Li Liu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
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23
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Abstract
Background Skin cutaneous melanoma (SKCM) is a highly malignant skin tumor. DIRAS2 is considered to be a tumor suppressor gene; however, its function in SKCM has not been explored. Methods The Gene Expression Profiling Interactive Analysis (GEPIA) was implemented to investigate the expression of DIRAS2 in SKCM, and plot the survival curve to determine the effect of DIRAS2 on the survival rates of SKCM patients. Then, the correlation between DIRAS2 and tumor immune infiltration was also discussed, and the expression of DIRAS2 and immune infiltration level in SKCM immune cells was determined using TIMER. The top 100 genes most associated with DIRAS2 expression were used for functional enrichment analysis. In order to confirm the anti-cancer effects of DIRAS2 in SKCM in the data analysis, in vitro assays as well as in vivo studies of DIRAS2 on SKCM tumor cell proliferation, migration, invasion, and metastasis were conducted. Western blot and immunofluorescence assay were employed to study the relationship between DIRAS2 and Wnt/β-catenin signaling pathway in SKCM. Results DIRAS2 expression was shown to be significantly correlated with tumor grade using univariate logistic regression analysis. DIRAS2 was found to be an independent prognostic factor for SKCM in multivariate analysis. Of note, DIRAS2 expression levels were positively correlated with the infiltration levels of B cells, CD4+ T cells, and CD8+ T cells in SKCM. The infiltration of B cells, CD4+ T cells, and CD8+ T cells was positively correlated with the cumulative survival rate of SKCM patients. In vitro experiments suggested that proliferation, migration, invasion, and metastasis of SKCM tumor cells were distinctly enhanced after DIRAS2 knockdown. Furthermore, DIRAS2 depletion promoted melanoma growth and metastasis in vivo. As for the mechanism, silencing DIRAS2 can activate the signal transduction of the Wnt/β-catenin signaling pathway. Conclusion DIRAS2 functions as a tumor suppressor gene in cases of SKCM by inhibiting the Wnt/β-catenin signaling. It is also associated with immune infiltration in SKCM.
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Affiliation(s)
- Wenli Xue
- Department of Dermatology, The First Hospital of Shanxi Medical University, Tai Yuan City, China
| | - Hongbo Zhu
- Department of Medical Oncology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Hongye Liu
- Department of Dermatology, The First Hospital of Shanxi Medical University, Tai Yuan City, China
| | - Hongxia He
- Department of Dermatology, The First Hospital of Shanxi Medical University, Tai Yuan City, China
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24
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Zhang Q, Liu YJ, Li JP, Zeng SH, Shen H, Han M, Guo S, Liu SL, Zou X. USP35 is a Potential Immunosuppressive Factor in Skin Cutaneous Melanoma. J Inflamm Res 2022; 15:3065-3082. [PMID: 35637872 PMCID: PMC9148213 DOI: 10.2147/jir.s362619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 12/15/2022] Open
Abstract
Background As one of the most immunogenic malignancies, skin cutaneous melanoma (SKCM) is mainly characterized by a high prevalence in immune-compromised patients and a brisk lymphocyte infiltration in the tumor microenvironment (TME). However, to date, studies on deubiquitination in SKCM are still very limited. Methods Public data with regard to this study in SKCM patients were acquired from The Cancer Genome Atlas (TCGA) and the Gene-Expression Omnibus (GEO) databases. We stratified TCGA-SKCM cases using consensus clustering and identified independent prognostic factors in deubiquitinating enzymes encoding genes (DECGs) by LASSO-Cox analysis. USP35 transcriptome level was examined using public data and validated by Immunohistochemical (IHC) staining at the protein level. Enrichment analysis was used to explore the potential functions of USP35, and the TISCH database, providing further evidence at the single-cell level. The CIBERSORT algorithm was used to assess the relationship between USP35 and the immune microenvironment, and IHC was used to further evaluate the relationship between USP35 and immunotherapy response. Finally, we used the cBioPortal and the Methsurv database to analyze the significance of genomic alterations of USP35 in melanoma. Results Our results showed that DECGs can be effectively used to stratify SKCM patients, suggesting their potential significance in the development of SKCM. Furthermore, USP35 overexpression was significantly associated with an unfavorable prognosis. We further revealed that USP35 may be involved in the activation of TORC1 signaling. Most importantly, USP35 was found to be significantly associated with an immunosuppressive TME, both in terms of negative correlation with the abundance of infiltrating CD8+ T cells and in terms of the fact that patients with high USP35 expression may benefit less from immunotherapy than those with low USP35 expression. Conclusion Deubiquitinating enzymes are of great importance in the diagnosis and treatment of SKCM, and USP35 is an extremely promising target for immunotherapy.
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Affiliation(s)
- Qian Zhang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People's Republic of China.,No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People's Republic of China
| | - Yuan-Jie Liu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People's Republic of China.,No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People's Republic of China
| | - Jie-Pin Li
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People's Republic of China.,No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People's Republic of China.,Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People's Republic of China
| | - Shu-Hong Zeng
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People's Republic of China.,No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People's Republic of China
| | - Hui Shen
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People's Republic of China
| | - Mei Han
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People's Republic of China
| | - Shun Guo
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People's Republic of China.,No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People's Republic of China
| | - Shen-Lin Liu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People's Republic of China.,No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People's Republic of China
| | - Xi Zou
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People's Republic of China.,No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People's Republic of China.,Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing, People's Republic of China
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25
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Ma Y, Wang N, Yang S. Skin cutaneous melanoma properties of immune-related lncRNAs identifying potential prognostic biomarkers. Aging (Albany NY) 2022; 14:3030-3048. [PMID: 35361740 PMCID: PMC9037265 DOI: 10.18632/aging.203982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/09/2022] [Indexed: 11/25/2022]
Abstract
Skin cutaneous melanoma (SKCM) is one of the most aggressive and life-threatening cancers with high incidence rate, metastasis rate and mortality. Early detection and stratification of risk assessment are essential to treat SKCM and to improve survival rate. The aim of this study is to construct an immune-related lncRNAs (immlncRNAs) prognosis risk model to identify immune biomarkers for early diagnosis, prognosis assessment and target immunotherapy of SKCM. For this purpose, we identified 46 immlncRNAs significantly correlated with SKCM prognosis to construct the prognostic risk model and patients were stratified into the high- and low-risk subgroups according to the developed model. The predictive efficiency of this model has been proved by K-M survival analysis and receiver operating characteristic curve. Moreover, CIBERSORT algorithms confirmed that there were differences in immune cell infiltration between the high- and low-risk groups. Functional enrichment analysis further indicated that immlncRNAs were related to a variety of immune response process signaling pathways, suggesting that relevant immlncRNAs could play an important role in the immune regulation of SKCM. Finally, subgroup analysis and multiple Cox regression analysis further proved the stability of the model. In summary, we successfully constructed a 46 immlncRNA-related prognostic risk score model with excellent predictive efficacy and provided more possibilities to investigate the immune regulation mechanisms and to develop immunotherapy of SKCM.
