501
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Cai HJ, Zhuang ZC, Wu Y, Zhang YY, Liu X, Zhuang JF, Yang YF, Gao Y, Chen B, Guan GX. Development and validation of a ferroptosis-related lncRNAs prognosis signature in colon cancer. Bosn J Basic Med Sci 2021; 21:569-576. [PMID: 33714257 PMCID: PMC8381210 DOI: 10.17305/bjbms.2020.5617] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 11/16/2022] Open
Abstract
Ferroptosis is a form of iron-dependent programmed cell death. Regulation of ferroptosis in tumor cells is a novel treatment modality. The present study aimed to investigate ferroptosis-related long non-coding RNAs (lncRNAs) and construct a prognostic model for colon adenocarcinoma (COAD). RNA- sequencing data and ferroptosis-related genes were obtained from The Cancer Genome Atlas database and FerrDb database. COAD patients were randomly assigned to training- and validation groups. The Least Absolute Shrinkage and Selection Operator regression and Cox regression model were used to determine and develop a predictive model. The model was corroborated using the validation group and the entire group. In total, 259 ferroptosis-related genes and 905 ferroptosis-related LncRNAs were obtained. Cox model revealed and constructed seven ferroptosis-related LncRNAs signature (LINC01503, AC004687.1, AC010973.2, AP001189.3, ARRDC1-AS1, OIP5-AS1, and NCK1-DT). Patients were assigned into two groups according to the median risk score. Kaplan-Meier survival curves showed that overall survival between high- and low-risk groups was statistically significant (P<0.01). Cox multivariate analysis seven ferroptosis-related LncRNAs signature was an independent risk factor for COAD outcomes (P<0.05). The relationship between seven ferroptosis-related LncRNAs and clinicopathological features was also examined. The principal component analysis showed a difference between high- and low-risk groups intuitively. With the aid of gene set enrichment analysis, the underlying mechanisms of seven ferroptosis-related LncRNAs were uncovered, including the MAPK signaling pathway, mTOR signaling pathway, and glutathione metabolism pathway. Finally, we established and validated seven ferroptosis-related lncRNAs signature for COAD patients to predict survival. These results may provide meaningful targets for future study.
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Affiliation(s)
- Hua-jun Cai
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Zhi-cheng Zhuang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yong Wu
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yi-yi Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xing Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jin-fu Zhuang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yuan-feng Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yuan Gao
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Bin Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Guo-xian Guan
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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502
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Liu X, Shi X, Guo W, Ke Y, Li Y, Pan S, Li X, Liu M, Liu M, Wang Y, Ruan Q, Ma H. A Promising Esophageal Cancer Prognostic Signature of Ferroptosis-Related LncRNA to Predict Immune Scenery and Immunotherapy Response. Int J Gen Med 2021; 14:5845-5862. [PMID: 34566425 PMCID: PMC8457888 DOI: 10.2147/ijgm.s327555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/23/2021] [Indexed: 12/28/2022] Open
Abstract
Purpose Ferroptosis and long non-coding RNA (lncRNA) expression signatures have been associated with the clinical progression and immune-contexture of different solid tumors. The study aimed to identify a prognostic signature of ferroptosis-related lncRNAs (falncRNAs) to forecast the immune scenery and immunotherapy response in esophageal cancer (EC). Patients and Methods Gene expression profiles of EC were extracted from The Cancer Genome Atlas (TCGA) database, and ferroptosis-related genes were downloaded from the FerrDb database, which identified differentially expressed falncRNAs (DEfalncRNAs) via differential analysis. DEfalncRNA pairs associated with prognosis were identified by constructing a matrix, univariate and least absolute shrinkage and selection operator (LASSO) analysis. The prognostic signature was constructed by multivariate analysis. We appraised the forecasting capability of prognostic signature in survival, clinicopathological features, immune landscape, efficacy of immunotherapy, and drug sensitivity. The potential molecular mechanism of signature was investigated by gene set enrichment analysis (GSEA). Results We obtained 18 DEfalncRNA pairs to define a novel prognostic signature that was determined on a discovery cohort of 158 tumor samples and 11 adjacent normal tissues from TCGA and internally validated, with the definition of high- vs low-risk groups based on 3 years overall survival. We demonstrated that the high- vs low-risk groups differed for clinical parameters and computationally predicted drug sensitivity and tumor immune contexture, with the high-risk group having worse survival, more aggressive disease (node involvement, metastasis), reduced drug sensitivity, higher tumor mutation load, and gene signatures of infiltration of pro-tumoral immune cell subsets. The GSEA results revealed that ferroptosis and immunoregulatory pathways were significantly enriched in the high-risk group. Conclusion The prognostic signature based on falncRNAs has the potential to forecast the survival, immune scenery, efficacy of immunotherapy, and drug sensitivity of EC, which is helpful for clinical prediction and individualized treatment.
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Affiliation(s)
- Xiaoxiao Liu
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Xiaobo Shi
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Wei Guo
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Yue Ke
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Yuxing Li
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Shupei Pan
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Xiaona Li
- Department of Dermatology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Mei Liu
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Mingzhu Liu
- Department of Gastroenterology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Yuchen Wang
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Qinli Ruan
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
| | - Hongbing Ma
- Department of Radiation Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, People's Republic of China
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503
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Zheng Z, Wu W, Lin Z, Liu S, Chen Q, Jiang X, Xue Y, Lin D. Identification of seven novel ferroptosis-related long non-coding RNA signatures as a diagnostic biomarker for acute myeloid leukemia. BMC Med Genomics 2021; 14:236. [PMID: 34579730 PMCID: PMC8474743 DOI: 10.1186/s12920-021-01085-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/13/2021] [Indexed: 12/22/2022] Open
Abstract
Background Ferroptosis is a newly discovered type of programmed cell death that participates in the biological processes of various cancers. However, the mechanism by which ferroptosis modulates acute myeloid leukemia (AML) remains unclear. This study aimed to investigate the role of ferroptosis-related long non-coding RNAs (lncRNAs) in AML and establish a corresponding prognostic model. Methods RNA-sequencing data and clinicopathological characteristics were obtained from The Cancer Genome Atlas database, and ferroptosis-related genes were obtained from the FerrDb database. The “limma” R package, Cox regression, and the least absolute shrinkage and selection operator were used to determine the ferroptosis-related lncRNA signature with the lowest Akaike information criteria (AIC). The risk score of ferroptosis-related lncRNAs was calculated and patients with AML were divided into high- and low-risk groups based on the median risk score. The Kaplan–Meier curve and Cox regression were used to evaluate the prognostic value of the risk score. Finally, gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA) were performed to explore the biological functions of the ferroptosis-related lncRNAs. Results Seven ferroptosis-related lncRNA signatures were identified in the training group, and Kaplan–Meier and Cox regression analyses confirmed that risk scores were independent prognostic predictors of AML in both the training and validation groups (All P < 0.05). In addition, the area under the curve (AUC) analysis confirmed that the signatures had a good predictive ability for the prognosis of AML. GSEA and ssGSEA showed that the seven ferroptosis-related lncRNAs were related to glutathione metabolism and tumor immunity. Conclusions In this study, seven novel ferroptosis-related lncRNA signatures (AP001266.2, AC133961.1, AF064858.3, AC007383.2, AC008906.1, AC026771.1, and KIF26B-AS1) were established. These signatures were shown to accurately predict the prognosis of AML, which would provide new insights into strategies for the development of new AML therapies. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01085-9.
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Affiliation(s)
- Zhiyuan Zheng
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, 350001, Fujian, China.,Medical Technology Experimental Teaching Center of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Wei Wu
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, 350001, Fujian, China.,Medical Technology Experimental Teaching Center of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Zehang Lin
- School of Computer and Information Engineering, Xiamen University of Technology, Xiamen, 361024, Fujian, China
| | - Shuhan Liu
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, 350001, Fujian, China.,Medical Technology Experimental Teaching Center of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Qiaoqian Chen
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, 350001, Fujian, China.,Medical Technology Experimental Teaching Center of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Xiandong Jiang
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, 350001, Fujian, China.,Medical Technology Experimental Teaching Center of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Yan Xue
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, 350001, Fujian, China.,Medical Technology Experimental Teaching Center of Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Donghong Lin
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, 350001, Fujian, China. .,Medical Technology Experimental Teaching Center of Fujian Medical University, Fuzhou, 350001, Fujian, China.
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504
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Sun J, Yue W, You J, Wei X, Huang Y, Ling Z, Hou J. Identification of a Novel Ferroptosis-Related Gene Prognostic Signature in Bladder Cancer. Front Oncol 2021; 11:730716. [PMID: 34557413 PMCID: PMC8455063 DOI: 10.3389/fonc.2021.730716] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/19/2021] [Indexed: 12/19/2022] Open
Abstract
Background Ferroptosis is a newly found non-apoptotic forms of cell death that plays an important role in tumors. However, the prognostic value of ferroptosis-related genes (FRG) in bladder cancer (BLCA) have not been well examined. Methods FRG data and clinical information were collected from The Cancer Genome Atlas (TCGA). Then, significantly different FRGs were investigated by functional enrichment analyses. The prognostic FRG signature was identified by univariate cox regression and least absolute shrinkage and selection operator (LASSO) analysis, which was validated in TCGA cohort and Gene Expression Omnibus (GEO) cohort. Subsequently, the nomogram integrating risk scores and clinical parameters were established and evaluated. Additionally, Gene Set Enrichment Analyses (GSEA) was performed to explore the potential molecular mechanisms underlying our prognostic FRG signature. Finally, the expression of three key FRGs was verified in clinical specimens. Results Thirty-two significantly different FRGs were identified from TCGA–BLCA cohort. Enrichment analyses showed that these genes were mainly related to the ferroptosis. Seven genes (TFRC, G6PD, SLC38A1, ZEB1, SCD, SRC, and PRDX6) were then identified to develop a prognostic signature. The Kaplan–Meier analysis confirmed the predictive value of the signature for overall survival (OS) in both TCGA and GEO cohort. A nomogram integrating age and risk scores was established and demonstrated high predictive accuracy, which was validated through calibration curves and receiver operating characteristic (ROC) curve [area under the curve (AUC) = 0.690]. GSEA showed that molecular alteration in the high- or low-risk group was closely associated with ferroptosis. Finally, experimental results confirmed the expression of SCD, SRC, and PRDX6 in BLCA. Conclusion Herein, we identified a novel FRG prognostic signature that maybe involved in BLCA. It showed high values in predicting OS, and targeting these FRGs may be an alternative for BLCA treatment. Further experimental studies are warranted to uncover the mechanisms that these FRGs mediate BLCA progression.
