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Lin X, Shao K, Lin Z, Liang Q, Li X, Chen H, Wu J. Identification of a ferroptosis-related gene signature for the prognosis of pediatric neuroblastoma. Transl Cancer Res 2024; 13:3678-3694. [PMID: 39145053 PMCID: PMC11319987 DOI: 10.21037/tcr-24-269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/24/2024] [Indexed: 08/16/2024]
Abstract
Background Ferroptosis-related genes are correlated with the prognosis of patients with neuroblastoma (NB) remains unknown. This study aims to establish a prognostic ferroptosis-related gene model for predicting prognostic value in pediatric NB patients. Methods The gene expression array and clinical characteristics of NB were downloaded from a public database. Correlations between ferroptosis-related genes and drug responses were analyzed by Childhood Cancer Therapeutics. The prognostic model was constructed by least absolute shrinkage and selection operator (LASSO) Cox regression and was validated in NB patients from the ICGC cohort. The survival analysis was performed by Cox regression analysis. single-sample gene set enrichment analysis (ssGSEA) was used to quantify the immune cell infiltration correlation. Results Overall, 70 genes were identified as ferroptosis-related differentially expressed genes (DEGs) from 247 samples. Then, 13 ferroptosis-related genes were correlated with OS in the univariate Cox regression analysis. Five prognostic ferroptosis-related DEGs (pFR-DEGs) (STEAP3, MAP1LC3A, ULK2, MTOR and TUBE1), which were defined as the intersection of DEGs and prognostic ferroptosis-related genes, were identified and utilized to construct the prognostic signature. The correlation between five pFR-DEGs and drug responses was analyzed, and the box plots indicated that MTOR gene expression was highest, suggesting that MTOR expression is related to progressive NB disease. The receiver operating characteristic (ROC) curve showed that the model had moderate predictive power. The survival analysis indicated that the high-risk group had poor overall survival (OS) (P=2.087×10-06). Univariate and multivariate analyses identified the risk score as a significant prognostic risk factor [P=0.003, hazard ratio (HR) =1.933]. Immune cell infiltration correlation analysis showed that the high-risk group was related to more immune cells. Conclusions The present study indicated a difference in ferroptosis-related gene expression between low- and high-risk NB patients. The ferroptosis-related signature could serve as a prognostic prediction tool. Additionally, immune infiltration might play an important role in different risk groups for NB patients.
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Affiliation(s)
- Xijin Lin
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Kongfeng Shao
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Zhuangbin Lin
- Department of Radiation Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qiandong Liang
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Xiaoyan Li
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Haiyan Chen
- Department of Radiation Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junxin Wu
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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Xu Y, Zeng C, Bin J, Tang H, Li W. Identifying novel circadian rhythm biomarkers for diagnosis and prognosis of melanoma by an integrated bioinformatics and machine learning approach. Aging (Albany NY) 2024; 16:11824-11842. [PMID: 39213172 PMCID: PMC11386929 DOI: 10.18632/aging.205961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/26/2023] [Indexed: 09/04/2024]
Abstract
Melanoma is a highly malignant skin tumor with poor prognosis. Circadian rhythm is closely related to melanoma pathogenesis. This study aimed to identify key circadian rhythm genes (CRGs) in melanoma and explore their potential as diagnostic and prognostic biomarkers. Microarray data of melanoma tissues and normal skins were obtained. Differentially expressed genes were identified and weighted gene co-expression network analysis (WGCNA) was performed to screen hub genes associated with melanoma. By overlapping hub genes with known CRGs, 125 melanoma-related CRGs were identified. Functional enrichment analysis revealed these CRGs were mainly involved in circadian rhythm and other cancer-related pathways. Three machine learning algorithms including LASSO regression, support vector machine-recursive feature elimination (SVM-RFE), and random forest were utilized to select key CRGs. Six CRGs (ABCC2, CA14, EGR3, FBXW7, LDHB, and PSEN2) were identified as key CRGs for melanoma diagnosis and prognosis. Diagnostic values of key CRGs were evaluated by ROC analysis in training and validation sets. Prognostic values of key CRGs were assessed by survival analysis and a multivariate Cox regression prognostic model was constructed. The prognostic model could effectively stratify melanoma patients into high- and low-risk groups with significantly different survival. A nomogram integrating clinical variables and risk score was built to predict 3-, 5- and 10-year overall survival of melanoma patients. In summary, six CRGs were identified as key genes associated with melanoma pathogenesis and may serve as promising diagnostic and prognostic biomarkers. The prognostic model and nomogram could facilitate personalized prognosis evaluation of melanoma patients.