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Affiliation(s)
- Yutong Ma
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, P.R. China
| | - Ning Wang
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, P.R. China
| | - Shude Yang
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, P.R. China
- Liaoning Provincial Key Laboratory of Oral Diseases, School of Stomatology, China Medical University, Shenyang 110001, Liaoning Province, P.R. China
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26
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Zhang H, Liu Y, Hu D, Liu S. Identification of Novel Molecular Therapeutic Targets and Their Potential Prognostic Biomarkers Based on Cytolytic Activity in Skin Cutaneous Melanoma. Front Oncol 2022; 12:844666. [PMID: 35345444 PMCID: PMC8957259 DOI: 10.3389/fonc.2022.844666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/09/2022] [Indexed: 12/13/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) attracts attention worldwide for its extremely high malignancy. A novel term cytolytic activity (CYT) has been introduced as a potential immunotherapy biomarker associated with counter-regulatory immune responses and enhanced prognosis in tumors. In this study, we extracted all datasets of SKCM patients, namely, RNA sequencing data and clinical information from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database, conducted differential expression analysis to yield 864 differentially expressed genes (DEGs) characteristic of CYT and used non-negative matrix factorization (NMF) method to classify molecular subtypes of SKCM patients. Among all genes, 14 hub genes closely related to prognosis for SKCM were finally screen out. Based on these genes, we constructed a 14-gene prognostic risk model and its robustness and strong predictive performance were further validated. Subsequently, the underlying mechanisms in tumor pathogenesis and prognosis have been defined from a number of perspectives, namely, tumor mutation burden (TMB), copy number variation (CNV), tumor microenvironment (TME), infiltrating immune cells, gene set enrichment analysis (GSEA) and immune checkpoint inhibitors (ICIs). Furthermore, combined with GTEx database and HPA database, the expression of genes in the model was verified at the transcriptional level and protein level, and the relative importance of genes in the model was described by random forest algorithm. In addition, the model was used to predict the difference in sensitivity of SKCM patients to chemotherapy and immunotherapy. Finally, a nomogram was constructed to better aid clinical diagnosis.
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Affiliation(s)
- Haoxue Zhang
- Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Yuyao Liu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Delin Hu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shengxiu Liu
- Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
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27
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Zuo S, Wang H, Li L, Pan H, Lu L. Thymidine Kinase 1 Drives Skin Cutaneous Melanoma Malignant Progression and Metabolic Reprogramming. Front Oncol 2022; 12:802807. [PMID: 35311151 PMCID: PMC8927676 DOI: 10.3389/fonc.2022.802807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/17/2022] [Indexed: 11/15/2022] Open
Abstract
Background Thymidine kinase 1 (TK1) is a cell cycle-dependent kinase that catalyzes the addition of a gamma-phosphate group to thymidine. The protumorigenic role of TK1 has been reported in various malignancies. However, the role of TK1 in skin cutaneous melanoma (SKCM) remains unclear. This study aimed to explore the molecular function of TK1 in SKCM progression. Methods Bioinformatics data were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Subcutaneous xenografts were established to observe the effect of TK1 knockdown on the proliferation of SKCM cells in vivo. RNA sequencing (RNA-seq; deposited in Sequence Read Archive, SRX10950283-SRX10950285 for A375 control cells and SRX10950286-SRX10950288 for TK1-silenced A375 cells) and immunoprecipitation–mass spectrometry (IP-MS) were used to analyze TK1-related genes and pathways. Seahorse XF Cell Mito tests and glycolysis stress assays were conducted for metabolic testing. Results TK1 was upregulated in malignant SKCM compared to that in normal tissues and cell lines. Elevated expression of TK1 was associated with poor prognosis. In vitro and in vivo assays demonstrated that TK1 promoted the proliferation and migration of SKCM cells. Moreover, TK1 was strongly associated with multiple intracellular metabolic pathways, facilitating cell mitochondrial respiration and glycolysis in SKCM malignant progression. Conclusions TK1 drives SKCM malignant progression and supports metabolic reprogramming, indicating that TK1 serves as a therapeutic target for SKCM.
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Affiliation(s)
- Sipeng Zuo
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Huixue Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Lin Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Hui Pan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Linna Lu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
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28
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Zou S, Zhang Y, Zhang L, Wang D, Xu S. Construction and validation of a prognostic risk model of angiogenesis factors in skin cutaneous melanoma. Aging (Albany NY) 2022; 14:1529-1548. [PMID: 35157610 PMCID: PMC8876895 DOI: 10.18632/aging.203895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022]
Abstract
Melanoma can secrete tumor angiogenesis factors, which is the essential factor for tumor growth and metastasis. However, there are few reports on the relationship between angiogenesis factors and prognosis risk in melanoma. This study aimed to develop a prognostic risk model of angiogenesis for melanoma. Forty-nine differentially expressed angiogenesis were identified from the TCGA database, which were mainly involved in PI3K/Akt pathway, focal adhesion, and MAPK signaling pathway. We then establish an eleven-gene signature. The model indicated a strong prognostic capability in both the discovery cohort and the validation cohort. Patients of smaller height (<170 cm) and lower weight (<80 kg) and those with advanced-stage and ulcerated melanoma had higher risk scores. The risk score was positively correlated with mutation load, homologous recombination defect, neoantigen load and chromosome instability. In addition, the high-risk group had a higher degree of immune cell infiltration, better response to immunotherapy and lower immune score. Therefore, these results indicate that the risk model is an effective method to predict the prognosis of melanoma.
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Affiliation(s)
- Songyun Zou
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Yonggang Zhang
- Department of Clinical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Limei Zhang
- Oncology Department, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Dengchuan Wang
- Office of Medical Ethics, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Shi Xu
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
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29
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Huang R, Li M, Zeng Z, Zhang J, Song D, Hu P, Yan P, Xian S, Zhu X, Chang Z, Zhang J, Guo J, Yin H, Meng T, Huang Z. The Identification of Prognostic and Metastatic Alternative Splicing in Skin Cutaneous Melanoma. Cancer Control 2022; 29:10732748211051554. [PMID: 34986671 PMCID: PMC8743934 DOI: 10.1177/10732748211051554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is a type of highly invasive cancer originated from melanocytes. It is reported that aberrant alternative splicing (AS) plays an important role in the neoplasia and metastasis of many types of cancer. Therefore, we investigated whether ASEs of pre-RNA have such an influence on the prognosis of SKCM and the related mechanism of ASEs in SKCM. The RNA-seq data and ASEs data for SKCM patients were obtained from the TCGA and TCGASpliceSeq database. The univariate Cox regression revealed 1265 overall survival-related splicing events (OS-SEs). Screened by Lasso regression, 4 OS-SEs were identified and used to construct an effective prediction model (AUC: .904), whose risk score was proved to be an independent prognostic factor. Furthermore, Kruskal-Wallis test and Mann-Whitney-Wilcoxon test showed that an aberrant splicing type of aminoacyl tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2) regulated by CDC-like kinase 1 (CLK1) was associated with the metastasis and stage of SKCM. Besides, the overlapped signal pathway for AIMP2 was galactose metabolism identified by the co-expression analysis. External database validation also confirmed that AIMP2, CLK1, and the galactose metabolism were associated with the metastasis and stage of SKCM patients. ChIP-seq and ATAC-seq methods further confirmed the transcription regulation of CLK1, AIMP2, and other key genes, whose cellular expression was detected by Single Cell Sequencing. In conclusion, we proposed that CLK1-regulated AIMP2-78704-ES might play a critical role in the tumorigenesis and metastasis of SKCM via galactose metabolism. Besides, we established an effective model with MTMR14-63114-ES, URI1-48867-ES, BATF2-16724-AP, and MED22-88025-AP to predict the metastasis and prognosis of SKCM patients.