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Affiliation(s)
- Jiale Sun
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wenchang Yue
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jiawei You
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xuedong Wei
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuhua Huang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhixin Ling
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Urology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
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505
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Zheng J, Guo J, Zhu L, Zhou Y, Tong J. Comprehensive analyses of glycolysis-related lncRNAs for ovarian cancer patients. J Ovarian Res 2021; 14:124. [PMID: 34560889 PMCID: PMC8464158 DOI: 10.1186/s13048-021-00881-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/13/2021] [Indexed: 11/10/2022] Open
Abstract
Background Not only glycolysis but also lncRNAs play a significant role in the growth, proliferation, invasion and metastasis of of ovarian cancer (OC). However, researches about glycolysis -related lncRNAs (GRLs) remain unclear in OC. Herein, we first constructed a GRL-based risk model for patients with OC. Methods The processed RNA sequencing (RNA-seq) profiles with clinicopathological data were downloaded from TCGA and glycolysis-related genes (GRGs) were obtained from MSigDB. Pearson correlation coefficient between glycolysis-related genes (GRGs) and annotated lncRNAs (|r| > 0.4 and p < 0.05) were calculated to identify GRLs. After screening prognostic GRLs, a risk model based on five GRLs was constructed using Univariate and Cox regression. The identified risk model was validated by two validation sets. Further, the differences in clinicopathology, biological function, hypoxia score, immune microenvironment, immune checkpoint, immune checkpoint blockade, chemotherapy drug sensitivity, N6-methyladenosine (m6A) regulators, and ferroptosis-related genes between risk groups were explored by abundant algorithms. Finally, we established networks based on co-expression, ceRNA, cis and trans interaction. Results A total of 535 GRLs were gained and 35 GRLs with significant prognostic value were identified. The prognostic signature containing five GRLs was constructed and validated and can predict prognosis. The nomogram proved the accuracy of the model for predicting prognosis. After computing hypoxia score of each sample by ssGSEA, we found patients with higher risk scores exhibited higher hypoxia score and high hypoxia score was a risk factor. It was revealed that a total of 21 microenvironment cells (such as Central memory CD4 T cell, Neutrophil, Regulatory T cell and so on) and Stromal score had significant differences between the two groups. Four immune checkpoint genes (CD274, LAG3, VTCN1, and CD47) showed disparate expression levels in the two groups. Besides, 16 m6A regulators and 126 ferroptosis-related genes were expressed higher in the low-risk group. GSEA revealed that the risk groups were associated with tumor-related pathways. The two risk groups were confirmed to be sensitive to several chemotherapeutic agents and patients in the low-risk group were more sensitive to ICB therapy. The networks based on co-expression, ceRNA, cis and trans interaction provided insights into the regulatory mechanisms of GRLs. Conclusions Our identified and validated risk model based on five GRLs is an independent prognostic factor for OC patients. Through comprehensive analyses, findings of our study uncovered potential biomarker and therapeutic target for the risk model based on the GRLs. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00881-2.
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Affiliation(s)
- Jianfeng Zheng
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, 310008, Zhejiang Province, China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, No.369 Kunpeng Road, Shangcheng District, Hangzhou, 310008, Zhejiang Province, China
| | - Jialu Guo
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, No.369 Kunpeng Road, Shangcheng District, Hangzhou, 310008, Zhejiang Province, China.,Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310006, Zhejiang Province, China
| | - Linling Zhu
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, No.369 Kunpeng Road, Shangcheng District, Hangzhou, 310008, Zhejiang Province, China
| | - Ying Zhou
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310008, Zhejiang Province, China
| | - Jinyi Tong
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, 310008, Zhejiang Province, China. .,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, No.369 Kunpeng Road, Shangcheng District, Hangzhou, 310008, Zhejiang Province, China.
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506
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Hu ZW, Wen YH, Ma RQ, Chen L, Zeng XL, Wen WP, Sun W. Ferroptosis Driver SOCS1 and Suppressor FTH1 Independently Correlate With M1 and M2 Macrophage Infiltration in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:727762. [PMID: 34527677 PMCID: PMC8437260 DOI: 10.3389/fcell.2021.727762] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
Objective To investigate the role of ferroptosis, an iron-dependent form of non-apoptotic cell death, in the head and neck squamous cell carcinoma (HNSCC) immune microenvironment. Materials and Methods A list of ferroptosis-related genes was obtained from the FerrDb database. Gene expression data were acquired from the cancer genome atlas (TCGA) and analyzed using the R language. Protein–protein interaction analysis was conducted using STRING and GeneMANIA. The correlations between gene expression levels and a patient’s survival were analyzed using GEPIA, the Kaplan–Meier estimate, and a multivariate Cox proportional hazards model. The expression results were verified using Oncomine and Human Protein Atlas data. We used the TIMER, GEPIA2, GEPIA2021, and TIMER2 databases to investigate the relationships between gene expression and infiltrating immune cells. Results Analysis of differentially expressed genes (DEGs) identified nine each ferroptosis drivers and ferroptosis suppressors, among which four genes correlated with survival as follows: two drivers (SOCS1, CDKN2A) associated with better survival and two suppressors (FTH1, CAV1) associated with poorer survival. Multivariate Cox survival analysis identified SOCS1 and FTH1 as independent prognostic factors for HNSCC, and their higher expression levels were verified using Oncomine and HPA data. The results acquired using TIMER, GEPIA2, GEPIA2021, and TIMER2 data revealed that the driver SOCS1 and the suppressor FTH1 independently correlated with M1 and M2 macrophage infiltration. Conclusions The ferroptosis driver SOCS1 and suppressor FTH1 are independent prognostic factors and that correlate with M1 and M2 macrophage infiltration in HNSCC. Targeting ferroptosis-immunomodulation may serve as a strategy to enhance the activity of immunotherapy.
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Affiliation(s)
- Zhang-Wei Hu
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Yi-Hui Wen
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Ren-Qiang Ma
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Lin Chen
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Xue-Lan Zeng
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
| | - Wei-Ping Wen
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China.,Department of Otolaryngology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Sun
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Otorhinolaryngology Institute, Sun Yat-sen University, Guangzhou, China
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507
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Zhou J, Wang X, Li Z, Jiang R. Construction and analysis of a novel ferroptosis-related gene signature predicting prognosis in lung adenocarcinoma. FEBS Open Bio 2021; 11:3005-3018. [PMID: 34499810 PMCID: PMC8564102 DOI: 10.1002/2211-5463.13288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/10/2021] [Accepted: 09/06/2021] [Indexed: 12/25/2022] Open
Abstract
Ferroptosis is a newly discovered, iron‐dependent, nonapoptotic form of programmed cell death that plays an important role in the development of lung adenocarcinoma (LUAD). In this study, ferroptosis‐related genes (FRGs) were identified from the FerrDb dataset, and the mRNA expression profiles and corresponding clinical data of LUAD patients were downloaded from the University of California, Santa Cruz (UCSC) databases. Data from LUAD patients from the Gene Expression Omnibus (GEO) dataset were used as the verification set. Cox and Lasso regression analyses were used to screen the FRGs with prognostic value, and six prognostic‐related FRGs were selected to construct prognostic risk score signatures. Immunohistochemistry was utilized to manifest the differential expression of six FRGs in tumor and normal tissues at the protein level. Functional enrichment analysis indicated that FRGs were mainly enriched in ferroptosis‐related pathways. Patients were divided into high‐ and low‐risk groups based on the median risk score. The Kaplan–Meier survival curves confirmed that patients with a high score had significantly worse overall survival. Receiver operating characteristic (ROC) curves proved that the prognostic signature has good sensitivity and specificity for predicting the prognosis of LUAD patients. Nomogram analysis showed that the prognostic signature has potential independent prognostic value. Moreover, the prognostic signature has been shown to be significantly associated with some clinical features (T stage, N stage, tumor stage, and survival status) as well as many immune‐activity‐related genes and immune‐checkpoint‐related genes. In conclusion, we constructed a prognostic signature consisting of six FGRs, which can provide a reference for predicting the prognosis of LUAD patients.
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Affiliation(s)
- Jing Zhou
- Tianjin Medical University Cancer Institute & 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, China.,Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, China
| | - Xinyue Wang
- Tianjin Medical University Cancer Institute & 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, China.,Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, China
| | - Zhaona Li
- Tianjin Medical University Cancer Institute & 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, China.,Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, China
| | - Richeng Jiang
- Tianjin Medical University Cancer Institute & 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, China.,Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, China
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508
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Pan J, Zhang X, Fang X, Xin Z. Construction on of a Ferroptosis-Related lncRNA-Based Model to Improve the Prognostic Evaluation of Gastric Cancer Patients Based on Bioinformatics. Front Genet 2021; 12:739470. [PMID: 34497636 PMCID: PMC8419360 DOI: 10.3389/fgene.2021.739470] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 07/29/2021] [Indexed: 01/07/2023] Open
Abstract
Background Gastric cancer is one of the most serious gastrointestinal malignancies with bad prognosis. Ferroptosis is an iron-dependent form of programmed cell death, which may affect the prognosis of gastric cancer patients. Long non-coding RNAs (lncRNAs) can affect the prognosis of cancer through regulating the ferroptosis process, which could be potential overall survival (OS) prediction factors for gastric cancer. Methods Ferroptosis-related lncRNA expression profiles and the clinicopathological and OS information were collected from The Cancer Genome Atlas (TCGA) and the FerrDb database. The differentially expressed ferroptosis-related lncRNAs were screened with the DESeq2 method. Through co-expression analysis and functional annotation, we then identified the associations between ferroptosis-related lncRNAs and the OS rates for gastric cancer patients. Using Cox regression analysis with the least absolute shrinkage and selection operator (LASSO) algorithm, we constructed a prognostic model based on 17 ferroptosis-related lncRNAs. We also evaluated the prognostic power of this model using Kaplan–Meier (K-M) survival curve analysis, receiver operating characteristic (ROC) curve analysis, and decision curve analysis (DCA). Results A ferroptosis-related “lncRNA–mRNA” co-expression network was constructed. Functional annotation revealed that the FOXO and HIF-1 signaling pathways were dysregulated, which might control the prognosis of gastric cancer patients. Then, a ferroptosis-related gastric cancer prognostic signature model including 17 lncRNAs was constructed. Based on the RiskScore calculated using this model, the patients were divided into a High-Risk group and a low-risk group. The K-M survival curve analysis revealed that the higher the RiskScore, the worse is the obtained prognosis. The ROC curve analysis showed that the area under the ROC curve (AUC) of our model is 0.751, which was better than those of other published models. The multivariate Cox regression analysis results showed that the lncRNA signature is an independent risk factor for the OS rates. Finally, using nomogram and DCA, we also observed a preferable clinical practicality potential for prognosis prediction of gastric cancer patients. Conclusion Our prognostic signature model based on 17 ferroptosis-related lncRNAs may improve the overall survival prediction in gastric cancer.
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Affiliation(s)
- Jiahui Pan
- The Key Laboratory of Zoonosis Research, Chinese Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Xinyue Zhang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xuedong Fang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhuoyuan Xin
- The Key Laboratory of Zoonosis Research, Chinese Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China.,Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
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509
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Zhang F, Liu H. Identification of ferroptosis-associated genes exhibiting altered expression in pulmonary arterial hypertension. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:7619-7630. [PMID: 34814266 DOI: 10.3934/mbe.2021377] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pulmonary arterial hypertension (PAH) is a life-threatening illness and ferroptosis is an iron-dependent form of regulated cell death, driven by the accumulation of lipid peroxides to levels that are sufficient to trigger cell death. However, only few studies have examined PAH-associated ferroptosis. In the present study, lung samples mRNA expression profiles (derived from 15 patients with PAH and 11 normal controls) were downloaded from a public database, and 514 differentially expressed genes (DEGs) were identified using the Wilcoxon rank-sum test and weighted gene correlation network analyses. These DEGs were screened for ferroptosis-associated genes using the FerrDb database: eight ferroptosis-associated genes were identified. Finally, the construction of gene-microRNA (miRNA) and gene-transcription factor (TF) networks, in conjunction with gene ontology and biological pathway enrichment analysis, were used to inform hypotheses regarding the molecular mechanisms underlying PAH-associated ferroptosis. Ferroptosis-associated genes were largely involved in oxidative stress responses and could be regulated by several identified miRNAs and TFs. This suggests the existence of modulatable pathways that are potentially involved in PAH-associated ferroptosis. Our findings provide novel directions for targeted therapy of PAH in regard to ferroptosis. These findings may ultimately help improve the therapeutic outcomes of PAH.