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Affiliation(s)
- Yi Xu
- Department of Plastic Surgery, Second People’s Hospital of Hunan Province, Changsha, Hunan, China
| | - Churuo Zeng
- Department of Plastic Surgery, Second People’s Hospital of Hunan Province, Changsha, Hunan, China
| | - Jie Bin
- Department of Plastic Surgery, Second People’s Hospital of Hunan Province, Changsha, Hunan, China
| | - Hua Tang
- Department of Plastic Surgery, Second People’s Hospital of Hunan Province, Changsha, Hunan, China
| | - Wei Li
- Department of Plastic Surgery, Second People’s Hospital of Hunan Province, Changsha, Hunan, China
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Qiu Z, Deng C, Zhou F, Chen Y, Chen X, Liu X, Ye C, Jin N. Ferroptosis heterogeneity within the tumor microenvironment revealed a genetic blueprint of breast cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:2741-2752. [PMID: 38251953 DOI: 10.1002/tox.24142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/25/2023] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
The tumor microenvironment (TME) significantly influences disease progression through immune infiltration, while ferroptosis, a recently discovered cell death mechanism, plays a crucial role in tumor suppression. However, its role in breast cancer is not clear. In this study, we analyzed bulk RNA and single-cell RNA sequencing data from 1217 samples, including 1104 breast cancer patients and 113 controls, to identify ferroptosis-related genes (FRGs) and construct a prognostic model. Using univariate cox regression, LASSO regression, and multivariate cox regression analysis, we discovered 21 FRGs and 3 TME-related immune cell types with prognostic value. Dimensionality reduction clustering and visualization were performed using the UMAP method, while the immune infiltration process was calculated with the TIP online tool. We employed GSEA enrichment analysis, WGCNA clustering analysis, and correlation analysis to examine functional differences, and the mutation analysis of the best and worst prognosis groups was conducted using the maftools package. Our findings revealed that knocking down the expression of the hub gene SLC39A7 significantly impacted cancer cell apoptosis and combining ferroptosis and TME scores yielded high prognostic power. Epithelial cells and B cells exhibited higher ferroptosis scores, which were independently associated with immune checkpoint blockade (ICB) response and ICB gene expression. This study provides a foundation for further exploration of the relationship between ferroptosis and ICB response in breast cancer. In conclusion, we developed a prognostic model based on ferroptosis and infiltrated immune cells that effectively stratified breast cancer patients and demonstrated the role of SLC39A7 in breast cancer pathogenesis through the regulation of apoptosis.
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Affiliation(s)
- Ziran Qiu
- Department of Surgical Oncology, Loudi, Hunan, China
| | - Chongwen Deng
- Department of Surgical Oncology, Loudi, Hunan, China
| | - Fuyin Zhou
- Department of Surgical Oncology, Loudi, Hunan, China
| | - Yuan Chen
- Department of Surgical Oncology, Loudi, Hunan, China
| | - XinLiang Chen
- Department of Surgical Oncology, Loudi, Hunan, China
| | - Xinyu Liu
- Department of Otolaryngology, Head and Neck Surgery, Loudi City Central Hospital, Loudi, Hunan, China
| | - Chunhua Ye
- Department of Surgical Oncology, Loudi, Hunan, China
| | - Na Jin
- Department of Surgical Oncology, Loudi, Hunan, China
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Liu X, Zhang HY, Deng HA. Transcriptome and single-cell transcriptomics reveal prognostic value and potential mechanism of anoikis in skin cutaneous melanoma. Discov Oncol 2024; 15:70. [PMID: 38460046 PMCID: PMC10924820 DOI: 10.1007/s12672-024-00926-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/05/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Skin cutaneous melanoma (SKCM) is a highly lethal cancer, ranking among the top four deadliest cancers. This underscores the urgent need for novel biomarkers for SKCM diagnosis and prognosis. Anoikis plays a vital role in cancer growth and metastasis, and this study aims to investigate its prognostic value and mechanism of action in SKCM. METHODS Utilizing consensus clustering, the SKCM samples were categorized into two distinct clusters A and B based on anoikis-related genes (ANRGs), with the B group exhibiting lower disease-specific survival (DSS). Gene set enrichment between distinct clusters was examined using Gene Set Variation Analysis (GSVA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. RESULTS We created a predictive model based on three anoikis-related differently expressed genes (DEGs), specifically, FASLG, IGF1, and PIK3R2. Moreover, the mechanism of these prognostic genes within the model was investigated at the cellular level using the single-cell sequencing dataset GSE115978. This analysis revealed that the FASLG gene was highly expressed on cluster 1 of Exhausted CD8( +) T (Tex) cells. CONCLUSIONS In conclusion, we have established a novel classification system for SKCM based on anoikis, which carries substantial clinical implications for SKCM patients. Notably, the elevated expression of the FASLG gene on cluster 1 of Tex cells could significantly impact SKCM prognosis through anoikis, thus offering a promising target for the development of immunotherapy for SKCM.
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Affiliation(s)
- Xing Liu
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Hong-Yan Zhang
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Hong-Ao Deng
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
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Roccuzzo G, Bongiovanni E, Tonella L, Pala V, Marchisio S, Ricci A, Senetta R, Bertero L, Ribero S, Berrino E, Marchiò C, Sapino A, Quaglino P, Cassoni P. Emerging prognostic biomarkers in advanced cutaneous melanoma: a literature update. Expert Rev Mol Diagn 2024; 24:49-66. [PMID: 38334382 DOI: 10.1080/14737159.2024.2314574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
INTRODUCTION Over the past two years, the scientific community has witnessed an exponential growth in research focused on identifying prognostic biomarkers for melanoma, both in pre-clinical and clinical settings. This surge in studies reflects the need of developing effective prognostic indicators in the field of melanoma. AREAS COVERED The aim of this work is to review the scientific literature on the most recent findings on the development or validation of prognostic biomarkers in melanoma, in the attempt of providing both clinicians and researchers with an updated broad synopsis of prognostic biomarkers in cutaneous melanoma. EXPERT OPINION While the field of prognostic biomarkers in melanoma appears promising, there are several complexities and limitations to address. The interdependence of clinical, histological, and molecular features requires accurate classification of different biomarker families. Correlation does not imply causation, and adjustments for confounding factors are often overlooked. In this scenario, large-scale studies based on high-quality clinical trial data can provide more reliable evidence. It is essential to avoid oversimplification by focusing on a single biomarker, as the interactions among multiple factors contribute to define the disease course and patient's outcome. Furthermore, implementing well-supported evidence in real-life settings can help advance prognostic biomarker research in melanoma.