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Affiliation(s)
- Runzhi Huang
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Zhengzhou University School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Mingxiao Li
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou University School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhiwei Zeng
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou University School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Jie Zhang
- Zhengzhou University School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Dianwen Song
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Peng Hu
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Penghui Yan
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuyuan Xian
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xiaolong Zhu
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou University School of Medicine, Zhengzhou University, Zhengzhou, China
| | | | - Jiayao Zhang
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Juanru Guo
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huabin Yin
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tong Meng
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
- Tongji University School of Mathematical Sciences, Tongji University, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
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Liang L, Mai S, Mai G, Chen Y, Liu L. DNA damage repair-related gene signature predicts prognosis and indicates immune cell infiltration landscape in skin cutaneous melanoma. Front Endocrinol (Lausanne) 2022; 13:882431. [PMID: 35957812 PMCID: PMC9361349 DOI: 10.3389/fendo.2022.882431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND DNA damage repair plays an important role in the onset and progression of cancers and its resistance to treatment therapy. This study aims to assess the prognostic potential of DNA damage repair markers in skin cutaneous melanoma (SKCM). METHOD In this study, we have analyzed the gene expression profiles being downloaded from TCGA, GTEx, and GEO databases. We sequentially used univariate and LASSO Cox regression analyses to screen DNA repair genes associated with prognosis. Then, we have conducted a multivariate regression analysis to construct the prognostic profile of DNA repair-related genes (DRRGs). The risk coefficient is used to calculate the risk scores and divide the patients into two cohorts. Additionally, we validated our prognosis model on an external cohort as well as evaluated the link between immune response and the DRRGs prognostic profiles. The risk signature is compared to immune cell infiltration, chemotherapy, and immune checkpoint inhibitors (ICIs) treatment. RESULTS An analysis using LASSO-Cox stepwise regression established a prognostic signature consisting of twelve DRRGs with strong predictive ability. Disease-specific survival (DSS) is found to be lower among high-risk patients group as compared to low-risk patients. The signature may be employed as an independent prognostic predictor after controlling for clinicopathological factors, as demonstrated by validation on one external GSE65904 cohort. A strong correlation is also found between the risk score and the immune microenvironment, along with the infiltrating immune cells, and ICIs key molecules. The gene enrichment analysis results indicate a wide range of biological activities and pathways to be exhibited by high-risk groups. Furthermore, Cisplatin exhibited a considerable response sensitivity in low-risk groups as opposed to the high-risk incidents, while docetaxel exhibited a considerable response sensitivity in high-risk groups. CONCLUSIONS Our findings provide a thorough investigation of DRRGs to develop an DSS-related prognostic indicator which may be useful in forecasting SKCM progression and enabling more enhanced clinical benefits from immunotherapy.
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Affiliation(s)
- Liping Liang
- Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shijie Mai
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Genghui Mai
- Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ye Chen
- Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, Integrated Clinical Microecology Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- *Correspondence: Le Liu, ; Ye Chen,
| | - Le Liu
- Department of Gastroenterology, Integrated Clinical Microecology Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- *Correspondence: Le Liu, ; Ye Chen,
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Abstract
Background The incidence of cutaneous melanoma (CM) is increasing, and its prognosis is not optimistic. Although immune checkpoint (ICP) inhibitors are effective in the treatment of CM patients, they are not effective for all CM patients. There is an urgent need for a marker to predict both the prognosis and the immunotherapy effect in patients with CM. Approaches Two groups of patients with greatly different prognosis and response to immunotherapy were identified by unwatched cluster exploration of TCGA on the basis of 34 ICPs. The prognosis and immunotherapy effect of CM were predicted by developing a precise and given signature on the basis of ICPs, and a multivariate Cox risk regression model was established from the TCGA cohort consisting of 454 CM samples. The model was validated in 210 and 231 samples in the test and verification cohorts, respectively. Results The prognosis in clinical subgroups was predicted by the classification system. High-risk patients had poorer responses to chemotherapy and immunotherapy. Finally, the signature was recognized as an independent prognostic factor. Based on checkpoint-based signature (ICPBS) and clinical characteristics, we constructed a nomogram for the prognosis in patients with CM, which was superior to ICPBS in efficacy than ICPBS alone. Conclusion As a useful prognostic tool to further improve cancer immunotherapy, the signature can accurately predict recurrence and overall survival among patients with CM.
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Affiliation(s)
- Rui Mao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Fan Yang
- Emergency Department, Peking University Third Hospital, Peking University School of Medicine, Beijing, China
| | - Tongtong Zhang
- The Center of Gastrointestinal and Minimally Invasive Surgery, The Third People’s Hospital of Chengdu, Chengdu, China
- Medical Research Center, The Third People’s Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, The Second Chengdu Hospital Affiliated to Chongqing Medical University, Chengdu, China
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
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Yang R, Liang B, Li J, Pi X, Yu K, Xiang S, Gu N, Chen X, Zhou S. Identification of a novel tumour microenvironment-based prognostic biomarker in skin cutaneous melanoma. J Cell Mol Med 2021; 25:10990-11001. [PMID: 34755462 PMCID: PMC8642691 DOI: 10.1111/jcmm.17021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/26/2021] [Accepted: 10/09/2021] [Indexed: 11/28/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is one of the most destructive skin malignancies and has attracted worldwide attention. However, there is a lack of prognostic biomarkers, especially tumour microenvironment (TME)-based prognostic biomarkers. Therefore, there is an urgent need to investigate the TME in SKCM, as well as to identify efficient biomarkers for the diagnosis and treatment of SKCM patients. A comprehensive analysis was performed using SKCM samples from The Cancer Genome Atlas and normal samples from Genotype-Tissue Expression. TME scores were calculated using the ESTIMATE algorithm, and differential TME scores and differentially expressed prognostic genes were successively identified. We further identified more reliable prognostic genes via least absolute shrinkage and selection operator regression analysis and constructed a prognostic prediction model to predict overall survival. Receiver operating characteristic analysis was used to evaluate the diagnostic efficacy, and Cox regression analysis was applied to explore the relationship with clinicopathological characteristics. Finally, we identified a novel prognostic biomarker and conducted a functional enrichment analysis. After considering ESTIMATEScore and tumour purity as differential TME scores, we identified 34 differentially expressed prognostic genes. Using least absolute shrinkage and selection operator regression, we identified seven potential prognostic biomarkers (SLC13A5, RBM24, IGHV3OR16-15, PRSS35, SLC7A10, IGHV1-69D and IGHV2-26). Combined with receiver operating characteristic and regression analyses, we determined PRSS35 as a novel TME-based prognostic biomarker in SKCM, and functional analysis enriched immune-related cells, functions and signalling pathways. Our study indicated that PRSS35 could act as a potential prognostic biomarker in SKCM by investigating the TME, so as to provide new ideas and insights for the clinical diagnosis and treatment of SKCM.
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Affiliation(s)
- Rong‐Hua Yang
- Department of Burn Surgery and Skin RegenerationThe First People’s Hospital of FoshanFoshanChina
| | - Bo Liang
- Nanjing University of Chinese MedicineNanjingChina
| | - Jie‐Hua Li
- Department of DermatologyThe First People’s Hospital of FoshanFoshanChina
| | - Xiao‐Bing Pi
- Department of DermatologyThe First People’s Hospital of FoshanFoshanChina
| | - Kai Yu
- Department of EmergencyThe Sun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Shi‐Jian Xiang
- Department of PharmacySeventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenChina
| | - Ning Gu
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese MedicineNanjingChina
| | - Xiao‐Dong Chen
- Department of Burn Surgery and Skin RegenerationThe First People’s Hospital of FoshanFoshanChina
| | - Si‐Tong Zhou
- Department of DermatologyThe First People’s Hospital of FoshanFoshanChina
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Zhao Q, Wang Q, Wang T, Xu J, Li T, Liu Q, Yao Q, Wang P. Pattern Recognition Receptors (PRRs) in Macrophages Possess Prognosis and Immunotherapy Potential for Melanoma. Front Immunol 2021; 12:765615. [PMID: 34858419 PMCID: PMC8630683 DOI: 10.3389/fimmu.2021.765615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Background Pattern recognition receptors (PRRs) family plays a vital role in the initial stage of innate immune response and the subsequent activation of adaptive immunity. Increasing evidences have indicated that several PRRs play critical roles in the progress of inflammation and tumorigenesis. However, the comprehensive significance of PRRs family in clinical prognosis of different cancers is still elusive. Methods We analyzed expression of 20 canonical PRRs in tumor samples from 9502 patients of 33 tumor types. Next, we used expression profiles of PRRs in skin cutaneous melanoma (SKCM) to build a Cox prognosis model. Then, we analyzed immune infiltration features and immune activity of high risk score and low risk score patients. Finally, we analyzed the single-cell sequencing data of different cancers and detected the expression of PRRs in mouse melanoma model to identify PRRs-expressing cell types. Results We found PRRs had a significantly positive correlation with prognosis in SKCM rather than other tumors, and PRR-based Cox model had a much better prognosis potential than any single PRR. Further analysis shows risk score could indicate immunocyte infiltration and immune activity in SKCM. We also found the expressions of some PRR genes were highly correlated with the expression of immune checkpoints molecules in SKCM, indicating they could be indicators for clinical immune therapy. Finally, we found only in SKCM samples, the expression of PRRs is especially high in a subpopulation of macrophages with a trait of CD206 low expression, probably explaining why PRRs have prognosis potential in melanoma. Conclusions Our study reveals PRR family in macrophages has a positive prognosis potential in melanoma and could be valuable for clinical prognosis and immune therapy.