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Affiliation(s)
- Fan Zhang
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Hongtao Liu
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou 510632, China
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510
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Cui DJ, Chen C, Yuan WQ, Yang YH, Han L. Integrative analysis of ferroptosis-related genes in ulcerative colitis. J Int Med Res 2021; 49:3000605211042975. [PMID: 34510961 PMCID: PMC8442491 DOI: 10.1177/03000605211042975] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/21/2021] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE The aim of this study was to identify and validate ferroptosis-related markers in ulcerative colitis (UC) to explore new directions for UC diagnosis and treatment. METHODS We screened UC chips and ferroptosis-related genes from the Gene Expression Omnibus (GEO), FerrDb, and GeneCards databases. The differentially expressed genes (DEGs) and ferroptosis-related DEGs between the UC group and normal controls were analyzed using bioinformatics methods. Enrichment analysis, protein-protein interaction analysis, and hub genes were screened. Peripheral blood chip and animal experiments were used to validate the ferroptosis-related hub genes. Finally, hub gene-transcription factor, hub gene-microRNA (miRNA), and hub gene-drug interaction networks were constructed. RESULTS Overall, 26 ferroptosis-related DEGs were identified that were significantly enriched in energy pathways and metabolism. We identified ten ferroptosis-related hub genes from the protein-protein interaction network: IL6, PTGS2, HIF1A, CD44, MUC1, CAV1, NOS2, CXCL2, SCD, and ACSL4. In the peripheral blood chip GSE94648, CD44 and MUC1 were upregulated, which was consistent with the expression trend in GSE75214. Animal experiments showed that CD44 expression was significantly increased in the colon. CONCLUSIONS Our findings indicate that CD44 and MUC1 may be ferroptosis-related markers in UC.
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Affiliation(s)
- De-jun Cui
- De-jun Cui, Department of Gastroenterology,
Guizhou Provincial People's Hospital, No. 83, East Zhongshan Road, Guiyang,
Guizhou Province 550002, PR China.
| | | | - Wen-qiang Yuan
- Department of Gastroenterology, National
Institution of Drug Clinical Trial, Guizhou Provincial People’s Hospital,
Medical College of Guizhou University, Guiyang, China
| | - Yun-han Yang
- Department of Gastroenterology, National
Institution of Drug Clinical Trial, Guizhou Provincial People’s Hospital,
Medical College of Guizhou University, Guiyang, China
| | - Lu Han
- Department of Gastroenterology, National
Institution of Drug Clinical Trial, Guizhou Provincial People’s Hospital,
Medical College of Guizhou University, Guiyang, China
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511
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Xu C, Chen H. A Ferroptosis-Related Gene Model Predicts Prognosis and Immune Microenvironment for Cutaneous Melanoma. Front Genet 2021; 12:697043. [PMID: 34447410 PMCID: PMC8384470 DOI: 10.3389/fgene.2021.697043] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Background Cutaneous melanoma is a common but aggressive tumor. Ferroptosis is a recently discovered cell death with important roles in tumor biology. Nevertheless, the prognostic power of ferroptosis-linked genes remained unclear in cutaneous melanoma. Methods Cutaneous melanoma patients of TCGA (The Cancer Genome Atlas) were taken as the training cohort while GSE65904 and GSE22153 as the validation cohorts. Multifactor Cox regression model was used to build a prognostic model, and the performance of the model was assessed. Functional enrichment and immune infiltration analysis were used to clarify the mechanisms. Results A five ferroptosis-linked gene predictive model was developed. ALOX5 and GCH1 were illustrated as independent predictive factors. Functional assessment showed enriched immune-linked cascades. Immune infiltrating analysis exhibited the distinct immune microenvironment. Conclusion Herein, a novel ferroptosis-related gene prognostic model was built in cutaneous melanoma. This model could be used for prognostic prediction, and maybe helpful for the targeted and immunotherapies.
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Affiliation(s)
- Congcong Xu
- Hospital of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Hao Chen
- Hospital of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
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512
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Cai J, Li C, Li H, Wang X, Zhou Y. Establishment of a ferroptosis-related gene signature for prognosis in lung adenocarcinoma patients. PeerJ 2021; 9:e11931. [PMID: 34434660 PMCID: PMC8351575 DOI: 10.7717/peerj.11931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/18/2021] [Indexed: 12/20/2022] Open
Abstract
Objective Lung cancer is the most common malignancy worldwide and exhibits both high morbidity and mortality. In recent years, scientists have made substantial breakthroughs in the early diagnosis and treatment of lung adenocarcinoma (LUAD), however, patient prognosis still shows vast individual differences. In this study, bioinformatics methods were used to identify and analyze ferroptosis-related genes to establish an effective signature for predicting prognosis in LUAD patients. Methods The gene expression profiles of LUAD patients with complete clinical and follow-up information were downloaded from two public databases, univariate Cox regression and multivariate Cox regression analysis were used to obtain ferroptosis-related genes for constructing the prognos tic risk model, AUC and calibration plot were used to evaluate the predictive accuracy of the FRGS and nomogram. Results A total of 74 ferroptosis-related differentially expressed genes (DEGs) were identi fied between LUAD and normal tissues from The Cancer Genome Atlas (TCGA) database. A five-gene panel for prediction of LUAD prognosis was established by multivariate regression and was verified using the GSE68465 cohort from the Gene Expression Omnibus (GEO) database. Patients were divided into two different risk groups according to the median risk score of the five genes. Based on Kaplan-Meier (KM) analysi, the OS rate of the high-risk group was markedly worse than that of the low-risk group. We also found that risk score was an independent prognostic indicator. The receiver operating characteristic ROC curve showed that the proposed model had good prediction ability. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses indicated that risk score was prominently enriched in ferroptosis processes. Moreover, at the score of immune-associated gene sets, significant differences were found between the two risk groups. Conclusions This study demonstrated that ferroptosis-related gene signatures can be used as a potential predictor for the prognosis of LUAD, thus providing a novel strategy for individualized treatment in LUAD patients.
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Affiliation(s)
- Jingjing Cai
- Molecular Diagnostics Center, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Chunyan Li
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Hongsheng Li
- Molecular Diagnostics Center, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Xiaoxiong Wang
- Molecular Diagnostics Center, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Yongchun Zhou
- Molecular Diagnostics Center, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
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513
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Ren Z, Hu M, Wang Z, Ge J, Zhou X, Zhang G, Zheng H. Ferroptosis-Related Genes in Lung Adenocarcinoma: Prognostic Signature and Immune, Drug Resistance, Mutation Analysis. Front Genet 2021; 12:672904. [PMID: 34434214 PMCID: PMC8381737 DOI: 10.3389/fgene.2021.672904] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/20/2021] [Indexed: 12/25/2022] Open
Abstract
It is reported that ferroptosis has close relation with tumorigenesis and drug resistance. However, the clinical significance of ferroptosis in lung adenocarcinoma (LUAD) remains elusive, and the potential targets for ferroptosis-based treatment are limited. In this study, we constructed a 15-gene prognostic signature predicting overall survival based on ferroptosis-related genes (ferroptosis driver genes VDAC2, GLS2, FLT3, TLR4, PHKG2, phosphogluconate dehydrogenase (PGD), PANX1, KRAS, PEBP1, ALOX15, and ALOX12B, and suppressor genes ACSL3, CISD1, FANCD2, and SLC3A2) in The Cancer Genome Atlas (TCGA)-LUAD cohort. The signature’s predictive ability was validated in the GSE68465 and GSE72094 cohorts by survival analysis and independent prognostic analysis with clinical features. Nomograms were provided for clinical reference. Functional analysis revealed that ferroptosis was closely related to cell cycle, cell metabolism, and immune pathways. Pan-cancer analysis comprehensively analyzed these 15 genes in 33 cancer types, indicating that the heterogeneity of 15 genes was evident across different cancer types. Besides, these genes were critical regulators modulating drug resistance, tumor microenvironment infiltration, and cancer stemness. Then, we screened 10 genes (TLR4, PHKG2, PEBP1, GLS2, FLT3, ALOX15, ACSL3, CISD1, FANCD2, and SLC3A2) as potential targets for further research because their biological functions in ferroptosis were consistent with their prognostic significance. Somatic mutation and copy number variation analysis revealed that the alteration rates of KRAS, PGD, and ALOX15 were more than 1% and significantly associated with overall survival in LUAD. Moreover, the expression of KRAS and PGD was positively related to tumor mutation burden, indicating that KRAS and PGD could serve as novel biomarkers for predicting immunotherapy response rate. Our study identified and validated a ferroptosis-related gene signature for LUAD, provided a 10-gene set for future research, and screened KRAS and PGD as potential novel immunotherapy biomarkers.
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Affiliation(s)
- Ziyuan Ren
- Basic Medical School, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Minghui Hu
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhonglin Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
| | - Junpeng Ge
- Department of Biology Engineering, Shandong Jianzhu University, Jinan, China
| | - Xiaoyan Zhou
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guoming Zhang
- Basic Medical School, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hongying Zheng
- Clinical Lab, The Affiliated Hospital of Qingdao University, Qingdao, China
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514
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Research Progress of Ferroptosis: A Bibliometrics and Visual Analysis Study. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:2178281. [PMID: 34413966 PMCID: PMC8370827 DOI: 10.1155/2021/2178281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/13/2021] [Accepted: 07/29/2021] [Indexed: 01/15/2023]
Abstract
Background Ferroptosis is a type of cell death with major topic of debate under current research and plays an important role in disease regulation. Objective In this study, the literature management software Bibexcel and knowledge graph tool VOSviewer were used to summarize and analyze the international research trends and hotspots about ferroptosis in recent years, which highlight the disease mechanism, diagnosis, and treatment related to ferroptosis. Material/Methods. The core collection database of Web of Science was used for retrieving ferroptosis research literature. The information such as the amount of text, the country, the period, the institution, the fund, and the keywords was extracted by the bibliometric tool Bibexcel. The cooccurrence and clustering function of VOSviewer were used to analyze the high-frequency keywords and the cooperative network of the author, institution, and country. Results The research of ferroptosis started late and was formally proposed in 2012. It has developed rapidly and presented an “exponential” growth trend. China, the United States, Germany, Japan, and France are the main national forces of ferroptosis research development. The United States and China have a relatively high degree of support and attention to ferroptosis. Exploring oxidative stress, inducers/inhibitors, synergistic antitumor effect, relationships with other cell death types, GSH/GPX4 and iron metabolism imbalance related mechanisms of ferroptosis, and ferroptosis in the nervous system disease, ischemia-reperfusion injury, tumor, inflammation, and age-related diseases are the hot research directions. Conclusion Ferroptosis has been a research hotspot in the field of biomedicine in recent years and has attracted the attention of scholars all over the world. The occurrence mechanism of ferroptosis and its application in neurological diseases, ischemia and reperfusion injury, tumors, inflammation, and aging are the hot directions of current research. In the future, ferroptosis can be appropriately considered for strengthening new approaches, new diseases, new inductors, new inhibitors, clinical transformation, and traditional medicine research.