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Affiliation(s)
- Gabriele Roccuzzo
- Department of Medical Sciences, Section of Dermatology, University of Turin, Turin, Italy
| | - Eleonora Bongiovanni
- Department of Medical Sciences, Section of Dermatology, University of Turin, Turin, Italy
| | - Luca Tonella
- Department of Medical Sciences, Section of Dermatology, University of Turin, Turin, Italy
| | - Valentina Pala
- Department of Medical Sciences, Section of Dermatology, University of Turin, Turin, Italy
| | - Sara Marchisio
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alessia Ricci
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Rebecca Senetta
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Simone Ribero
- Department of Medical Sciences, Section of Dermatology, University of Turin, Turin, Italy
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Pietro Quaglino
- Department of Medical Sciences, Section of Dermatology, University of Turin, Turin, Italy
| | - Paola Cassoni
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
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Song B, Wang K, Peng Y, Zhu Y, Cui Z, Chen L, Yu Z, Song B. Combined signature of G protein-coupled receptors and tumor microenvironment provides a prognostic and therapeutic biomarker for skin cutaneous melanoma. J Cancer Res Clin Oncol 2023; 149:18135-18160. [PMID: 38006451 DOI: 10.1007/s00432-023-05486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/19/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND G protein-coupled receptors (GPCRs) have been shown to have an important role in tumor development and metastasis, and abnormal expression of GPCRs is significantly associated with poor prognosis of tumor patients. In this study, we analyzed the GPCRs-related gene (GPRGs) and tumor microenvironment (TME) in skin cutaneous melanoma (SKCM) to construct a prognostic model to help SKCM patients obtain accurate clinical treatment strategies. METHODS SKCM expression data and clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Differential expression analysis, LASSO algorithm, and univariate and multivariate cox regression analysis were used to screen prognosis-related genes (GPR19, GPR146, S1PR2, PTH1R, ADGRE5, CXCR3, GPR143, and OR2I1P) and multiple prognosis-good immune cells; the data set was analyzed according to above results and build up a GPR-TME classifier. The model was further subjected to immune infiltration, functional enrichment, tumor mutational load, immunotherapy prediction, and scRNA-seq data analysis. Finally, cellular experiments were conducted to validate the functionality of the key gene GPR19 in the model. RESULTS The findings indicate that high expression of GPRGs is associated with a poor prognosis in patients with SKCM, highlighting the significant role of GPRGs and the tumor microenvironment (TME) in SKCM development. Notably, the group characterized by low GPR expression and a high TME exhibited the most favorable prognosis and immunotherapeutic efficacy. Furthermore, cellular assays demonstrated that knockdown of GPR19 significantly reduced the proliferation, migration, and invasive capabilities of melanoma cells in A375 and A2058 cell lines. CONCLUSION This study provides novel insights for the prognosis evaluation and treatment of melanoma, along with the identification of a new biomarker, GPR19.
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Affiliation(s)
- Binyu Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Kai Wang
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Yixuan Peng
- School of Basic Medicine, The Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China
| | - Yuhan Zhu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Zhiwei Cui
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Lin Chen
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China.
| | - Zhou Yu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China.
| | - Baoqiang Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China.
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Zhao S, Zhu Y, Liu H, He X, Xie J. System analysis based on the pyroptosis-related genes identifes GSDMD as a novel therapy target for skin cutaneous melanoma. J Transl Med 2023; 21:801. [PMID: 37950289 PMCID: PMC10636830 DOI: 10.1186/s12967-023-04513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/08/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Skin cutaneous melanoma (SKCM) is the most aggressive skin cancer, accounting for more than 75% mortality rate of skin-related cancers. As a newly identified programmed cell death, pyroptosis has been found to be closely associated with tumor progression. Nevertheless, the prognostic significance of pyroptosis in SKCM remains elusive. METHODS A total of 469 SKCM samples and 812 normal samples were obtained from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Firstly, differentially expressed pyroptosis-related genes (PRGs) between normal samples and SKCM samples were identified. Secondly, we established a prognostic model based on univariate Cox and LASSO Cox regression analyses, which was validated in the test cohort from GSE65904. Thirdly, a nomogram was used to predict the survival probability of SKCM patients. The R package "pRRophetic" was utilized to identify the drug sensitivity between the low- and high-risk groups. Tumor immune infiltration was evaluated using "immuneeconv" R package. Finally, the function of GSDMD and SB525334 was explored in A375 and A2058 cells. RESULTS Based on univariate Cox and LASSO regression analyses, we established a prognostic model with identified eight PRGs (AIM2, CASP3, GSDMA, GSDMC, GSDMD, IL18, NLRP3, and NOD2), which was validated in the test cohort. SKCM patients were divided into low- and high-risk groups based on the median of risk score. Kaplan-Meier survival analysis showed that high-risk patients had shorter overall survival than low-risk patients. Additionally, time-dependent ROC curves validated the accuracy of the risk model in predicting the prognosis of SKCM. More importantly, 4 small molecular compounds (SB525334, SR8278, Gemcitabine, AT13387) were identified, which might be potential drugs for patients in different risk groups. Finally, overexpression of GSDMD and SB525334 treatment inhibit the proliferation, migration, and invasion of SKCM cells. CONCLUSION In this study, we constructed a prognostic model based on PRGs and identified GSDMD as a potential therapeutic target, which provide new insights into SKCM treatment.