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Affiliation(s)
- Qihang Zhao
- National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Medical University, Shanghai, China
| | - Qiang Wang
- Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Tengjiao Wang
- Centre for Translational Medicine, Navy Medical University, Shanghai, China
| | - Junfang Xu
- National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Medical University, Shanghai, China
- Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tingting Li
- College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Qiuyan Liu
- National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Medical University, Shanghai, China
| | - Qinghua Yao
- Department of Integrated Chinese and Western Medicine, Cancer Hospital of University of Chinese Academy of Science, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Key Laboratory of Traditional Chinese Medicine Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Pin Wang
- National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Medical University, Shanghai, China
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Shi S, Fan Z, Liu Y, Huang C, Zhou J. Integration Analysis of m6A Related Genes in Skin Cutaneous Melanoma and the Biological Function Research of the SPRR1B. Front Oncol 2021; 11:729045. [PMID: 34737950 PMCID: PMC8560968 DOI: 10.3389/fonc.2021.729045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/27/2021] [Indexed: 01/22/2023] Open
Abstract
Melanoma has gradually entered the public view because of its high morbidity and rising prevalence rate, which is a serious threat to human life and health. Recently, N6-methyladenine (m6A) modification has been increasingly confirmed as a potential role in the development of tumogenesis. The purpose of this study is to explore the role and function of m6a-related regulators in the development of melanoma disease at the molecular, cellular and clinical levels through bioinformatics and traditional experiments. We screened and validated differential expression genes (DEGs) in m6A regulators via the GEO, GTEx, TCGA database. The biological processes and signaling pathway involved by DEGs were improved by constructing bioinformational methods such as PPI, GO enrichment, KEGG enrichment, GSEA enrichment, and immune infiltration analysis. And then, we explored the biological function of the key gene, SPRR1B, through cell invasion, migration, infiltration, and tissue chips. The gene IGF2BP3 which was differentially expressed in m6A regulatory factor gene was screened. The results of the enrichment analysis are significantly enriched in the biological processes and pathways of the skin barrier, epidermal differentiation, cytoskeleton, lymphocyte migration and other pathways, pointing to the direction of tumor immunity and tumor metastasis. Tumor immune-related genes YTHDC1, YTHDC2 and ALKBH5 were found. Knock SPRR1B reduction group had a significantly lower invasive ability, the ability to migrate. Nomogram prediction model shows that SPRR1B increased, expressing a worse prognosis. For this purpose, the relationship between m6A regulatory factor and melanoma progression was explored. At the same time, it was found that the abnormal up-regulated expression of SPRR1B before metastasis would lead to poor prognosis of melanoma. SPRR1B promotes the proliferation, invasion and migration of human melanoma cells.
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Affiliation(s)
- Shupeng Shi
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhihua Fan
- XiangYa School of Medicine, Central South University, Changsha, China
| | - Yang Liu
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Chengyu Huang
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jianda Zhou
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
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Zeng N, Ma L, Cheng Y, Xia Q, Li Y, Chen Y, Lu Z, Lu Q, Jiang F, Luo D. Construction of a Ferroptosis-Related Gene Signature for Predicting Survival and Immune Microenvironment in Melanoma Patients. Int J Gen Med 2021; 14:6423-6438. [PMID: 34675611 PMCID: PMC8502037 DOI: 10.2147/ijgm.s327348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/14/2021] [Indexed: 12/25/2022] Open
Abstract
Objective In this research, we studied the genes associated with ferroptosis to develop a prognostic model and find out an association with tumor immune microenvironment in skin cutaneous melanoma (SKCM) patients. Methods To find SKCM-related ferroptosis genes, we used Cox regression and LASSO approach on 60 genes related to ferroptosis and SKCM-related RNA-seq. Following that, a ferroptosis-related gene signature was created. Time-dependent ROC curve and Kaplan–Meier analysis were calculated to determine its capability of prediction. Besides, several assessments were used to evaluate overall survival (OS), accompanied by the creation of a nomogram for the clinicopathologic factors and the ferroptosis-related gene signature we established. We also investigated the relationship between ferroptosis-related gene signature with three immune checkpoints and immune cell infiltration. Results Our prognostic model included two genes (ALOX5, CHAC1). In both TCGA and GEO cohorts, OS was lower in high-risk category. Using our gene signature, we can reliably predict OS. Additionally, our gene signature can predict immune cell infiltration and SKCM immunotherapy response. Conclusion Our gene signature has shown to be a reliable predictor of OS, reflect the immune microenvironment, and predict the effectiveness of immunotherapy for SKCM patients.
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Affiliation(s)
- Ni Zeng
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China.,Department of Dermatology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, People's Republic of China
| | - Liwen Ma
- Department of Dermatology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yuxin Cheng
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Qingyue Xia
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yueyue Li
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yihe Chen
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Zhiyu Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Qian Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Feng Jiang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, People's Republic of China
| | - Dan Luo
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
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Zhou S, Sun Y, Chen T, Wang J, He J, Lyu J, Shen Y, Chen X, Yang R. The Landscape of the Tumor Microenvironment in Skin Cutaneous Melanoma Reveals a Prognostic and Immunotherapeutically Relevant Gene Signature. Front Cell Dev Biol 2021; 9:739594. [PMID: 34660598 PMCID: PMC8517264 DOI: 10.3389/fcell.2021.739594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 08/23/2021] [Indexed: 01/15/2023] Open
Abstract
The tumorigenesis of skin cutaneous melanoma (SKCM) remains unclear. The tumor microenvironment (TME) is well known to play a vital role in the onset and progression of SKCM. However, the dynamic mechanisms of immune regulation are insufficient. We conducted a comprehensive analysis of immune cell infiltration in the TME. Based on the differentially expressed genes (DEGs) in clusters grouped by immune infiltration status, a set of hub genes related to the clinical prognosis of SKCM and tumor immune infiltration was explored. Methods: We analyzed immune cell infiltration in two independent cohorts and assessed the relationship between the internal pattern of immune cell infiltration and SKCM characteristics, including clinicopathological features, potential biological pathways, and gene mutations. Genes related to the infiltration pattern of TME immune cells were determined. Furthermore, the unsupervised clustering method (k-means) was used to divide samples into three different categories according to TME, which were defined as TME cluster-A, -B, and -C. DEGs among three groups of samples were analyzed as signature genes. We further distinguished common DEGs between three groups of samples according to whether differences were significant and divided DEGs into the Signature gene-A group with significant differences and the Signature gene-B group with insignificant differences. The Signature gene-A gene set mainly had exon skipping in SKCM, while the Signature gene-B gene set had no obvious alternative splicing form. Subsequently, we analyzed genetic variations of the two signatures and constructed a competing endogenous RNA (ceRNA) regulatory network. LASSO Cox regression was used to determine the immune infiltration signature and risk score of SKCM. Finally, we obtained 13 hub genes and calculated the risk score based on the coefficient of each gene to explore the impact of the high- and low-risk scores on biologically related functions and prognosis of SKCM patients further. The correlation between the risk score and clinicopathological characteristics of SKCM patients indicated that a low-risk score was associated with TME cluster-A classification (p < 0.001) and metastatic SKCM (p < 0.001). Thirteen hub genes also showed different prognostic effects in pan-cancer. The results of univariate and multivariate Cox analyses revealed that risk score could be used as an independent risk factor for predicting the prognosis of SKCM patients. The nomogram that integrated clinicopathological characteristics and immune characteristics to predict survival probability was based on multivariate Cox regression. Finally, 13 hub genes that showed different prognostic effects in pan-cancers were obtained. According to immunohistochemistry staining results, Ube2L6, SRPX2, and IFIT2 were expressed at higher levels, while CLEC4E, END3, and KIR2DL4 were expressed at lower levels in 25 melanoma specimens. Conclusion: We performed a comprehensive assessment of the immune-associated TME. To elucidate the potential development of immune-genomic features in SKCM, we constructed an unprecedented set of immune characteristic genes (EDN3, CLEC4E, SRPX2, KIR2DL4, UBE2L6, and IFIT2) related to the immune landscape of TME. These genes are related to different prognoses and drug responses of SKCM. The immune gene signature constructed can be used as a robust prognostic biomarker of SKCM and a predictor of an immunotherapy effect.