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515
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Guo Q, Zhang X, Shen T, Wang X. Identification of Autophagy- and Ferroptosis-Related lncRNAs Functioned through Immune-Related Pathways in Head and Neck Squamous Carcinoma. Life (Basel) 2021; 11:life11080835. [PMID: 34440579 PMCID: PMC8399325 DOI: 10.3390/life11080835] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/30/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
The interplay between autophagy and ferroptosis has been highlighted as an important event to decide cancer cell fate. However, the underlying mechanisms remain largely unclear. In this study, we systematically explored the expression, prognostic value and functional roles of lncRNA in autophagy and ferroptosis. By a set of bioinformatics analyses, we identified 363 autophagy- and ferroptosis-related lncRNAs (AF-lncRNAs) and found 17 of them are dramatically related to the prognosis of head and neck squamous cell carcinoma (HNSC) patients, named as prognosis-related AF-lncRNAs (PAF-lncRNAs). Based on six key PAF-lncRNAs, a risk score model was developed and used to categorize the TCGA-retrieved HNSC patients into two groups (high-risk vs. low-risk). Functional analysis showed the differentially expressed genes (DEGs) between the two groups were mainly enriched in immune-related pathways and regulated by a PAF-lncRNA-directed ceRNA (competitive endogenous RNA) network. Combined with a variety of immune infiltration analyses, we also found a decreased landscape of immune cell infiltration in high-risk groups. Together, by revealing PAF-lncRNAs with tumor prognostic features functioned through immune-related pathways, our work would contribute to show the pathogenesis of a lncRNA-directed interplay among autophagy, ferroptosis and tumor immunity in HNSC and to develop potential prognostic biomarkers and targets for tumor immunotherapy.
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Affiliation(s)
- Qi Guo
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Q.G.); (X.Z.)
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230026, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xuehan Zhang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Q.G.); (X.Z.)
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230026, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Tao Shen
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Q.G.); (X.Z.)
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230026, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Correspondence: (T.S.); (X.W.); Tel./Fax: +86-551-63600080 (T.S. & X.W.)
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Q.G.); (X.Z.)
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230026, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Correspondence: (T.S.); (X.W.); Tel./Fax: +86-551-63600080 (T.S. & X.W.)
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516
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Identification of Ferroptosis-Related Long Noncoding RNA and Construction of a Novel Prognostic Signature for Gastric Cancer. DISEASE MARKERS 2021; 2021:7724997. [PMID: 34394774 PMCID: PMC8357526 DOI: 10.1155/2021/7724997] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/20/2021] [Indexed: 12/19/2022]
Abstract
Background Gastric cancer is the most common malignant tumor of the digestive system. It has a poor prognosis and is clinically challenging to treat. Ferroptosis is a newly defined mode of programmed cell death. The roles and prognostic value of ferroptosis-related long noncoding RNAs (lncRNAs) in gastric cancer remain unknown. Results In the current study, 20 ferroptosis-related lncRNAs were identified via univariate Cox analysis, least absolute shrinkage, and selection operator Cox regression analysis and used to construct a prognostic signature and classify gastric cancer patients into high-risk and low-risk groups. The signature was validated using TCGA training and testing cohorts. The risk signature was an independent prognostic indicator of survival and accurately predicted the prognoses of patients with gastric cancer. It was also associated with immune cell infiltration. Gene set enrichment analysis was used to investigate underlying mechanisms that the 20 ferroptosis-related lncRNAs were involved in. Chemosensitivity and immune checkpoint inhibitor analyses indicated that high-risk patients were more sensitive to the immune checkpoint inhibitor programmed cell death protein 1. Conclusions The important role of ferroptosis-related lncRNAs in immune infiltration identified in the current study may assist the determination of personalized prognoses and treatments in patients with gastric cancer. These 20 lncRNAs can be used as the diagnostic and prognostic markers for gastric cancer.
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517
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Wang Y, Chen W, Zhu M, Xian L. Ferroptosis-Related Gene Signature and Patterns of Immune Infiltration Predict the Overall Survival in Patients With Lung Adenocarcinoma. Front Mol Biosci 2021; 8:692530. [PMID: 34395526 PMCID: PMC8360867 DOI: 10.3389/fmolb.2021.692530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) is a malignant tumor with high heterogeneity and poor prognosis. Ferroptosis, a form of regulated cell-death–related iron, has been proven to trigger inflammation-associated immunosuppression in the tumor microenvironment, which promotes tumor growth. Therefore, the clinical prognostic value of ferroptosis-related genes in LUAD needs to be further explored. Method: In this study, we downloaded the mRNA expression profiles and corresponding clinical data of LUAD patients from the Cancer Genome Atlas database. The least absolute shrinkage and selection operator (LASSO) Cox regression model was utilized to construct ferroptosis-related gene signature. Based on these, we established the nomograms for prognosis prediction and validated the model in the GSE72094 dataset. The cell type was identified using the CIBERSORT algorithm for estimating relative subsets of RNA transcripts, which was then used to screen significant tumor immune-infiltrating cells associated with the LUAD prognosis prediction model. Subsequently, we applied co-expression analysis to reveal the relationship between ferroptosis-related genes and significant immune cells. Results: The univariate COX regression analysis showed that 20 genes were associated with the overall survival (OS) as prognostic differentially expressed genes (DEGs) (FDR <0.05). Patients were divided into two risk groups using a 13-gene signature, with the high-risk group having a significantly worse OS than their low-risk counterparts (p < 0.001). We used receiver operating characteristic (ROC) curve analysis to confirm the predictive capacity of the signature. Besides, we identified seven pairs of ferroptosis-related genes and tumor-infiltrating immune cells associated with the prognosis of LUAD patients. Conclusion: In this study, we construct a ferroptosis-related gene signature that can be used for prognostic prediction in LUAD. In addition, we reveal a potential connection between ferroptosis and tumor-infiltrating immune cells.
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Affiliation(s)
- Yuxuan Wang
- Guangxi Medical University, Nanning, China.,Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University, Thoracic and Cardiovascular Surgery, Nanning, China
| | - Weikang Chen
- Guangxi Medical University, Nanning, China.,Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University, Thoracic and Cardiovascular Surgery, Nanning, China
| | - Minqi Zhu
- Guangxi Medical University, Nanning, China.,Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University, Thoracic and Cardiovascular Surgery, Nanning, China
| | - Lei Xian
- Guangxi Medical University, Nanning, China.,Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University, Thoracic and Cardiovascular Surgery, Nanning, China
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518
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Gao Y, Li J, Wu Q, Wang S, Yang S, Li X, Chen N, Li L, Zhang L. Tetrahydroxy stilbene glycoside ameliorates Alzheimer's disease in APP/PS1 mice via glutathione peroxidase related ferroptosis. Int Immunopharmacol 2021; 99:108002. [PMID: 34333354 DOI: 10.1016/j.intimp.2021.108002] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/11/2021] [Accepted: 07/18/2021] [Indexed: 02/08/2023]
Abstract
Amyloid beta peptide (Aβ) has been confirmed to be an essential reason of Alzheimer's disease (AD) for a long time. Ferroptosis is a newly recognized oxidative cell death mechanism, which is highly related to AD. Recently, tetrahydroxy stilbene glycoside (TSG) has been beneficial in alleviating learning and memory of AD and aged mouse model. Unfortunately, the underlying mechanisms between TSG and ferroptosis in AD are poorly understood. Herein, we investigated whether neural cells in cerebral cortex and hippocampus that were seriously afflicted in APP/PS1 mice might be vulnerable to ferroptosis. Treatment with non-toxic TSG dose-dependently resisted Aβ-caused cytotoxic death in neuronal cells by regulating ferroptosis related proteins and enzymes in APP/PS1 mice. TSG also alleviated cellular oxidative stress and inflammatory damage in response to Aβ by attenuating the levels of oxidation products. Importantly, TSG administration abrogated Aβ-caused brain damage, indicating that TSG rescued brain cells. Subsequently, TSG promoted the activation of GSH/GPX4/ROS and Keap1/Nrf2/ARE signaling pathways. Notably, markers related to ferroptosis including increased lipid peroxidation, enhanced neuroinflammation such as NLRP3, and also the expression of DMT1, ACSL4 and NCOA4, were reduced by TSG administration. In addition, TSG enhanced antioxidative stress via the upregulation of SOD, and the expression of FTH1, CD98 and xCT. Taken together, our data indicated a novel mechanism of TSG in reversing Aβ-caused injury through restoring mitochondrial function via several signaling pathways, implying a promising candidate against neurodegenerative diseases especially AD. Hence, TSG should be taken into consideration during treatment of AD in the future.
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Affiliation(s)
- Yan Gao
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing Engineering Research Center for Nervous System Drugs, Beijing Institute for Brain Disorders, Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing 100053, China; State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica and Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Yantai University, Yantai 264005, China
| | - Juntong Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Qinglin Wu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Shasha Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Songwei Yang
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Xun Li
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Naihong Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica and Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; College of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Lin Li
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing Engineering Research Center for Nervous System Drugs, Beijing Institute for Brain Disorders, Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing 100053, China
| | - Lan Zhang
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing Engineering Research Center for Nervous System Drugs, Beijing Institute for Brain Disorders, Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing 100053, China.
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519
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Guo Y, Qu Z, Li D, Bai F, Xing J, Ding Q, Zhou J, Yao L, Xu Q. Identification of a prognostic ferroptosis-related lncRNA signature in the tumor microenvironment of lung adenocarcinoma. Cell Death Discov 2021; 7:190. [PMID: 34312372 PMCID: PMC8313561 DOI: 10.1038/s41420-021-00576-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/16/2021] [Accepted: 07/03/2021] [Indexed: 12/12/2022] Open
Abstract
Ferroptosis is closely linked to various cancers, including lung adenocarcinoma (LUAD); however, the factors involved in the regulation of ferroptosis-related genes are not well established. In this study, we identified and characterized ferroptosis-related long noncoding RNAs (lncRNAs) in LUAD. In particular, a coexpression network of ferroptosis-related mRNAs and lncRNAs from The Cancer Genome Atlas (TCGA) was constructed. Univariate and multivariate Cox proportional hazards analyses were performed to establish a prognostic ferroptosis-related lncRNA signature (FerRLSig). We obtained a prognostic risk model consisting of 10 ferroptosis-related lncRNAs: AL606489.1, AC106047.1, LINC02081, AC090559.1, AC026355.1, FAM83A-AS1, AL034397.3, AC092171.5, AC010980.2, and AC123595.1. High risk scores according to the FerRLSig were significantly associated with poor overall survival (hazard ratio (HR) = 1.412, 95% CI = 1.271–1.568; P < 0.001). Receiver operating characteristic (ROC) curves and a principal component analysis further supported the accuracy of the model. Next, a prognostic nomogram combining FerRLSig with clinical features was established and showed favorable predictive efficacy for survival risk stratification. In addition, gene set enrichment analysis (GSEA) revealed that FerRLSig is involved in many malignancy-associated immunoregulatory pathways. Based on the risk model, we found that the immune status and response to immunotherapy, chemotherapy, and targeted therapy differed significantly between the high-risk and low-risk groups. These results offer novel insights into the pathogenesis of LUAD, including the contribution of ferroptosis-related lncRNAs, and reveal a prognostic indicator with the potential to inform immunological research and treatment.