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Affiliation(s)
- Shixin Zhao
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yongkang Zhu
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hengdeng Liu
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xuefeng He
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Julin Xie
- Department of Burns, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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Song B, Peng Y, Zheng Y, Zhu Y, Liu W, Wang K, Cui Z, Song B. Role of single-cell ferroptosis regulation in intercellular communication and skin cutaneous melanoma progression and immunotherapy. Cancer Immunol Immunother 2023; 72:3523-3541. [PMID: 37638981 DOI: 10.1007/s00262-023-03504-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND The involvement of ferroptosis in the pathogenesis and progression of various cancers has been well established. However, limited studies have investigated the role of ferroptosis-mediated tumor microenvironment (TME) in skin cutaneous melanoma (SKCM). METHODS By leveraging single-cell RNA sequencing data, the nonnegative matrix factorization (NMF) approach was employed to comprehensively characterize and identify distinct gene signatures within ferroptosis-associated TME cell clusters. Prognostic and treatment response analyses were conducted using both bulk datasets and external cancer cohort to evaluate the clinical implications of TME clusters. RESULTS This NMF-based analysis successfully delineated fibroblasts, macrophages, T cells, and B cells into multiple clusters, enabling the identification of unique gene expression patterns and the annotation of distinct TME clusters. Furthermore, pseudotime trajectories, enrichment analysis, cellular communication analysis, and gene regulatory network analysis collectively demonstrated significant intercellular communication between key TME cell clusters, thereby influencing tumor cell development through diverse mechanisms. Importantly, our bulk RNA-seq analysis revealed the prognostic significance of ferroptosis-mediated TME cell clusters in SKCM patients. Moreover, our analysis of immune checkpoint blockade highlighted the crucial role of TME cell clusters in tumor immunotherapy, facilitating the discovery of potential immunotherapeutic targets. CONCLUSIONS In conclusion, this pioneering study employing NMF-based analysis unravels the intricate cellular communication mediated by ferroptosis within the TME and its profound implications for the pathogenesis and progression of SKCM. We provide compelling evidence for the prognostic value of ferroptosis-regulated TME cell clusters in SKCM, as well as their potential as targets for immunotherapy.
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Affiliation(s)
- Binyu Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Yixuan Peng
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
- School of Basic Medicine, The Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China
| | - Yu Zheng
- Hospital for Skin Disease (Institute of Dermatology), Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Yuhan Zhu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Wei Liu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Kai Wang
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Zhiwei Cui
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Baoqiang Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Chanle West Road, Xi'an, 710032, Shaanxi Province, China.
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Feng J, Wang J, Xu Y, Lu F, Zhang J, Han X, Zhang C, Wang G. Construction and validation of a novel cuproptosis-mitochondrion prognostic model related with tumor immunity in osteosarcoma. PLoS One 2023; 18:e0288180. [PMID: 37405988 DOI: 10.1371/journal.pone.0288180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND The purpose of this study was to develop a new prognostic model for osteosarcoma based on cuproptosis-mitochondrion genes. MATERIALS AND METHODS The data of osteosarcoma were obtained from TARGET database. By using Cox regression and LASSO regression analysis, a novel risk score was constructed based on cuproptosis-mitochondrion genes. Kaplan-Meier, ROC curve and independent prognostic analyses were performed to validate the risk score in GSE21257 dataset. Then, a predictive nomogram was constructed and further validated by calibration plot, C-index and ROC curve. Based on the risk score, all patients were divided into high-risk and low-risk group. GO and KEGG enrichment, immune correlation and drug sensitivity analyses were performed between groups. Real-time quantitative PCR verified the expression of cuproptosis-mitochondrion prognostic model genes in osteosarcoma. And we explored the function of FDX1 in osteosarcoma by western blotting, CCK8, colony formation assay, wound healing assay and transwell assays. RESULTS A total of six cuproptosis-mitochondrion genes (FDX1, COX11, MFN2, TOMM20, NDUFB9 and ATP6V1E1) were identified. A novel risk score and associated prognostic nomogram were constructed with high clinical application value. Strong differences in function enrichment and tumor immune microenvironment were shown between groups. Besides, the correlation of cuproptosis-mitochondrion genes and drug sensitivity were revealed to search for potential therapeutic target. The expression of FDX1, COX11, MFN2, TOMM20 and NDUFB9 at mRNA level was elevated in osteosarcoma cells compared with normal osteoblast hFOB1.19. The mRNA expression level of ATP6V1E1 was decreased in osteosarcoma. Compared with hFOB1.19, western blotting revealed that the expression of FDX1 was significantly elevated in osteosarcoma cells. Functional experiments indicated that FDX1 mainly promoted the migration of osteosarcoma rather than proliferation. CONCLUSIONS We developed a novel prognostic model of osteosarcoma based on cuproptosis-mitochondrion genes, which provided great guidance in survival prediction and individualized treatment decision making for patients with osteosarcoma.
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Affiliation(s)
- Jinyan Feng
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jinwu Wang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yao Xu
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Feng Lu
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jin Zhang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xiuxin Han
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Chao Zhang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Guowen Wang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
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10
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Li G, Zhang H, Zhao J, Liu Q, Jiao J, Yang M, Wu C. Machine learning-based construction of immunogenic cell death-related score for improving prognosis and response to immunotherapy in melanoma. Aging (Albany NY) 2023; 15:2667-2688. [PMID: 37036471 PMCID: PMC10120887 DOI: 10.18632/aging.204636] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/24/2023] [Indexed: 04/09/2023]
Abstract
BACKGROUND Immunogenic cell death (ICD) is a form of regulated cell death (RCD) which could drive the activation of the innate and adaptive immune responses. In this work, we aimed to develop an ICD-related signature to facilitate the assessment of prognosis and immunotherapy response for melanoma patients. METHODS A set of machine learning methods, including consensus clustering, non-negative matrix factorization (NMF) method and least absolute shrinkage and selection operator (LASSO) logistic regression model, and bioinformatics analytic tools were integrated to construct an ICD-related risk score (ICDscore). CIBERSORT and ESTIMATE algorithm were used to evaluate the infiltration of immune cells. The 'pRRophetic' package in R and 6 cohorts of melanoma patients receiving immunotherapy were used for therapy sensitivity analyses. The predictive performance between ICDscore with other mRNA signatures were also compared. RESULTS The ICDscore could predict prognosis and immunotherapy response in multiple cohorts, and displayed superior performance than other forms of cell death-related signatures or 52 published signatures. The melanoma patients with low ICDscore were marked with high infiltration of immune cells, high expression of immune checkpoint inhibitor-related genes, and increased tumor mutation burden. CONCLUSIONS In conclusion, we constructed a stable and robust ICD-related signature for evaluating the prognosis and benefits of immunotherapy, and it could serve as a promising tool to guide decision-making and surveillance for individual melanoma patients.