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Affiliation(s)
- Sitong Zhou
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Yidan Sun
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Tianqi Chen
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jingru Wang
- Department of Burn Surgery and Skin Regeneration, The First People's Hospital of Foshan, Foshan, China
| | - Jia He
- Department of Burn Surgery and Skin Regeneration, The First People's Hospital of Foshan, Foshan, China
| | - Jin Lyu
- Department of Pathology, The First People's Hospital of Foshan, Foshan, China
| | - Yanna Shen
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
| | - Xiaodong Chen
- Department of Burn Surgery and Skin Regeneration, The First People's Hospital of Foshan, Foshan, China
| | - Ronghua Yang
- Department of Burn Surgery and Skin Regeneration, The First People's Hospital of Foshan, Foshan, China
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Nurzat Y, Su W, Min P, Li K, Xu H, Zhang Y. Identification of Therapeutic Targets and Prognostic Biomarkers Among Integrin Subunits in the Skin Cutaneous Melanoma Microenvironment. Front Oncol 2021; 11:751875. [PMID: 34660316 PMCID: PMC8514842 DOI: 10.3389/fonc.2021.751875] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
The roles of different integrin alpha/beta (ITGA/ITGB) subunits in skin cutaneous melanoma (SKCM) and their underlying mechanisms of action remain unclear. Oncomine, UALCAN, GEPIA, STRING, GeneMANIA, cBioPortal, TIMER, TRRUST, and Webgestalt analysis tools were used. The expression levels of ITGA3, ITGA4, ITGA6, ITGA10, ITGB1, ITGB2, ITGB3, ITGB4, and ITGB7 were significantly increased in SKCM tissues. The expression levels of ITGA1, ITGA4, ITGA5, ITGA8, ITGA9, ITGA10, ITGB1, ITGB2, ITGB3, ITGB5, ITGB6 and ITGB7 were closely associated with SKCM metastasis. The expression levels of ITGA1, ITGA4, ITGB1, ITGB2, ITGB6, and ITGB7 were closely associated with the pathological stage of SKCM. The expression levels of ITGA6 and ITGB7 were closely associated with disease-free survival time in SKCM, and the expression levels of ITGA6, ITGA10, ITGB2, ITGB3, ITGB6, ITGB7, and ITGB8 were markedly associated with overall survival in SKCM. We also found significant correlations between the expression of integrin subunits and the infiltration of six types of immune cells (B cells, CD8+ T cells, CD4+T cells, macrophages, neutrophils, and dendritic cells). Finally, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed, and protein-protein interaction (PPI) networks were constructed. We have identified abnormally-expressed genes and gene regulatory networks associated with SKCM, improving understanding of the underlying pathogenesis of SKCM.
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Affiliation(s)
- Yeltai Nurzat
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Weijie Su
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Peiru Min
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Ke Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Heng Xu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Yixin Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
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Fan Y, Liang X, Yu D. Low expression of endoplasmic reticulum stress-related gene SERP1 is associated with poor prognosis and immune infiltration in skin cutaneous melanoma. Aging (Albany NY) 2021; 13:23036-23071. [PMID: 34613934 PMCID: PMC8544316 DOI: 10.18632/aging.203594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023]
Abstract
Stress-associated endoplasmic reticulum protein 1 (SERP1) is a gene induced by endoplasmic reticulum (ER) stress and a major contributor to multiple tumor types. Skin cutaneous melanoma (SKCM) is a highly aggressive and fatal cancer with poor treatment outcomes after progression. In this study, we evaluated SERP1's role in tumorigenesis, prognosis, and immune infiltration in SKCM. Patients with SKCM had low SERP1 expression. We identified differentially expressed genes between high- and low-SERP1 expression groups and conducted functional, pathway, and gene enrichment analyses. Protein-protein (PPI) and gene-gene interaction (GGI) networks were constructed via STRING and GeneMANIA, respectively. SERP1 mutation information was obtained through cBioPortal; location in the skin was identified through the Human Protein Atlas. Kaplan-Meier analysis revealed an association between low SERP1 expression and overall survival (OS), disease-specific survival (DSS), progress-free interval (PFI) rates, and worse prognosis in patients with multiple clinicopathological features. Cox regression analysis and nomograms further presented SERP1 level as an independent prognostic factor for patients with SKCM. Furthermore, there were significant correlations between SERP1 expression and immune infiltrates; thus, low SERP1 expression is associated with immune cell infiltration and can be considered a poor prognostic biomarker in patients with SKCM. Stress-associated endoplasmic reticulum protein 1 (SERP1) is a gene induced by endoplasmic reticulum (ER) stress and a major contributor to multiple tumor types. Skin cutaneous melanoma (SKCM) is a highly aggressive and fatal cancer with poor treatment outcomes after progression. In this study, we evaluated SERP1's role in tumorigenesis, prognosis, and immune infiltration in SKCM. Patients with SKCM had low SERP1 expression. We identified differentially expressed genes between high- and low-SERP1 expression groups and conducted functional, pathway, and gene enrichment analyses. Protein-protein (PPI) and gene-gene interaction (GGI) networks were constructed via STRING and GeneMANIA, respectively. SERP1 mutation information was obtained through cBioPortal; location in the skin were identified through the Human Protein Atlas. Kaplan-Meier analysis revealed an association between low SERP1 expression and overall survival (OS), disease-specific survival (DSS), progress-free interval (PFI) rates, and worse prognosis in patients with multiple clinicopathological features. Cox regression analysis and nomograms further presented SERP1 level as an independent prognostic factor for patients with SKCM. Furthermore, there were significant correlations between SERP1 expression and immune infiltrates; thus, low SERP1 expression is associated with immune cell infiltration and can be considered a poor prognostic biomarker in patients with SKCM.
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Affiliation(s)
- Yuchao Fan
- Department of Anesthesiology, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Xiao Liang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Deshui Yu
- Department of Anesthesiology, The Second People’s Hospital of Yibin, Yibin, Sichuan Province, China
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Meng J, Huang X, Qiu Y, Yu M, Lu J, Yao J. Characterization of m6A-Related Genes Landscape in Skin Cutaneous Melanoma to Aid Immunotherapy and Assess Prognosis. Int J Gen Med 2021; 14:5345-5361. [PMID: 34522131 PMCID: PMC8434882 DOI: 10.2147/ijgm.s328522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/24/2021] [Indexed: 01/21/2023] Open
Abstract
Background Skin cutaneous melanoma (SKCM) is the most malignant tumor among skin cancers. Immunotherapy has shown a great role in the advantageous prognosis of SKCM. However, only a small percentage of people can benefit from immunotherapy. To date, there has been insufficient evidence to reveal the prognostic value of m6A in SKCM and its relationship with the infiltration of immune cells and the efficacy of immunotherapy. Methods Here, we synthetically analyzed 23 m6A regulators from SKCM samples collected from the TCGA and GEO databases. We defined three m6A modification patterns and constructed m6A scores using principal component analysis (PCA). Results We found significant differences in overall survival (OS) and immune infiltration between different m6A subclusters. Besides, m6A score was positively correlated with regulatory T-cell and helper T-cell content, which may account for the association of high m6A scores with superior prognosis. Multivariate Cox regression analysis revealed that the m6A score was an independent prognostic indicator. Moreover, patients with high m6A scores showed a better response to immunotherapy, and this result was further validated in two independent immunotherapy cohorts receiving anti-PD-1/PD-L1 therapy. Conclusion The findings suggested the m6A score can screen suitable candidates for immunotherapy and can predict immunotherapy response. This analysis of different m6A patterns in a large sample of SKCM expanded our understanding of TME and provided new ideas for prognostic assessment and personalized immunotherapy strategies for SKCM patients.