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Affiliation(s)
- Yugang Guo
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Nanyang Normal University, Nanyang, China
| | - Zhongyu Qu
- Henan Provincial Nanyang Central Hospital, Nanyang, China
| | - Dandan Li
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Nanyang Normal University, Nanyang, China
| | - Fanghui Bai
- Henan Provincial Nanyang Central Hospital, Nanyang, China
| | - Juan Xing
- Henan Provincial Nanyang Central Hospital, Nanyang, China
| | - Qian Ding
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Nanyang Normal University, Nanyang, China
| | - Jiawei Zhou
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Nanyang Normal University, Nanyang, China.,School of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Nanyang Normal University, Nanyang, China
| | - Qian Xu
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Nanyang Normal University, Nanyang, China.
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520
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Primary Aldosteronism: Metabolic Reprogramming and the Pathogenesis of Aldosterone-Producing Adenomas. Cancers (Basel) 2021; 13:cancers13153716. [PMID: 34359615 PMCID: PMC8345059 DOI: 10.3390/cancers13153716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/29/2021] [Accepted: 07/21/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Primary aldosteronism is a common form of endocrine hypertension often caused by a hyper-secreting tumor of the adrenal cortex called an aldosterone-producing adenoma. Metabolic reprogramming plays a role in tumor progression and influences the tumor immune microenvironment by limiting immune-cell infiltration and suppressing its anti-tumor function. We hypothesized that the development of aldosterone-producing adenomas involves metabolic adaptations of its component tumor cells and intrinsically influences tumor pathogenesis. Herein, we use state-of-the-art computational tools for the comprehensive analysis of array-based gene expression profiles to demonstrate metabolic reprogramming and remodeling of the immune microenvironment in aldosterone-producing adenomas compared with paired adjacent adrenal cortical tissue. Our findings suggest metabolic alterations may function in the pathogenesis of aldosterone-producing adenomas by conferring survival advantages to their component tumor cells. Abstract Aldosterone-producing adenomas (APAs) are characterized by aldosterone hypersecretion and deregulated adrenocortical cell growth. Increased energy consumption required to maintain cellular tumorigenic properties triggers metabolic alterations that shape the tumor microenvironment to acquire necessary nutrients, yet our knowledge of this adaptation in APAs is limited. Here, we investigated adrenocortical cell-intrinsic metabolism and the tumor immune microenvironment of APAs and their potential roles in mediating aldosterone production and growth of adrenocortical cells. Using multiple advanced bioinformatics methods, we analyzed gene expression datasets to generate distinct metabolic and immune cell profiles of APAs versus paired adjacent cortex. APAs displayed activation of lipid metabolism, especially fatty acid β-oxidation regulated by PPARα, and glycolysis. We identified an immunosuppressive microenvironment in APAs, with reduced infiltration of CD45+ immune cells compared with adjacent cortex, validated by CD45 immunohistochemistry (3.45-fold, p < 0.001). APAs also displayed an association of lipid metabolism with ferroptosis and upregulation of antioxidant systems. In conclusion, APAs exhibit metabolic reprogramming towards fatty acid β-oxidation and glycolysis. Increased lipid metabolism via PPARα may serve as a key mechanism to modulate lipid peroxidation, a hallmark of regulated cell death by ferroptosis. These findings highlight survival advantages for APA tumor cells with metabolic reprogramming properties.
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521
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Zheng Z, Zhang Q, Wu W, Xue Y, Liu S, Chen Q, Lin D. Identification and Validation of a Ferroptosis-Related Long Non-coding RNA Signature for Predicting the Outcome of Lung Adenocarcinoma. Front Genet 2021; 12:690509. [PMID: 34367250 PMCID: PMC8339970 DOI: 10.3389/fgene.2021.690509] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ferroptosis is a recently recognized type of programmed cell death that is involved in the biological processes of various cancers. However, the mechanism of ferroptosis in lung adenocarcinoma (LUAD) remains unclear. This study aimed to determine the role of ferroptosis-associated long non-coding RNAs (lncRNAs) in LUAD and to establish a prognostic model. METHODS We downloaded ferroptosis-related genes from the FerrDb database and RNA sequencing data and clinicopathological characteristics from The Cancer Genome Atlas. We randomly divided the data into training and validation sets. Ferroptosis-associated lncRNA signatures with the lowest Akaike information criteria were determined using COX regression analysis and the least absolute shrinkage and selection operator. The risk scores of ferroptosis-related lncRNAs were calculated, and patients with LUAD were assigned to high- and low-risk groups based on the median risk score. The prognostic value of the risk scores was evaluated using Kaplan-Meier curves, Cox regression analyses, and nomograms. We then explored relationships between ferroptosis-related lncRNAs and the immune response using gene set enrichment analysis (GSEA). RESULTS Ten ferroptosis-related lncRNA signatures were identified in the training group, and Kaplan-Meier and Cox regression analyses confirmed that the risk scores were independent predictors of LUAD outcome in the training and validation sets (all P < 0.05). The area under the curve confirmed that the signatures could determine the prognosis of LUAD. The predictive accuracy of the established nomogram model was verified using the concordance index and calibration curve. The GSEA showed that the 10 ferroptosis-related lncRNAs might be associated with tumor immune response. CONCLUSION We established a novel signature involving 10 ferroptosis-related lncRNAs (LINC01843, MIR193BHG, AC091185.1, AC027031.2, AL021707.2, AL031667.3, AL606834.1, AC026355.1, AC124045.1, and AC025048.4) that can accurately predict the outcome of LUAD and are associated with the immune response. This will provide new insights into the development of new therapies for LUAD.
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Affiliation(s)
| | | | | | | | | | | | - Donghong Lin
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, China
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522
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Yang C, Huang S, Cao F, Zheng Y. Role of ferroptosis-related genes in prognostic prediction and tumor immune microenvironment in colorectal carcinoma. PeerJ 2021; 9:e11745. [PMID: 34316400 PMCID: PMC8286063 DOI: 10.7717/peerj.11745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/19/2021] [Indexed: 01/11/2023] Open
Abstract
Background and Aim Colorectal cancer (CRC) ranks the second most common cause of cancer-related mortality worldwide. Ferroptosis, a recently discovered form of programmed cell death different from other, raises promising novel opportunities for therapeutic intervention of CRC. This study intended to systematically assess the prognosis value and multiple roles of the ferroptosis-related genes in the tumor immune microenvironment of CRC. Materials and Methods Of 1,192 CRC patients with complete information from the public datasets (TCGA CRC, GEO GSE39582 and GSE17538 cohorts) were selected for analysis. Firstly, K-means consensus clustering was performed to identify ferroptosis-associated subtypes in CRC patients. Subsequently, we constructed a risk signature based on ferroptosis-related genes in TCGA cohort and acquired its validation in two GEO cohorts. Additionally, we established a nomogram integrating the risk signature and clinical factors to improve risk assessment of CRC patients. Results Five molecular subtypes were identified by consensus clustering for ferroptosis-related genes. There were significant differences in the overall survival, immune cells infiltration status and PD1/PD-L1 mRNA among the five clusters. Then, a risk signature based on the ten-gene was constructed which could distinguish effectively high-risk group among CRC patients in both training and validation sets. The high-risk patients were more likely to have an inhibitory immune microenvironment and lower stemness features. A prognostic nomogram integrated risk signature and clinicopathological features could be used as a more accurate prognostic prediction visualization tool than TNM stage alone. Conclusion This ferroptosis risk signature may accurately differentiate between different risk populations and predict the prognosis of CRC. Besides, this study elucidated the crucial role of ferroptosis in tumor immune microenvironment.
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Affiliation(s)
- Chao Yang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shuoyang Huang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fengyu Cao
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yongbin Zheng
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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523
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Tian Q, Zhou Y, Zhu L, Gao H, Yang J. Development and Validation of a Ferroptosis-Related Gene Signature for Overall Survival Prediction in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:684259. [PMID: 34307361 PMCID: PMC8294813 DOI: 10.3389/fcell.2021.684259] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/18/2021] [Indexed: 12/28/2022] Open
Abstract
Background: Ferroptosis is an iron-dependent programmed cell death process. Recent studies have found that ferroptosis inducers hold promising potential in the treatment of lung adenocarcinoma (LUAD). However, the comprehensive analysis about the prognostic value of ferroptosis-related genes in LUAD remains to be elucidated. Methods: The RNA sequencing data and corresponding clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A total of 259 ferroptosis-related genes were extracted from FerrDb website. The ferroptosis-related prognostic signature was developed by least absolute shrinkage and selection operator (LASSO) Cox regression analysis in TCGA LUAD cohort, and then validated by 5 independent GEO cohorts. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were performed to identify the difference in biological processes and functions between different risk groups. The expression levels of core prognostic genes were then verified in LUAD samples by immunohistochemistry (IHC) and erastin-treated LUAD cell lines by real-time polymerase chain reaction (PCR). The potential roles of GPX2 and DDIT4 as ferroptosis drivers in LUAD cell line were further confirmed by in vitro experiments. Results: A total of 20 intersecting genes between 70 ferroptosis-related DEGs and 45 potential prognostic genes were obtained for LASSO Cox regression analysis. The ferroptosis-related prognostic signature was developed by 7 core prognostic DEGs, and stratified LUAD patients into two risk groups. Kaplan-Meier analysis showed that the overall survival (OS) of LUAD patients in the high-risk group was significantly worse than that of the low-risk group. External validation of 5 independent GEO cohorts further confirmed that the ferroptosis-related prognostic signature was an ideal biomarker for predicting the survival of LUAD patients. Significant enrichment of fatty acid metabolism and cell cycle-related pathways were found in different risk groups. The expression patterns of 7 core prognostic genes in LUAD and adjacent normal lung tissues were validated by IHC, which was almost consistent with the results from public database. Furthermore, the changes related to cell cycle and ferroptosis after erastin treatment were also validated in LUAD cell lines. In addition, silencing GPX2 or DDIT4 could partially reverse the erastin-induced ferroptosis. Conclusion: In summary, the ferroptosis-related prognostic signature based on 7 core prognostic DEGs indicated superior predictive performance of LUAD patients. Targeting ferroptosis holds potential to be a therapeutic alternative for LUAD.
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Affiliation(s)
- Qi Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yan Zhou
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lizhe Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jin Yang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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524
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Yao J, Chen X, Liu X, Li R, Zhou X, Qu Y. Characterization of a ferroptosis and iron-metabolism related lncRNA signature in lung adenocarcinoma. Cancer Cell Int 2021; 21:340. [PMID: 34217273 PMCID: PMC8254945 DOI: 10.1186/s12935-021-02027-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/15/2021] [Indexed: 02/09/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are increasingly recognized as the crucial mediators in the regulation of ferroptosis and iron metabolism. A systematic understanding of ferroptosis and iron-metabolism related lncRNAs (FIRLs) in lung adenocarcinoma (LUAD) is essential for new diagnostic and therapeutic strategies. Methods FIRLs were obtained through Pearson correlation analysis between ferroptosis and iron-metabolism related genes and all lncRNAs. Univariate and multivariate Cox regression analysis were used to identify optimal prognostic lncRNAs. Next, a novel signature was constructed and risk score of each patient was calculated. Survival analysis and ROC analysis were performed to evaluate the predictive performance using The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) and Gene Expression Omnibus (GEO) datasets, respectively. Furthermore, multivariate Cox and stratification analysis were used to assess prognostic value of this signature in whole cohort and various subgroups. The correlation of risk signature with immune infiltration and gene mutation was also discussed. The expression of lncRNAs was verified by quantitative real-time PCR (qRT-PCR). Results A 7-FIRLs signature including ARHGEF26-AS1, LINC01137, C20orf197, MGC32805, TMPO-AS1, LINC00324, and LINC01116 was established in the present study to assess the overall survival (OS) of LUAD. The survival analysis and ROC curve indicated good predictive performance of the signature in both the TCGA training set and the GEO validation set. Multivariate Cox and stratification analysis indicated that the 7‐FIRLs signature was an independent prognostic factor for OS. Nomogram exhibited robust validity in prognostic prediction. Differences in immune cells, immune functions and gene mutation were also found between high-risk and low-risk groups. Conclusions This risk signature based on the FIRLs may be promising for the clinical prediction of prognosis and immunotherapeutic responses in LUAD patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02027-2.