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Affiliation(s)
- Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Key Laboratory of Modern Teaching Technology, Ministry of Education, Shaanxi Normal University, Xi’an, Shaanxi, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Huina Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jin Zhao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Qiongwen Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinke Jiao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Mingsheng Yang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Changjing Wu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
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Study of Ferroptosis Transmission by Small Extracellular Vesicles in Epithelial Ovarian Cancer Cells. Antioxidants (Basel) 2023; 12:antiox12010183. [PMID: 36671044 PMCID: PMC9854685 DOI: 10.3390/antiox12010183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynecological cancer. The current treatment for EOC involves surgical debulking of the tumors followed by a combination of chemotherapy. While most patients achieve complete remission, many EOCs will recur and develop chemo-resistance. The cancer cells can adapt to several stress stimuli, becoming resistant. Because of this, new ways to fight resistant cells during the disease are being studied. However, the clinical outcomes remain unsatisfactory. Recently, ferroptosis, a novel form of regulated cell death trigged by the accumulation of iron and toxic species of lipid metabolism in cells, has emerged as a promising anti-tumor strategy for EOC treatment. This process has a high potential to become a complementary treatment to the current anti-tumor strategies to eliminate resistant cells and to avoid relapse. Cancer cells, like other cells in the body, release small extracellular vesicles (sEV) that allow the transport of substances from the cells themselves to communicate with their environment. To achieve this, we analyzed the capacity of epithelial ovarian cancer cells (OVCA), treated with ferroptosis inducers, to generate sEV, assessing their size and number, and study the transmission of ferroptosis by sEV. Our results reveal that OVCA cells treated with ferroptotic inducers can modify intercellular communication by sEV, inducing cell death in recipient cells. Furthermore, these receptor cells are able to generate a greater amount of sEV, contributing to a much higher ferroptosis paracrine transmission. Thus, we discovered the importance of the sEV in the communication between cells in OVCA, focusing on the ferroptosis process. These findings could be the beginning form to study the molecular mechanism ferroptosis transmission through sEV.
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12
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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] [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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Leng J, Xing Z, Li X, Bao X, Zhu J, Zhao Y, Wu S, Yang J. Assessment of Diagnosis, Prognosis and Immune Infiltration Response to the Expression of the Ferroptosis-Related Molecule HAMP in Clear Cell Renal Cell Carcinoma. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:913. [PMID: 36673667 PMCID: PMC9858726 DOI: 10.3390/ijerph20020913] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/20/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Hepcidin antimicrobial peptide (HAMP) is a key factor in maintaining iron metabolism, which may induce ferroptosis when upregulated. However, its prognostic value and relation to immune infiltrating cells remains unclear. METHODS This study analyzed the expression levels of HAMP in the Oncomine, Timer and Ualcan databases, and examined its prognostic potential in KIRC with R programming. The Timer and GEPIA databases were used to estimate the correlations between HAMP and immune infiltration and the markers of immune cells. The intersection genes and the co-expression PPI network were constructed via STRING, R programming and GeneMANIA, and the hub genes were selected with Cytoscape. In addition, we analyzed the gene set enrichment and GO/KEGG pathways by GSEA. RESULTS Our study revealed higher HAMP expression levels in tumor tissues including KIRC, which were related to poor prognosis in terms of OS, DSS and PFI. The expression of HAMP was positively related to the immune infiltration level of macrophages, Tregs, etc., corresponding with the immune biomarkers. Based on the intersection genes, we constructed the PPI network and used the 10 top hub genes. Further, we performed a pathway enrichment analysis of the gene sets, including Huntington's disease, the JAK-STAT signaling pathway, ammonium ion metabolic process, and so on. CONCLUSION In summary, our study gave an insight into the potential prognosis of HAMP, which may act as a diagnostic biomarker and therapeutic target related to immune infiltration in KIRC.
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Affiliation(s)
- Jing Leng
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Zixuan Xing
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Xiang Li
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Xinyue Bao
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Junzheya Zhu
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yunhan Zhao
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Shaobo Wu
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Jiao Yang
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
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Tang Y, Ge S, Zheng X, Zheng J. High Hepcidin expression predicts poor prognosis in patients with clear cell renal cell carcinoma. Diagn Pathol 2022; 17:100. [PMID: 36585741 PMCID: PMC9805116 DOI: 10.1186/s13000-022-01274-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/19/2022] [Indexed: 01/01/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a growing public health challenge worldwide. Hepcidin antimicrobial peptide (HAMP) is differentially expressed in various tumors. However, the roles and functions of HAMP in ccRCC remain unclear. In the present study, we integrated systematic bioinformatics approaches to investigate the roles and functions of HAMP and its association with immune cell infiltration in ccRCC. Compared with paracancerous tissue, HAMP expression was significantly upregulated in ccRCC patients. Meanwhile, we found good diagnostic performance of HAMP for ccRCC patients and its close associations with the clinicopathological features of ccRCC patients. In addition, we found that HAMP is closely related to multiple immune pathways and positively correlated with various immune cells. HAMP was a significant independent predictor for ccRCC. High expression of HAMP was associated with worse clinical prognosis and more immune cell infiltration in ccRCC patients. HAMP may offer potential as a biomarker to predict prognosis and the clinical treatment outcome of ccRCC patients.