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Affiliation(s)
- Jinzhi Meng
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Xing Huang
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Yue Qiu
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Miao Yu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Jinfeng Lu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Jun Yao
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
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Yang R, Wang Z, Li J, Pi X, Gao R, Ma J, Qing Y, Zhou S. The Identification of the Metabolism Subtypes of Skin Cutaneous Melanoma Associated With the Tumor Microenvironment and the Immunotherapy. Front Cell Dev Biol 2021; 9:707677. [PMID: 34458265 PMCID: PMC8397464 DOI: 10.3389/fcell.2021.707677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023] Open
Abstract
Skin cutaneous melanoma (SKCM) is a highly aggressive and resistant cancer with immense metabolic heterogeneity. Here, we performed a comprehensive examination of the diverse metabolic signatures of SKCM based on non-negative matrix factorization (NMF) categorization, clustering SKCM into three distinct metabolic subtypes (C1, C2, and C3). Next, we evaluated the metadata sets of the metabolic signatures, prognostic values, transcriptomic features, tumor microenvironment signatures, immune infiltration, clinical features, drug sensitivity, and immunotherapy response of the subtypes and compared them with those of prior publications for classification. Subtype C1 was associated with high metabolic activity, low immune scores, and poor prognosis. Subtype C2 displayed low metabolic activity, high immune infiltration, high stromal score, and high expression of immune checkpoints, demonstrating the drug sensitivity to PD-1 inhibitors. The C3 subtype manifested moderate metabolic activity, high enrichment in carcinogenesis-relevant pathways, high levels of CpG island methylator phenotype (CIMP), and poor prognosis. Eventually, a 90-gene classifier was produced to implement the SKCM taxonomy and execute a consistency test in different cohorts to validate its reliability. Preliminary validation was performed to ascertain the role of SLC7A4 in SKCM. These results indicated that the 90-gene signature can be replicated to stably identify the metabolic classification of SKCM. In this study, a novel SKCM classification approach based on metabolic gene expression profiles was established to further understand the metabolic diversity of SKCM and provide guidance on precisely targeted therapy to patients with the disease.
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Affiliation(s)
- Ronghua Yang
- Department of Burn Surgery and Skin Regeneration, The First People's Hospital of Foshan, Foshan, China
| | - Zhengguang Wang
- Department of Orthopedics, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jiehua Li
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Xiaobing Pi
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Runxing Gao
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, China
| | - Jun Ma
- Department of Burns, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Qing
- Department of Oncology, Affiliated Hospital of Chengdu University, Chengdu, China
| | - Sitong Zhou
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
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41
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Li Y, Lyu S, Gao Z, Zha W, Wang P, Shan Y, He J, Huang S. Identification of Potential Prognostic Biomarkers Associated With Cancerometastasis in Skin Cutaneous Melanoma. Front Genet 2021; 12:687979. [PMID: 34367245 PMCID: PMC8337057 DOI: 10.3389/fgene.2021.687979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is a highly aggressive tumor. The mortality and drug resistance among it are high. Thus, exploring predictive biomarkers for prognosis has become a priority. We aimed to find immune cell-based biomarkers for survival prediction. Here 321 genes were differentially expressed in immune-related groups after ESTIMATE analysis and differential analysis. Two hundred nineteen of them were associated with the metastasis of SKCM via weighted gene co-expression network analysis. Twenty-six genes in this module were hub genes. Twelve of the 26 genes were related to overall survival in SKCM patients. After a multivariable Cox regression analysis, we obtained six of these genes (PLA2G2D, IKZF3, MS4A1, ZC3H12D, FCRL3, and P2RY10) that were independent prognostic signatures, and a survival model of them performed excellent predictive efficacy. The results revealed several essential genes that may act as significant prognostic factors of SKCM, which could deepen our understanding of the metastatic mechanisms and improve cancer treatment.
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Affiliation(s)
- Yang Li
- Dermatology, The Third People's Hospital of Hangzhou, Hangzhou, China
| | - Shanshan Lyu
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhe Gao
- Dermatology, The Third People's Hospital of Hangzhou, Hangzhou, China
| | - Weifeng Zha
- Dermatology, The Third People's Hospital of Hangzhou, Hangzhou, China
| | - Ping Wang
- Dermatology, The Third People's Hospital of Hangzhou, Hangzhou, China
| | - Yunyun Shan
- Dermatology, The Third People's Hospital of Hangzhou, Hangzhou, China
| | - Jianzhong He
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Suyang Huang
- Dermatology, The Third People's Hospital of Hangzhou, Hangzhou, China
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Ju A, Tang J, Chen S, Fu Y, Luo Y. Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis. Front Oncol 2021; 11:709077. [PMID: 34327145 PMCID: PMC8313829 DOI: 10.3389/fonc.2021.709077] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/30/2021] [Indexed: 01/17/2023] Open
Abstract
Skin cutaneous melanoma (SKCM) is a chronically malignant tumor with a high mortality rate. Pyroptosis, a kind of pro-inflammatory programmed cell death, has been linked to cancer in recent studies. However, the value of pyroptosis in the diagnosis and prognosis of SKCM is not clear. In this study, it was discovered that 20 pyroptosis-related genes (PRGs) differed in expression between SKCM and normal tissues, which were related to diagnosis and prognosis. Firstly, based on these genes, nine machine-learning algorithms were shown to perform well in constructing diagnostic classifiers, including K-Nearest Neighbor (KNN), logistic regression, Support Vector Machine (SVM), Artificial Neural Network (ANN), decision tree, random forest, XGBoost, LightGBM, and CatBoost. Secondly, the least absolute shrinkage and selection operator (LASSO) Cox regression analysis was applied and the prognostic model was constructed based on 9 PRGs. Subgroups in low and high risks determined by the prognostic model were shown to have different survival. Thirdly, functional enrichment analyses were performed by applying the gene set enrichment analysis (GSEA), and results suggested that the risk was related to immune response. In conclusion, the expression signatures of pyroptosis-related genes are effective and robust in the diagnosis and prognosis of SKCM, which is related to immunity.
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Affiliation(s)
- Anji Ju
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing, China.,Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaze Tang
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing, China.,Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuohua Chen
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing, China.,Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Fu
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing, China.,Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yongzhang Luo
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing, China.,Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
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43
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Ying H, Lin A, Liang J, Zhang J, Luo P. Association Between FSIP2 Mutation and an Improved Efficacy of Immune Checkpoint Inhibitors in Patients With Skin Cutaneous Melanoma. Front Mol Biosci 2021; 8:629330. [PMID: 34113648 PMCID: PMC8186463 DOI: 10.3389/fmolb.2021.629330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/06/2021] [Indexed: 12/24/2022] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) have shown remarkable success in treating skin cutaneous melanoma (SKCM); however, the response to treatment varies greatly between patients. Considering that the efficacy of ICI treatment is influenced by many factors, we selected the Fibrosheath interacting protein 2 (FSIP2) gene and systematically analyzed its potential to predict the efficacy of ICI treatment. Methods Patient data were collected from an ICI treatment cohort (n = 120) and a The Cancer Genome Atlas (TCGA)-SKCM cohort (n = 467). The data were divided into an FSIP2-mutant (MT) group and FSIP2-wild-type (WT) group according to FSIP2 mutation status. In this study, we analyzed the patients' overall survival rate, tumor mutational burden (TMB), neoantigen load (NAL), copy number variation (CNV), cell infiltration data and immune-related genes. We used gene set enrichment analysis (GSEA) to delineate biological pathways and processes associated with the efficacy of immunotherapy. Results The efficacy of ICI treatment of SKCM patients with FSIP2 mutation was significantly better than that of patients without FSIP2 mutation. The patients in the FSIP2-MT group had higher tumor immunogenicity and lower regulatory T cell (Treg) infiltration. Results of GSEA showed that pathways related to tumor progression (MAPK and FGFR), immunomodulation, and IL-2 synthesis inhibition were significantly downregulated in the FSIP2-MT group. Conclusion Our research suggests that the FSIP2 gene has the potential to predict the efficacy of ICI treatment. The high tumor immunogenicity and low Treg levels observed may be closely related to the fact that patients with FSIP2-MT can benefit from ICI treatment.