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Affiliation(s)
- Jie Yao
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Xiao Chen
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Respiratory Medicine, Tai'an City Central Hospital, Tai'an, China.,Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Xijia Zhou
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Yiqing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China. .,Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China.
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525
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Qi X, Wang R, Lin Y, Yan D, Zuo J, Chen J, Shen B. A Ferroptosis-Related Gene Signature Identified as a Novel Prognostic Biomarker for Colon Cancer. Front Genet 2021; 12:692426. [PMID: 34276794 PMCID: PMC8280527 DOI: 10.3389/fgene.2021.692426] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023] Open
Abstract
Background Colon cancer (CC) is a common gastrointestinal malignant tumor with high heterogeneity in clinical behavior and response to treatment, making individualized survival prediction challenging. Ferroptosis is a newly discovered iron-dependent cell death that plays a critical role in cancer biology. Therefore, identifying a prognostic biomarker with ferroptosis-related genes provides a new strategy to guide precise clinical decision-making in CC patients. Methods Alteration in the expression profile of ferroptosis-related genes was initially screened in GSE39582 dataset involving 585 CC patients. Univariate Cox regression analysis and LASSO-penalized Cox regression analysis were combined to further identify a novel ferroptosis-related gene signature for overall survival prediction. The prognostic performance of the signature was validated in the GSE17536 dataset by Kaplan-Meier survival curve and time-dependent ROC curve analyses. Functional annotation of the signature was explored by integrating GO and KEGG enrichment analysis, GSEA analysis and ssGSEA analysis. Furthermore, an outcome risk nomogram was constructed considering both the gene signature and the clinicopathological features. Results The prognostic signature biomarker composed of 9 ferroptosis-related genes accurately discriminated high-risk and low-risk patients with CC in both the training and validation datasets. The signature was tightly linked to clinicopathological features and possessed powerful predictive ability for distinct clinical subgroups. Furthermore, the risk score was confirmed to be an independent prognostic factor for CC patients by multivariate Cox regression analysis (p < 0.05). Functional annotation analyses showed that the prognostic signature was closely correlated with pivotal cancer hallmarks, particularly cell cycle, transcriptional regulation, and immune-related functions. Moreover, a nomogram with the signature was also built to quantify outcome risk for each patient. Conclusion The novel ferroptosis-related gene signature biomarker can be utilized for predicting individualized prognosis, optimizing survival risk assessment and facilitating personalized management of CC patients.
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Affiliation(s)
- Xin Qi
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Rui Wang
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Yuxin Lin
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Donghui Yan
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Jiachen Zuo
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Jiajia Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Bairong Shen
- Institute for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
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526
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Yifan C, Jianfeng S, Jun P. Development and Validation of a Random Forest Diagnostic Model of Acute Myocardial Infarction Based on Ferroptosis-Related Genes in Circulating Endothelial Cells. Front Cardiovasc Med 2021; 8:663509. [PMID: 34262953 PMCID: PMC8274450 DOI: 10.3389/fcvm.2021.663509] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/20/2021] [Indexed: 12/22/2022] Open
Abstract
The high incidence and mortality of acute myocardial infarction (MI) drastically threaten human life and health. In the past few decades, the rise of reperfusion therapy has significantly reduced the mortality rate, but the MI diagnosis is still by means of the identification of myocardial injury markers without highly specific biomarkers of microcirculation disorders. Ferroptosis is a novel reported type of programmed cell death, which plays an important role in cancer development. Maintaining iron homeostasis in cells is essential for heart function, and its role in the pathological process of ischemic organ damages remains unclear. Being quickly detected through blood tests, circulating endothelial cells (CECs) have the potential for early judgment of early microcirculation disorders. In order to explore the role of ferroptosis-related genes in the early diagnosis of acute MI, we relied on two data sets from the GEO database to first detect eight ferroptosis-related genes differentially expressed in CECs between the MI and healthy groups in this study. After comparing different supervised learning algorithms, we constructed a random forest diagnosis model for acute MI based on these ferroptosis-related genes with a compelling diagnostic performance in both the validation (AUC = 0.8550) and test set (AUC = 0.7308), respectively. These results suggest that the ferroptosis-related genes might play an important role in the early stage of MI and have the potential as specific diagnostic biomarkers for MI.
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527
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Shao Y, Jia H, Huang L, Li S, Wang C, Aikemu B, Yang G, Hong H, Yang X, Zhang S, Sun J, Zheng M. An Original Ferroptosis-Related Gene Signature Effectively Predicts the Prognosis and Clinical Status for Colorectal Cancer Patients. Front Oncol 2021; 11:711776. [PMID: 34249766 PMCID: PMC8264263 DOI: 10.3389/fonc.2021.711776] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignant tumors in the world. Ferroptosis is a newly defined form of cell death, distinguished by different morphology, biochemistry, and genetics, and involved in CRC progression and treatment. This study aims to establish a predictive model to elucidate the relationship between ferroptosis and prognosis of CRC patients, to explore the potential value of ferroptosis in therapeutic options. Methods The ferroptosis-related genes were obtained from the GeneCards and FerrDb websites. The limma R package was used to screen the differential ferroptosis-related genes (DEGs) in CRC from The Cancer Genome Atlas (TCGA) dataset. The least absolute shrinkage and selection operator (LASSO) and multivariate Cox regressions were to establish the 10-gene prognostic signature. The survival and receiver operating characteristic (ROC) curves were illustrated to evaluate the predictive effect of the signature. Besides, independent prognostic factors, downstream functional enrichment, drug sensitivity, somatic mutation status, and immune feature were analyzed. Moreover, all these conclusions were verified by using multiple datasets in International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO). Results Ten ferroptosis-related gene signature (TFAP2C, SLC39A8, NOS2, HAMP, GDF15, FDFT1, CDKN2A, ALOX12, AKR1C1, ATP6V1G2) was established to predict the prognosis of CRC patients by Lasso cox analysis, demonstrating a good performance on Receiver operating characteristic (ROC) and Kaplan–Meier (K–M) analyses. The CRC patients in the high- or low-risk group showed significantly different fractions of immune cells, such as macrophage cells and CD8+ T cells. Drug sensitivity and somatic mutation status like TP53 were also closely associated with the risk scores. Conclusions In this study, we identified a novel ferroptosis-related 10-gene signature, which could effectively predict the prognosis and survival time of CRC patients, and provide meaningful clinical implications for targeted therapy or immunotherapy. Targeting ferroptosis is a good therapeutic option for CRC patients. Further studies are needed to reveal the underlying mechanisms of ferroptosis in CRC.
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Affiliation(s)
- Yanfei Shao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongtao Jia
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ling Huang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuchun Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenxing Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Batuer Aikemu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hiju Hong
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sen Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minhua Zheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhang A, Yang J, Ma C, Li F, Luo H. Development and Validation of a Robust Ferroptosis-Related Prognostic Signature in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:616271. [PMID: 34249899 PMCID: PMC8264775 DOI: 10.3389/fcell.2021.616271] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 05/31/2021] [Indexed: 12/25/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer. Ferroptosis is a newly recognized process of cell death, which is different from other forms of cell death in morphology, biochemistry, and genetics, and has played a vital role in cancer biology. This study aimed to identify a ferroptosis-related gene signature associated with LUAD prognosis. Methods Dataset TCGA-LUAD which came from the TCGA portal was taken as the training cohort. GSE72094 and GSE68465 from the GEO database were treated as validation cohorts. Two hundred fifty-nine ferroptosis-related genes were retrieved from the FerrDb database. In the training cohort, Kaplan–Meier and univariate Cox analyses were conducted for preliminary screening of ferroptosis-related genes with potential prognostic capacity. These genes then entered into the LASSO Cox regression model, constructing a gene signature. The latter was then evaluated in the training and validation cohorts via Kaplan–Meier, Cox, and ROC analyses. In addition, the correlations between risk score and autophagy were examined by Pearson correlation coefficient. The analyses of GSEA and immune infiltrating were performed for better studying the function annotation of the gene signature and the character of each kind of immune cells played in the tumor microenvironment. Results A 15-gene signature was found from the training cohort and validated by Kaplan–Meier and Cox regression analyses, revealing its independent prognosis value in LUAD. Moreover, the ROC analysis was conducted, confirming a strong predictive ability that this signature owned for LUAD prognosis. One hundred fifty-one of 222 (68.01%) autophagy-related genes were discovered significantly correlated with risk scores. Analyses of GSEA and immune infiltration exhibited in detail the specific pathways that associate with the 15-gene signature and identified the crucial roles of resting mast cells and resting dendritic cells owned in the prognosis of the 15-gene signature. Conclusion In this present study, a novel ferroptosis-related 15-gene signature (RELA, ACSL3, YWHAE, EIF2S1, CISD1, DDIT4, RRM2, PANX1, TLR4, ARNTL, LPIN1, HERPUD1, NCOA4, PEBP1, and GLS2) was built. It could accurately predict the prognosis of LUAD and was related to resting mast cells and resting dendritic cells, which provide potential for the personalized outcome prediction and the development of new therapies in LUAD population.
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Affiliation(s)
- Anran Zhang
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Jinpo Yang
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Chao Ma
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Feng Li
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany.,Department of Surgery, Competence Center of Thoracic Surgery, Charité University Hospital Berlin, Berlin, Germany
| | - Huan Luo
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
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529
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Zhu L, Tian Q, Jiang S, Gao H, Yu S, Zhou Y, Yan Y, Ren Y, He J, Wang B. A Novel Ferroptosis-Related Gene Signature for Overall Survival Prediction in Patients With Breast Cancer. Front Cell Dev Biol 2021; 9:670184. [PMID: 34222241 PMCID: PMC8247647 DOI: 10.3389/fcell.2021.670184] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/14/2021] [Indexed: 01/27/2023] Open
Abstract
Introduction Breast cancer is the most common malignant tumor in women worldwide. However, advanced multidisciplinary therapy cannot rescue the mortality of high-risk breast cancer metastasis. Ferroptosis is a newly discovered form of regulating cell death that related to cancer treatment, especially in eradicating aggressive malignancies that are resistant to traditional therapies. However, the prognostic value of ferroptosis-related gene in breast cancer remains unknown. Materials and Methods In this study, a total of 1,057 breast cancer RNA expression data with clinical and follow-up information were downloaded from the TCGA cohort, multivariate Cox regression was used to construct the 11-gene prognostic ferroptosis-related gene signature. The breast cancer patients from the GEO cohort were used for validation. The expression levels of core prognostic genes were also verified in erastin-treated breast cancer cell lines by real-time polymerase chain action (PCR). Results and Discussion Our results showed that 78% ferroptosis-related genes were differentially expressed between breast cancer tumor tissue and adjacent non-tumorous tissues, including 29 of them which were significantly correlated with OS in the univariate Cox regression analysis. Patients were divided into high-risk group and low-risk group by the 11-gene signature. Patients with high-risk scores had a higher probability of death earlier than the low-risk group both in the TCGA construction cohort and in the GEO validation cohort (all P < 0.001). Meanwhile, the risk score was proved to be an independent predictor for OS in both univariate and multivariate Cox regression analyses (HR > 1, P < 0.01). The predictive efficacy of the prognostic signature for OS was further verified by the time-dependent ROC curves. Moreover, we also enriched many immune-related biological processes in later functional analysis; the immune status showed a statistical difference between the two risk groups. In addition, the differences in expression levels of 11 core prognostic genes were examined in ferroptosis inducer-treated breast cancer cell lines. Conclusion In conclusion, a novel ferroptosis-related gene model can be used for prognostic prediction in breast cancer. New ferroptosis-related genes may be used for breast cancer targeting therapy in the future.