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Affiliation(s)
- Yuting Tang
- grid.412540.60000 0001 2372 7462Department of Rehabilitation, Municipal Hospital of Traditional Chinese Medicine, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200071 People’s Republic of China
| | - Shengdong Ge
- grid.284723.80000 0000 8877 7471Department of Urology, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Southern Medical University, Guangzhou, China
| | - Xiao Zheng
- grid.412540.60000 0001 2372 7462Department of Rehabilitation, Municipal Hospital of Traditional Chinese Medicine, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200071 People’s Republic of China
| | - Jiejiao Zheng
- grid.413597.d0000 0004 1757 8802Department of Rehabilitation, HuaDong Hospital, FuDan University, Shanghai, 200040 People’s Republic of China
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Qin J, Sharma A, Wang Y, Tobar-Tosse F, Dakal TC, Liu H, Liu H, Ke B, Kong C, Liu T, Zhao C, Schmidt-Wolf IGH, Jin C. Systematic discrimination of the repetitive genome in proximity of ferroptosis genes and a novel prognostic signature correlating with the oncogenic lncRNA CRNDE in multiple myeloma. Front Oncol 2022; 12:1026153. [PMID: 36605450 PMCID: PMC9808058 DOI: 10.3389/fonc.2022.1026153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023] Open
Abstract
Emerging insights into iron-dependent form of regulated cell death ferroptosis in cancer have opened a perspective for its use in cancer therapy. Of interest, a systematic profiling of ferroptosis gene signatures as prognostic factors has gained special attention in several cancers. Herein, we sought to investigate the presence of repetitive genomes in the vicinity of ferroptosis genes that may influence their expression and to establish a prognostic gene signature associated with multiple myeloma (MM). Our analysis showed that genes associated with ferroptosis were enriched with the repetitive genome in their vicinity, with a strong predominance of the SINE family, followed by LINE, of which the most significant discriminant values were SINE/Alu and LINE/L1, respectively. In addition, we examined in detail the performance of these genes as a cancer risk prediction model and specified fourteen ferroptosis-related gene signatures, which identified MM high-risk patients with lower immune/stromal scores with higher tumor purity in their immune microenvironment. Of interest, we also found that lncRNA CRNDE correlated with a risk score and was highly associated with the majority of genes comprising the signature. Taken together, we propose to investigate the molecular impact of the repetitive genome we have highlighted on the local transcriptome of ferroptosis genes in cancer. Furthermore, we revealed a genomic signature/biomarker related to ferroptosis that can be used to predict the risk of survival in MM patients.
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Affiliation(s)
- Jiading Qin
- Medical College of Nanchang University, Nanchang, China,Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Soochow, China
| | - Amit Sharma
- Department of Integrated Oncology, Center for Integrated Oncology, University Hospital of Bonn, Bonn, Germany,Department of Neurosurgery, University Hospital of Bonn, Bonn, Germany
| | - Yulu Wang
- Department of Integrated Oncology, Center for Integrated Oncology, University Hospital of Bonn, Bonn, Germany
| | - Fabian Tobar-Tosse
- Department of Basic Sciences for Health, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, India
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Hongjia Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Bo Ke
- Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China
| | - Chunfang Kong
- Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China
| | - Tingting Liu
- Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China
| | - Chunxia Zhao
- School of Nursing, Nanchang University, Nanchang, China
| | - Ingo G. H. Schmidt-Wolf
- Department of Integrated Oncology, Center for Integrated Oncology, University Hospital of Bonn, Bonn, Germany
| | - Chenghao Jin
- Medical College of Nanchang University, Nanchang, China,Department of Hematology, Jiangxi Provincial People’s Hospital, Nanchang, China,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Soochow, China,*Correspondence: Chenghao Jin,
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Shi WK, Liu YX, Qiu XY, Zhou JY, Zhou JL, Lin GL. Construction and validation of a novel Ferroptosis-related gene signature predictive model in rectal Cancer. BMC Genomics 2022; 23:764. [DOI: 10.1186/s12864-022-08996-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
Abstract
Background
Rectal cancer (RC) is one of the most common malignant tumors. Ferroptosis is an iron-dependent form of cell death, which plays an important role in various cancers. However, the correlation between ferroptosis-related genes (FRGs) and prognosis in RC remains unclear.
Methods
Gene expression data from The Cancer Genome Atlas Rectum adenocarcinoma (TCGA-READ) and GSE87211 were downloaded. Clustering and functional enrichment were evaluated. A FRGs risk score was established based on the univariate Cox analysis and the Least absolute shrinkage and selection operator (LASSO) analysis. K-M analysis and ROC analysis were conducted to determine prognostic values. qRT-PCR was performed to validate levels of mRNA expression. Multivariate Cox analysis was used to build a prognostic prediction model based on the risk score.
Results
Based on FRGs, RC patients were grouped into two clusters. In the functional enrichment of differentially expressed genes between the two clusters, immune-related pathways dominated. A novel FRGs signature with 14 genes related to the overall survival (OS) of RC was established. qRT-PCR of the 14 genes identified TP63, ISCU, PLIN4, MAP3K5, OXSR, FANCD2 and ATM were overexpressed in RC tissue; HSPB1, MAPK1, ABCC1, PANX1, MAPK9 and ATG7 were underexpressed; TUBE1 had no difference. The high-risk group had a significantly lower OS than the low-risk group (P < 0.001), and ROC curve analysis confirmed the signature’s predictive capacity. Multivariate analysis demonstrated that the risk score and age were independent prognostic factors.
Conclusion
A novel FRGs model can be used to predict the prognosis in RC, as well as to guide individual treatment.