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Affiliation(s)
- Haoxuan Ying
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Southern Medical University, Guangzhou, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Junyi Liang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Shin HJ, Lee KJ, Gil M. Multiomic Analysis of Cereblon Expression and Its Prognostic Value in Kidney Renal Clear Cell Carcinoma, Lung Adenocarcinoma, and Skin Cutaneous Melanoma. J Pers Med 2021; 11:jpm11040263. [PMID: 33916291 PMCID: PMC8065640 DOI: 10.3390/jpm11040263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/09/2021] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
Cereblon (CRBN) is a component of the E3 ubiquitin ligase complex that plays crucial roles in various cellular processes. However, no systematic studies on the expression and functions of CRBN in solid tumors have been conducted to date. Here, we analyzed CRBN expression and its clinical value using several bioinformatic databases. CRBN mRNA expression was downregulated in various cancer types compared to normal cells. Survival analysis demonstrated that overall survival was significantly positively correlated with CRBN expression in some cancer types including lung adenocarcinoma (LUAD), kidney renal clear cell carcinoma (KIRC), and skin cutaneous melanoma (SKCM). CRBN expression was downregulated regardless of clinicopathological characteristics in LUAD and KIRC. Analysis of genes that are commonly correlated with CRBN expression among KIRC, LUAD, and SKCM samples elucidated the potential CRBN-associated mechanisms of cancer progression. Overall, this study revealed the prognostic value of CRBN and its potential associated mechanisms, which may facilitate the development of anti-cancer therapeutic agents.
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Affiliation(s)
- Hyo Jae Shin
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea;
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea
| | - Kyung Jin Lee
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea
- Department of Life Science, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.J.L.); (M.G.)
| | - Minchan Gil
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
- Correspondence: (K.J.L.); (M.G.)
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Zhou X, Peng M, He Y, Peng J, Zhang X, Wang C, Xia X, Song W. CXC Chemokines as Therapeutic Targets and Prognostic Biomarkers in Skin Cutaneous Melanoma Microenvironment. Front Oncol 2021; 11:619003. [PMID: 33767987 PMCID: PMC7985846 DOI: 10.3389/fonc.2021.619003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Background Skin Cutaneous Melanoma (SKCM) is a tumor of the epidermal melanocytes induced by gene activation or mutation. It is the result of the interaction between genetic, constitutional, and environmental factors. SKCM is highly aggressive and is the most threatening skin tumor. The incidence of the disease is increasing year by year, and it is the main cause of death in skin tumors around the world. CXC chemokines in the tumor microenvironment can regulate the transport of immune cells and the activity of tumor cells, thus playing an anti-tumor immunological role and affecting the prognosis of patients. However, the expression level of CXC chemokine in SKCM and its effect on prognosis are still unclear. Method Oncomine, UALCAN, GEPIA, STRING, GeneMANIA, cBioPortal, TIMER, TRRUST, DAVID 6.8, and Metascape were applied in our research. Result The transcription of CXCL1, CXCL5, CXCL8, CXCL9, CXCL10, and CXCL13 in SKCM tissues were significantly higher than those in normal tissues. The pathological stage of SKCM patients is closely related to the expression of CXCL4, CXCL9, CXCL10, CXCL11, CXCL12, and CXCL13. The prognosis of SKCM patients with low transcription levels of CXCL4, CXCL9, CXCL10, CXCL11, and CXCL13 is better. The differential expression of CXC chemokines is mainly associated with inflammatory response, immune response, and cytokine mediated signaling pathways. Our data indicate that the key transcription factors of CXC chemokines are RELA, NF-κB1 and SP1. The targets of CXC chemokines are mainly LCK, LYN, SYK, MAPK2, MAPK12, and ART. The relationship between CXC chemokine expression and immune cell infiltration in SKCM was closed. Conclusions Our research provides a basis for screening SKCM biomarkers, predicting prognosis, and choosing immunotherapy.
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Affiliation(s)
- Xuezhi Zhou
- Hunan Key Laboratory of Ophthalmology, Eye Center of Xiangya Hospital, Central South University, Changsha, China
| | - Manjuan Peng
- Hunan Key Laboratory of Ophthalmology, Eye Center of Xiangya Hospital, Central South University, Changsha, China
| | - Ye He
- Hunan Key Laboratory of Ophthalmology, Eye Center of Xiangya Hospital, Central South University, Changsha, China
| | - Jingjie Peng
- Hunan Key Laboratory of Ophthalmology, Eye Center of Xiangya Hospital, Central South University, Changsha, China
| | - Xuan Zhang
- Hunan Key Laboratory of Ophthalmology, Eye Center of Xiangya Hospital, Central South University, Changsha, China
| | - Chao Wang
- Hunan Key Laboratory of Ophthalmology, Eye Center of Xiangya Hospital, Central South University, Changsha, China
| | - Xiaobo Xia
- Hunan Key Laboratory of Ophthalmology, Eye Center of Xiangya Hospital, Central South University, Changsha, China
| | - Weitao Song
- Hunan Key Laboratory of Ophthalmology, Eye Center of Xiangya Hospital, Central South University, Changsha, China
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Dong X, Song J, Chen B, Qi Y, Jiang W, Li H, Zheng D, Wang Y, Zhang X, Liu H. Exploration of the Prognostic and Immunotherapeutic Value of B and T Lymphocyte Attenuator in Skin Cutaneous Melanoma. Front Oncol 2021; 10:592811. [PMID: 33718105 PMCID: PMC7953043 DOI: 10.3389/fonc.2020.592811] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/22/2020] [Indexed: 01/05/2023] Open
Abstract
B and T lymphocyte attenuator (BTLA) is a newly identified immune checkpoint molecular belonging to the CD28 immunoglobulin superfamily. However, the expression and clinical value of BTLA in skin cutaneous melanoma (SKCM) has not been widely characterized. We found that BTLA levels were upregulated in metastatic melanoma compared to normal skin tissues and primary melanoma. Higher BTLA was also correlated with improved prognosis in SKCM based on several datasets. The multivariate Cox regression model revealed that BTLA was an independent survival indicator in metastatic melanoma. Tumor microenvironment analysis indicated BTLA was positively associated with the infiltrating levels of different immune cells and the activity of the anti-cancer immunity cycle. Importantly, BTLA accurately predicted the outcome of melanoma patients treated with MAGE-A3 blocker or first-line anti-PD-1. The present findings disclose that BTLA is a reliable biomarker for prognosis and immunotherapeutic response and might contribute to developing novel SKCM immunological treatment strategies.
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Affiliation(s)
- Xubin Dong
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jingjing Song
- Department of Children’s Health Care, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Buran Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yufeng Qi
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenjie Jiang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huihui Li
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Danni Zheng
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yinghao Wang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaohua Zhang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Haiguang Liu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Abstract
Skin cutaneous melanoma (SKCM) is a prevalent skin cancer whose metastatic form is dangerous due to its high morbidity and mortality. Previous studies have systematically established the vital role of oxidative stress (OS) in melanoma progression. This study aimed to identify prognostic OS genes closely associated with SKCM and illustrate their potential mechanisms. Transcriptome data and corresponding clinical traits of patients with SKCM were retrieved from The Cancer Genome Atlas and Gene Expression Omnibus databases. A weighted gene co-expression network analysis was conducted to identify relationships between clinical features and OS genes in specific modules. Subsequently, Cox regression analysis was performed on candidate OS genes; four hub prognosis-associated OS genes (AKAP9, VPS13C, ACSL4, and HMOX2) were identified to construct a prognostic model. After a series of bioinformatics analysis, our prognostic model was identified significantly associated with the overall survival of patients with SKCM and metastatic ability of the cancer. Furthermore, our risk model demonstrated improved diagnostic accuracy in the Cancer Genome Atlas and Gene Expression Omnibus cohorts. In addition, we established 2 nomograms based on either risk score or hub genes, which displayed favorable discriminating ability for SKCM. Our results provide novel insight into the potential applications of OS-associated genes in SKCM.