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Affiliation(s)
- Lizhe Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qi Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Siyuan Jiang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shibo Yu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yudong Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Yan
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Ren
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bin Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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530
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He F, Chen Z, Deng W, Zhan T, Huang X, Zheng Y, Yang H. Development and validation of a novel ferroptosis-related gene signature for predicting prognosis and immune microenvironment in head and neck squamous cell carcinoma. Int Immunopharmacol 2021; 98:107789. [PMID: 34130150 DOI: 10.1016/j.intimp.2021.107789] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/26/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022]
Abstract
Ferroptosis plays an important role across variable cancer types. However, few studies have focused on the prognostic patterns of ferroptosis-related genes in HNSCC. Cohorts with mRNA expression profiles, as well as corresponding clinical data of HNSCC patients from published studies, were collected and consolidated from public databases. We performed random survival forest analysis, Kaplan-Meier (KM) analysis of best combinations, and Cox regression analysis on 231 ferroptosis-related genes to construct a gene signature in the discovery cohort (TCGA), and later validated it in the validation cohort (GEO). The 7-gene signature was constructed to stratify patients into two groups according to their level of risk. Poorer overall survival (OS) was detected in the high risk (HRisk) group than in the low risk (LRisk) group in both the TCGA cohort (P < 0.0001, HR = 1.71, 95%CI:1.41-2.07) and the GEO cohort (P < 0.001, HR = 1.68, 95%CI:1.32-2.13). The risk score was identified as an independent predictive factor of OS in multivariate Cox regression analyses (HR > 1, P < 0.0001) in both cohorts. The signature's predictive capacity was proven by the time-dependent receiver operating characteristic (ROC) curve analysis and nomogram analysis. Functional enrichment analysis revealed that immunosuppressive pathways such as matrix extracellular space, and (transforming growth factor-β)TGF-β were enriched. The HRisk group was strongly associated with upregulation of both cancer-related pathways and stromal scores, while higher proportions of anti-tumor immune cells and immune signatures were enriched in the LRisk group. In conclusion, the signature based on 7 ferroptosis-related genes could be applicable for predicting the prognosis of HNSCC, indicating that ferroptosis may be a potential therapeutic target for HNSCC.
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Affiliation(s)
- Feinan He
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Department of Hearing and Speech Science, Xinhua College, Sun Yat-Sen University, Guangzhou, China
| | - Zhigang Chen
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wenting Deng
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Department of Hearing and Speech Science, Xinhua College, Sun Yat-Sen University, Guangzhou, China
| | - Ting Zhan
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Department of Hearing and Speech Science, Xinhua College, Sun Yat-Sen University, Guangzhou, China
| | - Xiaotong Huang
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Department of Hearing and Speech Science, Xinhua College, Sun Yat-Sen University, Guangzhou, China
| | - Yiqing Zheng
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Department of Hearing and Speech Science, Xinhua College, Sun Yat-Sen University, Guangzhou, China.
| | - Haidi Yang
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Department of Hearing and Speech Science, Xinhua College, Sun Yat-Sen University, Guangzhou, China.
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Liang J, Zhi Y, Deng W, Zhou W, Li X, Cai Z, Zhu Z, Zeng J, Wu W, Dong Y, Huang J, Zhang Y, Xu S, Feng Y, Ding F, Zhang J. Development and validation of ferroptosis-related lncRNAs signature for hepatocellular carcinoma. PeerJ 2021; 9:e11627. [PMID: 34178478 PMCID: PMC8202323 DOI: 10.7717/peerj.11627] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) with high heterogeneity is one of the most frequent malignant tumors throughout the world. However, there is no research to establish a ferroptosis-related lncRNAs (FRlncRNAs) signature for the patients with HCC. Therefore, this study was designed to establish a novel FRlncRNAs signature to predict the survival of patients with HCC. Method The expression profiles of lncRNAs were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. FRlncRNAs co-expressed with ferroptosis-related genes were utilized to establish a signature. Cox regression was used to construct a novel three FRlncRNAs signature in the TCGA cohort, which was verified in the GEO validation cohort. Results Three differently expressed FRlncRNAs significantly associated with prognosis of HCC were identified, which composed a novel FRlncRNAs signature. According to the FRlncRNAs signature, the patients with HCC could be divided into low- and high-risk groups. Patients with HCC in the high-risk group displayed shorter overall survival (OS) contrasted with those in the low-risk group (P < 0.001 in TCGA cohort and P = 0.045 in GEO cohort). This signature could serve as a significantly independent predictor in Cox regression (multivariate HR > 1, P < 0.001), which was verified to a certain extent in the GEO cohort (univariate HR > 1, P < 0.05). Meanwhile, it was also a useful tool in predicting survival among each stratum of gender, age, grade, stage, and etiology,etc. This signature was connected with immune cell infiltration (i.e., Macrophage, Myeloid dendritic cell, and Neutrophil cell, etc.) and immune checkpoint blockade targets (PD-1, CTLA-4, and TIM-3). Conclusion The three FRlncRNAs might be potential therapeutic targets for patients, and their signature could be utilized for prognostic prediction in HCC.
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Affiliation(s)
- Jiaying Liang
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Yaofeng Zhi
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Wenhui Deng
- Guangzhou University of Chinese Medicine, The fourth Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Weige Zhou
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Xuejun Li
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Zheyou Cai
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Zhijian Zhu
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Jinxiang Zeng
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Wanlan Wu
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Ying Dong
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Jin Huang
- Guangzhou University of Chinese Medicine, Clinic of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuzhuo Zhang
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Shichao Xu
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Yixin Feng
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Fuping Ding
- Guangzhou University of Chinese Medicine, School of Nursing, Guangzhou, China
| | - Jin Zhang
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
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532
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Zhang K, Ping L, Du T, Liang G, Huang Y, Li Z, Deng R, Tang J. A Ferroptosis-Related lncRNAs Signature Predicts Prognosis and Immune Microenvironment for Breast Cancer. Front Mol Biosci 2021; 8:678877. [PMID: 34164433 PMCID: PMC8215711 DOI: 10.3389/fmolb.2021.678877] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/25/2021] [Indexed: 01/10/2023] Open
Abstract
Background: Ferroptosis, a regulated cell death which is driven by the iron-dependent peroxidation of lipids, plays an important role in cancer. However, studies about ferroptosis-related Long non-coding RNAs (lncRNAs) in breast cancer (BC) are limited. Besides, the prognostic role of ferroptosis-related lncRNAs and their relationship to immune microenvironment in breast cancer remain unclear. This study aimed to explore the potential prognostic value of ferroptosis-related lncRNAs and their relationship to immune microenvironment in breast cancer. Methods: RNA-sequencing data of female breast cancer patients were downloaded from TCGA database. 937 patients were randomly separated into training or validation cohort in 2:1 ratio. Ferroptosis-related lncRNAs were screened by Pearson correlation analysis with 239 reported ferroptosis-related genes. A ferroptosis-related lncRNAs signature was constructed with univariate and multivariate Cox regression analyses in the training cohort, and its prognostic value was further tested in the validation cohort. Results: An 8-ferroptosis-related-lncRNAs signature was developed by multivariate Cox regression analysis to divide patients into two risk groups. Patients in the high-risk group had worse prognosis than patients in the low-risk group. Multivariate Cox regression analysis showed the risk score was an independent prognostic indicator. Receiver operating characteristic curve (ROC) analysis proved the predictive accuracy of the signature. The area under time-dependent ROC curve (AUC) reached 0.853 at 1 year, 0.802 at 2 years, 0.740 at 5 years in the training cohort and 0.791 at 1 year, 0.778 at 2 years, 0.722 at 5 years in the validation cohort. Further analysis demonstrated that immune-related pathways were significantly enriched in the high-risk group. Analysis of the immune cell infiltration landscape showed that breast cancer in the high-risk group tended be immunologically “cold”. Conclusion: We identified a novel ferroptosis-related lncRNA signature which could precisely predict the prognosis of breast cancer patients. Ferroptosis-related lncRNAs may have a potential role in the process of anti-tumor immunity and serve as therapeutic targets for breast cancer.
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Affiliation(s)
- Kaiming Zhang
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Liqin Ping
- Department of Medical Oncology, State Key Laboratory of On cology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Tian Du
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Gehao Liang
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yun Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhiling Li
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Rong Deng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jun Tang
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
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533
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Yu Z, He H, Chen Y, Ji Q, Sun M. A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma. Sci Rep 2021; 11:11486. [PMID: 34075060 PMCID: PMC8169824 DOI: 10.1038/s41598-021-90126-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
Ovarian cancer (OV) is a common type of carcinoma in females. Many studies have reported that ferroptosis is associated with the prognosis of OV patients. However, the mechanism by which this occurs is not well understood. We utilized Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) to identify ferroptosis-related genes in OV. In the present study, we applied Cox regression analysis to select hub genes and used the least absolute shrinkage and selection operator to construct a prognosis prediction model with mRNA expression profiles and clinical data from TCGA. A series of analyses for this signature was performed in TCGA. We then verified the identified signature using International Cancer Genome Consortium (ICGC) data. After a series of analyses, we identified six hub genes (DNAJB6, RB1, VIMP/ SELENOS, STEAP3, BACH1, and ALOX12) that were then used to construct a model using a training data set. The model was then tested using a validation data set and was found to have high sensitivity and specificity. The identified ferroptosis-related hub genes might play a critical role in the mechanism of OV development. The gene signature we identified may be useful for future clinical applications.
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Affiliation(s)
- Zhixiang Yu
- Basic Medicine College, The Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Haiyan He
- Department of Obstetrics and Gynecology, Tangdu Hospital, The Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Yanan Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine,Nanjing University, Nanjing, Jiangsu, China
| | - Qiuhe Ji
- Department of Endocrinology and Metabolism, Xijing Hospital, The Air Force Military Medical University, Xi'an, Shaanxi, China.
| | - Min Sun
- Department of Obstetrics and Gynecology, Tangdu Hospital, The Air Force Military Medical University, Xi'an, Shaanxi, China.