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Pan B, Li Y, Xu Z, Miao Y, Yin H, Kong Y, Zhang X, Liang J, Xia Y, Wang L, Li J, Wu J, Xu W. Identifying a novel ferroptosis-related prognostic score for predicting prognosis in chronic lymphocytic leukemia. Front Immunol 2022; 13:962000. [PMID: 36275721 PMCID: PMC9582233 DOI: 10.3389/fimmu.2022.962000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) is the most common leukemia in the western world. Although the treatment landscape for CLL is rapidly evolving, there are still some patients who develop drug resistance or disease refractory. Ferroptosis is a type of lipid peroxidation–induced cell death and has been suggested to have prognostic value in several cancers. Our research aims to build a prognostic model to improve risk stratification in CLL patients and facilitate more accurate assessment for clinical management. Methods The differentially expressed ferroptosis-related genes (FRGs) in CLL were filtered through univariate Cox regression analysis based on public databases. Least absolute shrinkage and selection operator (LASSO) Cox algorithms were performed to construct a prognostic risk model. CIBERSORT and single-sample gene set enrichment analysis (ssGSEA) were performed to estimate the immune infiltration score and immune-related pathways. A total of 36 CLL patients in our center were enrolled in this study as a validation cohort. Moreover, a nomogram model was established to predict the prognosis. Results A total of 15 differentially expressed FRGs with prognostic significance were screened out. After minimizing the potential risk of overfitting, we constructed a novel ferroptosis-related prognostic score (FPS) model with nine FRGs (AKR1C3, BECN1, CAV1, CDKN2A, CXCL2, JDP2, SIRT1, SLC1A5, and SP1) and stratified patients into low- and high-risk groups. Kaplan–Meier analysis showed that patients with high FPS had worse overall survival (OS) (P<0.0001) and treatment-free survival (TFS) (P<0.0001). ROC curves evaluated the prognostic prediction ability of the FPS model. Additionally, the immune cell types and immune-related pathways were correlated with the risk scores in CLL patients. In the validation cohort, the results confirmed that the high-risk group was related to worse OS (P<0.0001), progress-free survival (PFS) (P=0.0140), and TFS (P=0.0072). In the multivariate analysis, only FPS (P=0.011) and CLL-IPI (P=0.010) were independent risk indicators for OS. Furthermore, we established a nomogram including FPS and CLL-IPI that could strongly and reliably predict individual prognosis. Conclusion A novel FPS model can be used in CLL for prognostic prediction. The model index may also facilitate the development of new clinical ferroptosis-targeted therapies in patients with CLL.
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Zhang X, Ding C, Zhao Z. Exploring a 7-gene prognostic model based on ferroptosis for efficiently guiding immunotherapy in melanoma patients. Adv Med Sci 2022; 67:364-378. [PMID: 36155341 DOI: 10.1016/j.advms.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/01/2022]
Abstract
PURPOSE Although skin cutaneous melanoma (SKCM) is a relatively immunotherapy-sensitive tumor type, there is still a certain fraction that benefits less from treatment. Ferroptosis has been demonstrated to modulate tumor progression in many cancer types. This study focused on ferroptosis-related genes to construct a prognostic model for SKCM patients. MATERIALS AND METHODS Gene expression profiles of SKCM samples were obtained from public databases. Unsupervised consensus clustering was used to determine molecular subtypes related to ferroptosis. Least absolute shrinkage and selection operator (LASSO) and stepwise Akaike information criterion (stepAIC) were applied to construct a prognostic model based on differentially expressed genes between two molecular subtypes. RESULTS C1 and C2 subtypes were identified with differential prognosis and immune infiltration. A 7-gene prognostic model was constructed to classify samples into high-FPRS and low-FPRS groups. Low-FPRS group with favorable prognosis had higher immune infiltration and more enriched immune-related pathways than the high-FPRS group. The two groups showed distinct sensitivity to immunotherapy, with the low-FPRS group predicted to have more positive response to immunotherapy than the high-FPRS group. A nomogram based on the FPRS score and clinical features was built for more convenient use. CONCLUSIONS The critical role of ferroptosis involved in SKCM development was further validated in this study. The prognostic model was efficient and stable to be applied in clinical conditions to support clinicians in determining personalized therapy for SKCM patients especially those with metastasis.
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Affiliation(s)
- Xin Zhang
- Department of Dermatology, The First Medical Center of PLA General Hospital, Beijing, China
| | - Changrui Ding
- Department of Dermatology, The First Affiliated Hospital of Qiqihar Medical College, Qiqihar City, Heilongjiang Province, China
| | - Zigang Zhao
- Department of Dermatology, Hainan Hospital of PLA General Hospital, Sanya City, Hainan Province, China.