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Affiliation(s)
- Xianpei Wu
- Department of Orthopedics Trauma and Hand Surgery
| | - Jinmin Zhao
- Department of Orthopedics Trauma and Hand Surgery
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration
- Guangxi Collaborative Innovation Center for Biomedicine
- Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
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Si Y, Lin A, Ding W, Meng H, Luo P, Zhang J. CARD11 alteration as a candidate biomarker of skin cutaneous melanoma treated with immune checkpoint blockade. Am J Transl Res 2021; 13:286-300. [PMID: 33527024 PMCID: PMC7847528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) can be problematic, including a lack of sustained clinical response, in the treatment of skin cutaneous melanoma (SKCM) patients; therefore, predictive biomarkers are urgently needed. Recently, gene mutations identified by melanoma genomic analysis have shown great predictive potential. METHODS We collected an immunotherapy cohort and The Cancer Genome Atlas (TCGA)-SKCM cohort from published studies and tested the predictive function of the CARD11 mutation. We then further studied the association between the CARD11 mutation and tumor immunogenicity by studying related genes and pathways in the tumor microenvironment (TME). RESULTS In the immunotherapy and TCGA-SKCM cohorts, patients with CARD11-mutant (MT) tumors had longer overall survival (OS) and a better prognosis than those with CARD11-wild-type (WT) tumors. CARD11-MT tumors had higher immunogenicity, and gene expression related to immunosuppression was significantly downregulated in CARD11-MT tumors. We found that immunosuppression-related pathways were significantly downregulated in CARD11-MT tumors, while immune activation-related pathways were significantly upregulated. Additionally, CARD11-MT tumors had more DNA damage response and repair (DDR) pathway mutations. CONCLUSIONS CARD11 mutation is associated with longer OS and a better prognosis after ICI treatment. Therefore, the CARD11 gene can be used as a biomarker for predicting the efficacy of ICIs in SKCM patients.
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Affiliation(s)
- Yutian Si
- Department of Oncology, Zhujiang Hospital, Southern Medical UniversityGuangzhou 510282, China
- Southern Medical UniversityGuangzhou 510282, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical UniversityGuangzhou 510282, China
| | - Weimin Ding
- Department of Oncology, Zhujiang Hospital, Southern Medical UniversityGuangzhou 510282, China
| | - Hui Meng
- Department of Oncology, Zhujiang Hospital, Southern Medical UniversityGuangzhou 510282, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical UniversityGuangzhou 510282, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical UniversityGuangzhou 510282, China
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Xie R, Dong S, Jiang J, Yang C, Li L, Zhao S, Li Y, Wang C, Li S, Xiao Y, Chen L. Development and Validation of an Immune-Related Gene Pair Signature in Skin Cutaneous Melanoma. Clin Cosmet Investig Dermatol 2020; 13:973-986. [PMID: 33364806 PMCID: PMC7751297 DOI: 10.2147/ccid.s281364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Skin cutaneous melanoma (SKCM) is a common skin malignancy worldwide, and its metastasis and mortality rates are high. The molecular characteristics exhibited by tumor-immune interactions have drawn the attention from researchers. Therefore, increased knowledge and new strategies to identify effective immune-related biomarkers may improve the clinical management of SKCM by providing more accurate prognostic information. PATIENTS AND METHODS In this study, we established a prognostic immune-related gene pair (IRGP) signature for predicting the survival of SKCM patients. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases provided gene expression profiles together with clinical information, and the samples were randomly divided into three groups including the training, testing, and validation datasets. The regression model of least absolute shrinkage and selection operator (LASSO) helped to identify a 13-IRGP signature with a significant relation to the survival of SKCM patients. RESULTS The training, TCGA, and independent sets have an average value of area under the curve of 0.79, 0.76, and 0.82, respectively. In addition, this 13-IRGP signature can noticeably divide SKCM patients into high-risk group and low-risk group with significantly different prognoses. Many biological activities such as gene family were enriched among the genes in our IRGP signature. While analyzing the risk signature and clinical characteristics, there was a large difference in the risk score between T stage and tumor stage grouping. Finally, we constructed a nomogram and forest plots of the risk score and clinical features. CONCLUSION In summary, we developed a robust 13-IRGP prognostic signature in SKCM, which can identify and provide new insights into immunological biomarkers.
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Affiliation(s)
- Ran Xie
- PET/CT Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Cancer Center of Yunnan Province, Kunming, Yunnan, People's Republic of China
| | - Suwei Dong
- Second Orthopedic Ward, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Cancer Center of Yunnan Province, Kunming, Yunnan, People's Republic of China
| | - Jie Jiang
- Graduate School, Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Conghui Yang
- PET/CT Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Cancer Center of Yunnan Province, Kunming, Yunnan, People's Republic of China
| | - Lanjiang Li
- Department of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Sheng Zhao
- PET/CT Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Cancer Center of Yunnan Province, Kunming, Yunnan, People's Republic of China
| | - Yunlei Li
- Graduate School, Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Chun Wang
- PET/CT Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Cancer Center of Yunnan Province, Kunming, Yunnan, People's Republic of China
| | - Shujuan Li
- PET/CT Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Cancer Center of Yunnan Province, Kunming, Yunnan, People's Republic of China
| | - Yanbin Xiao
- Second Orthopedic Ward, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Cancer Center of Yunnan Province, Kunming, Yunnan, People's Republic of China
| | - Long Chen
- PET/CT Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Cancer Center of Yunnan Province, Kunming, Yunnan, People's Republic of China
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Zhang J, Liu H, Zhang W, Li Y, Fan Z, Jiang H, Luo J. Identification of lncRNA-mRNA Regulatory Module to Explore the Pathogenesis and Prognosis of Melanoma. Front Cell Dev Biol 2020; 8:615671. [PMID: 33392203 PMCID: PMC7773644 DOI: 10.3389/fcell.2020.615671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 12/21/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is an aggressive form of skin cancer that results in high mortality rate worldwide. It is vital to discover effective prognostic biomarkers and therapeutic targets for the treatment of melanoma. Long non-coding RNA (lncRNA) has been verified to play an essential role in the regulation of gene expression in diseases and tumors. Therefore, it is significant to explore the function of lncRNAs in the development and progression of SKCM. In this paper, a set of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were first screened out using 471 cutaneous melanoma samples and 813 normal skin samples. Gene Ontology and KEGG pathway enrichment analysis were performed to obtain the significant function annotations and pathways of DEmRNAs. We also ran survival analysis on both DElncRNAs and DEmRNAs to identify prognostic-related lncRNAs and mRNAs. Next, a set of hub genes derived from protein-protein interaction (PPI) network analysis and lncRNA target genes screened from starbase-ENCORI database were integrated to construct a lncRNA-mRNA regulatory module, which includes 6 lncRNAs 4 target mRNAs. We further checked the capacity of these lncRNA and mRNA in the diagnosis of melanoma, and found that single lncRNA can effectively distinguish tumor and normal tissue. Moreover, we ran CMap analysis to select a list of small molecule drugs for SKCM, such as EGFR inhibitor AG-490, growth factor receptor inhibitor GW-441756 and apoptosis stimulant betulinic-acid, which have shown therapeutic effect in the treatment of melanoma.
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Affiliation(s)
- Jiaqi Zhang
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Department of Dermatology, Graduate School of Dalian Medical University, Dalian, China
| | - Hui Liu
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Wenhao Zhang
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Yinfang Li
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Zhigang Fan
- Department of Oncology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, China
| | - Hua Jiang
- Department of Oncology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Judong Luo
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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