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Yang J, Tang Y, Liu X, Zhang J, Zahoor Khan M, Mi S, Wang C, Yu Y. Characterization of peripheral white blood cells transcriptome to unravel the regulatory signatures of bovine subclinical mastitis resistance. Front Genet 2022; 13:949850. [PMID: 36204322 PMCID: PMC9530456 DOI: 10.3389/fgene.2022.949850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Subclinical bovine mastitis is a pathogenic infection of the breast characterized by a marked decrease in milk production and quality. As it has no obvious clinical symptoms, diagnosis and treatment are challenging. Therefore, searching for biomarkers in cows’ peripheral white blood cells is valuable for preventing and treating subclinical mastitis. Thus, in this study, the transcriptome of peripheral blood from healthy and subclinical mastitis cows was characterized to find the regulatory signatures of bovine subclinical mastitis using RNA-seq. A total of 287 differentially expressed genes (DEGs) and 70 differentially expressed lncRNAs (DELs) were detected, and 37 DELs were documented near known Quantitative Trait Loci (QTL) associated with the mastitis of cows. Bioinformatic analysis indicated that lncRNAs MSTRG25101.2, MSTRG.56327.1, and MSTRG.18968.1, which are adjacent to the SCS QTL and SCC QTL, may be candidate lncRNAs that influence the pathogenesis of mastitis in cows by up-regulating the expression of genes TLR4, NOD2, CXCL8, and OAS2. Moreover, the alternative splicing (AS) pattern of transcriptional sequence differences between healthy cows and subclinical mastitis cows suggested a molecular mechanism of mastitis resistance and susceptibility. A total of 2,212 differential alternative splicing (DAS) events, corresponding to 1,621 unique DAS genes, were identified in both groups and significantly enriched in immune and inflammatory pathways. Of these, 29 DAS genes were subject to regulation by 32 alternative splicing SNPs, showing diverse and specific splicing patterns and events. It is hypothesized that the PIK3C2B and PPRPF8 splice variants associated with AS SNPs (rs42705933 and rs133847062) may be risk factors for susceptibility to bovine subclinical mastitis. Altogether, these key blood markers associated with resistance to subclinical mastitis and SNPs associated with alternative splicing of genes provide the basis for genetic breeding for resistance to subclinical mastitis in cows.
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Affiliation(s)
- Jinyan Yang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yongjie Tang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xueqin Liu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinning Zhang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Muhammad Zahoor Khan
- Department of Animal Sciences, Faculty of Veterinary and Animal Sciences, University of Agriculture, Dera Ismail Khan, Pakistan
| | - Siyuan Mi
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Ying Yu,
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Qian B, Wu K, Lou X, Li K, Wu L, Zhang D. Ferroptosis Associates With Diagnosis and Prognosis by Promoting Antitumor Immune Response in Melanoma. Front Cell Dev Biol 2022; 10:915198. [PMID: 35874826 PMCID: PMC9304890 DOI: 10.3389/fcell.2022.915198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Immunotherapy has greatly improved the clinical benefits of cancer treatment, especially in melanoma. Ferroptosis is a novel mechanism of cell death which relates to immunity. This study aimed at understanding the potential link between ferroptosis and cancer immunocompetent in melanoma using multiple bioinformatics analyses. By the WGCNA assay, we first constructed a key module–gene of ferroptosis, which was strongly correlated with the diagnosis, prognosis, and infiltration of immune cells in melanoma. The elevated module–gene could effectively distinguish melanoma from normal tissues and acted as a good prognostic marker. The module–gene of ferroptosis was positively correlated with the infiltration of immune cells. In particular, the module was positively correlated with the expression of PD-L1 and sensitively increased after effective anti-PD-1 treatment. Furthermore, the differential expression of the module–gene between normal and tumor tissues was observed in pan-cancer. The similarity correlations of the module–gene with infiltration of immune cells and the expressions of PD-L1 were confirmed in the pan-cancer level. Our study demonstrated that the key module–gene of ferroptosis was closely related with diagnosis, prognosis, and anti-immune response in melanoma, as well as in pan-cancer.
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Affiliation(s)
- Benheng Qian
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kui Wu
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaoying Lou
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - kexin Li
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lianpin Wu
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Lianpin Wu, ; Donghong Zhang,
| | - Donghong Zhang
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Lianpin Wu, ; Donghong Zhang,
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Lv H, Liu X, Zeng X, Liu Y, Zhang C, Zhang Q, Xu J. Comprehensive Analysis of Cuproptosis-Related Genes in Immune Infiltration and Prognosis in Melanoma. Front Pharmacol 2022; 13:930041. [PMID: 35837286 PMCID: PMC9273972 DOI: 10.3389/fphar.2022.930041] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 12/16/2022] Open
Abstract
Skin cutaneous melanoma (SKCM, hereafter referred to as melanoma) is the most lethal skin cancer with increasing incidence. Regulated cell death plays an important role in tumorigenesis and serves as an important target for almost all treatment strategies. Cuproptosis is the most recently identified copper-dependent regulated cell death form that relies on mitochondria respiration. However, its role in tumorigenesis remains unknown. The correlation of cuproptosis-related genes with tumor prognosis is far to be understood, either. In the present study, we explored the correlation between cuproptosis-related genes with the prognosis of melanoma by accessing and analyzing a public database and found 11 out 12 genes were upregulated in melanoma tissues and three genes (LIPT1, PDHA1, and SLC31A1) have predictive value for the prognosis. The subgroup of melanoma patients with higher cuproptosis-related gene expression showed longer overall survival than those with lower gene expression. We chose LIPT1 for further exploration. LIPT1 expression was increased in melanoma biopsies and was an independent favorable prognostic indicator for melanoma patients. Moreover, LIPT1 expression was positively correlated with PD-L1 expression and negatively associated with Treg cell infiltration. The melanoma patients with higher LIPT1 expression showed longer overall survival than those with lower LIPT1 expression after receiving immunotherapy, indicating the prognostic predictive value of LIPT1. Finally, a pan-cancer analysis indicated that LIPT1 was differentially expressed in diverse cancers as compared to normal tissues and correlated with the expression of multiple immune checkpoints, especially PD-L1. It could serve as a favorable prognosis indicator in some cancer types. In conclusion, our study demonstrated the prognostic value of cuproptosis-related genes, especially LIPT1, in melanoma, and revealed the correlation between LIPT1 expression and immune infiltration in melanoma, thus providing new clues on the prognostic assessment of melanoma patients and providing a new target for the immunotherapy of melanoma.
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Affiliation(s)
- Haozhen Lv
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiao Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xuanhao Zeng
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yating Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Canjing Zhang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qi Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Qi Zhang, ; Jinhua Xu,
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Dermatology, Shanghai, China
- *Correspondence: Qi Zhang, ; Jinhua Xu,
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