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534
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Deng S, Zheng Y, Mo Y, Xu X, Li Y, Zhang Y, Liu J, Chen J, Tian Y, Ke Y. Ferroptosis Suppressive Genes Correlate with Immunosuppression in Glioblastoma. World Neurosurg 2021; 152:e436-e448. [PMID: 34062295 DOI: 10.1016/j.wneu.2021.05.098] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Glioblastoma (GBM) is the most lethal primary tumor in the central nervous system. Ferroptosis is a type of programmed iron-dependent cell death. In the present study, we aimed to identify prognostic ferroptosis-related genes and their role in tumor immunity. METHODS We used differential and survival analysis and The Cancer Genome Atlas (TCGA) GBM RNA sequencing data. We also used systematic bioinformatic methods. RESULTS Using differential and survival analysis, we found that a ferroptosis suppressor was predominant within ferroptosis-related genes in TCGA GBM RNA sequencing data. By integrating TCGA and gene expression omnibus GBM cohorts, 12 dysregulated ferroptosis suppressors were detected. Among the suppressors, CD44, heat shock protein family B (small) member 1 (HSPB1), and solute carrier family 40 member 1 (SLC40A1) were relevant to overall survival. Using systematic bioinformatic methods, we observed that ferroptosis suppressor expression correlated with immunosuppression, which could be attributed to T-cell exhaustion and cytotoxic T-lymphocyte evasion. Finally, we observed that a potential ferroptosis-inducing drug, acetaminophen, interacted with CD44, HSPB1, and SLC40A1. CONCLUSIONS The ferroptosis suppressors CD44, HSPB1, and SLC40A1 were significantly associated with prognosis in GBM and correlated with immunosuppression (i.e., T-cell exhaustion and cytotoxic T-lymphocyte evasion). Acetaminophen might have an antitumor function in GBM by regulating CD44, HSPB1, and SLC40A1 to induce ferroptosis. Our results are expected to be of great significance in developing new immunotherapy strategies for GBM.
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Affiliation(s)
- Shaokang Deng
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yaofeng Zheng
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yunzhao Mo
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiangdong Xu
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yan Li
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuxuan Zhang
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Liu
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jianqiu Chen
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yixin Tian
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yiquan Ke
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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535
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Wu ZH, Tang Y, Yu H, Li HD. The role of ferroptosis in breast cancer patients: a comprehensive analysis. Cell Death Discov 2021; 7:93. [PMID: 33947836 PMCID: PMC8097021 DOI: 10.1038/s41420-021-00473-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/22/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) affects the breast tissue and is the second most common cause of mortalities among women. Ferroptosis is an iron-dependent cell death mode that is characterized by intracellular accumulation of reactive oxygen species (ROS). We constructed a prognostic multigene signature based on ferroptosis-associated differentially expressed genes (DEGs). Moreover, we comprehensively analyzed the role of ferroptosis-associated miRNAs, lncRNAs, and immune responses. A total of 259 ferroptosis-related genes were extracted. KEGG function analysis of these genes revealed that they were mainly enriched in the HIF-1 signaling pathway, NOD-like receptor signaling pathway, central carbon metabolism in cancer, and PPAR signaling pathway. Fifteen differentially expressed genes (ALOX15, ALOX15B, ANO6, BRD4, CISD1, DRD5, FLT3, G6PD, IFNG, NGB, NOS2, PROM2, SLC1A4, SLC38A1, and TP63) were selected as independent prognostic factors for BC patients. Moreover, T cell functions, including the CCR score, immune checkpoint, cytolytic activity, HLA, inflammation promotion, para-inflammation, T cell co-stimulation, T cell co-inhibition, and type II INF responses were significantly different between the low-risk and high-risk groups of the TCGA cohort. Immune checkpoints between the two groups revealed that the expressions of PDCD-1 (PD-1), CTLA4, LAG3, TNFSF4/14, TNFRSF4/8/9/14/18/25, and IDO1/2 among others were significantly different. A total of 1185 ferroptosis-related lncRNAs and 219 ferroptosis-related miRNAs were also included in this study. From the online database, we identified novel ferroptosis-related biomarkers for breast cancer prognosis. The findings of this study provide new insights into the development of new reliable and accurate cancer treatment options.
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Affiliation(s)
- Zeng-Hong Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yun Tang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Hong Yu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Hua-Dong Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
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536
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Wang Y, Xia HB, Chen ZM, Meng L, Xu AM. Identification of a ferroptosis-related gene signature predictive model in colon cancer. World J Surg Oncol 2021; 19:135. [PMID: 33926457 PMCID: PMC8086290 DOI: 10.1186/s12957-021-02244-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023] Open
Abstract
Background The prognosis of colon cancer (CC) is challenging to predict due to its highly heterogeneous nature. Ferroptosis, an iron-dependent form of cell death, has roles in various cancers; however, the correlation between ferroptosis-related genes (FRGs) and prognosis in CC remains unclear. Methods The expression profiles of FRGs and relevant clinical information were retrieved from the Cancer Genome Atlas (TCGA) database. Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) regression model were performed to build a prognostic model in TCGA cohort. Results Ten FRGs, five of which had mutation rates ≥ 3%, were found to be related to the overall survival (OS) of patients with CC. Patients were divided into high- and low-risk groups based on the results of Cox regression and LASSO analysis. Patients in the low-risk group had a significantly longer survival time than patients in the high-risk group (P < 0.001). Enrichment analyses in different risk groups showed that the altered genes were associated with the extracellular matrix, fatty acid metabolism, and peroxisome. Age, risk score, T stage, N stage, and M stage were independent predictors of patient OS based on the results of Cox analysis. Finally, a nomogram was constructed to predict 1-, 3-, and 5-year OS of patients with CC based on the above five independent factors. Conclusion A novel FRG model can be used for prognostic prediction in CC and may be helpful for individualized treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-021-02244-z.
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Affiliation(s)
- Ye Wang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People's Republic of China
| | - Heng-Bo Xia
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People's Republic of China
| | - Zhang-Ming Chen
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People's Republic of China
| | - Lei Meng
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People's Republic of China
| | - A-Man Xu
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People's Republic of China.
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537
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Huang W, Duan Y, Yang X, Shang C, Chen X, Zhang H, Li F. Identification of Novel Prognostic Risk Signatures of Soft Tissue Sarcoma Based on Ferroptosis-Related Genes. Front Oncol 2021; 11:629868. [PMID: 33889544 PMCID: PMC8056866 DOI: 10.3389/fonc.2021.629868] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/08/2021] [Indexed: 01/01/2023] Open
Abstract
Background The role of ferroptosis in tumorigenesis has been confirmed in previous studies. However, the comprehensive analysis of ferroptosis-related gene (FRG) to study the role of FRG in soft tissue sarcoma (STS) is lacking. Methods RNA sequencing profile of TCGA-SARC cohort and GTEx were used to select differentially expressed FRGs (DEFRGs). Univariate, LASSO, and multivariate Cox analyses were selected to determine overall survival (OS)- and disease-free survival (PFS)-related FRGs. Two prognostic signatures were established and validated in two independent sets from Gene Expression Omnibus (GEO). Finally, the expression of key FRGs were validated with RT-qPCR. Results In total, 198 FRGs (90.4%) were abnormally expressed in STS. Twelve DEFRGs were incorporated in the final signatures and showed favorable discrimination in both training and validation cohorts. Patients in the different risk groups not only showed different prognosis, but also showed different infiltration of immune cells. Two nomograms combining signature and clinical variables were established and the C-indexes were 0.852 and 0.752 for the OS and DFS nomograms, respectively. Finally, the expression of NOX5, HELLS, and RPL8 were validated with RT-qPCR. Conclusion This comprehensive analysis of the FRG landscape in STS revealed novel FRGs related to carcinogenesis and prognosis. These findings have implications for prognosis and therapeutic responses, which revealed potential prognostic biomarkers and promote precision medicine.
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Affiliation(s)
- Wenjing Huang
- Department of Pediatric Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuhe Duan
- Department of Pediatric Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiuwei Yang
- Department of Infectious Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Cong Shang
- Department of Pediatric Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xin Chen
- Department of Pediatric Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Huanyu Zhang
- Department of Pediatric Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Fujiang Li
- Department of Pediatric Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
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538
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Jiang X, Yan Q, Xie L, Xu S, Jiang K, Huang J, Wen Y, Yan Y, Zheng J, Tang S, Nie K, Zheng Z, Pan J, Liu P, Huang Y, Yan X, Zou Y, Chen X, Liu F, Li P, Zhuang K. Construction and Validation of a Ferroptosis-Related Prognostic Model for Gastric Cancer. JOURNAL OF ONCOLOGY 2021; 2021:6635526. [PMID: 33727924 PMCID: PMC7937463 DOI: 10.1155/2021/6635526] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/05/2021] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Gastric cancer (GC), an extremely aggressive tumor with a very different prognosis, is the third leading cause of cancer-related mortality. We aimed to construct a ferroptosis-related prognostic model that can be distinguished prognostically. METHODS The gene expression and the clinical data of GC patients were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database (GEO). The ferroptosis-related genes were obtained from the FerrDb. Using the "limma" R package and univariate Cox analysis, ferroptosis-related genes with differential expression and prognostic value were identified in the TCGA cohort. Last absolute shrinkage and selection operator (LASSO) Cox regression was applied to shrink ferroptosis-related predictors and construct a prognostic model. Functional enrichment, ESTIMATE algorithm, and single-sample gene set enrichment analysis (ssGSEA) were applied for exploring the potential mechanism. GC patients from the GEO cohort were used for validation. RESULTS An 8-gene prognostic model was constructed and stratified GC patients from TCGA and meta-GEO cohort into high-risk groups or low-risk groups. GC patients in high-risk groups have significantly poorer OS compared with those in low-risk groups. The risk score was identified as an independent predictor for OS. Functional analysis revealed that the risk score was mainly associated with the biological function of extracellular matrix (ECM) organization and tumor immunity. CONCLUSION In conclusion, the ferroptosis-related model can be utilized for the clinical prognostic prediction in GC.
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Affiliation(s)
- Xiaotao Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Qiaofeng Yan
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- No. 1 Traditional Chinese Medicine Hospital in Changde, Changde 415000, Hunan, China
| | - Linling Xie
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Shijie Xu
- Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Kailin Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Jiahua Huang
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Yi Wen
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Yanhua Yan
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Junhui Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Shuting Tang
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Kechao Nie
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Zhihua Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Jinglin Pan
- Department of Gastroenterology, Hainan Provincial Hospital of Traditional Chinese Medicine, Haikou 570100, Hainan, China
| | - Peng Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Yuancheng Huang
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Xingrui Yan
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Yushan Zou
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Xuan Chen
- Ningde Hospital of Traditional Chinese Medicine Affiliated to Fujian University of Traditional Chinese Medicine, Ningde 352100, Fujian, China
| | - Fengbin Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
- Baiyun Hospital of The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510470, Guangdong, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Peiwu Li
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
| | - Kunhai Zhuang
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China
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539
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Lu T, Xu R, Li Q, Zhao JY, Peng B, Zhang H, Guo JD, Zhang SQ, Li HW, Wang J, Zhang LY. Systematic profiling of ferroptosis gene signatures predicts prognostic factors in esophageal squamous cell carcinoma. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:134-143. [PMID: 33981829 PMCID: PMC8080401 DOI: 10.1016/j.omto.2021.02.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
We developed a predictive model associated with ferroptosis to provide a more comprehensive view of esophageal squamous cell carcinoma (ESCC) immunotherapy. Gene expression data and corresponding clinical outcomes were obtained from the GEO and The Cancer Genome Atlas (TCGA) databases, and a ferroptosis-related gene set was obtained from the FerrDb database. We identified 45 ferroptosis-related genes that were differentially expressed, including enrichment in genes involved in the immune system process. We established a ferroptosis-related gene-based prognostic model based on the results of univariate Cox regression and multivariate Cox regression analyses, with an area under the curve (AUC) of 0.76 (3 years). We found that the patients with low-risk scores showed a higher proportion of CD8+ T cells, CD4+ memory activated T cells, etc. Finally, a predictive ferroptosis-related prognostic nomogram, which included the predictive values of age, gender, grade, TNM stage, and risk score, was established to predict overall survival. In sum, we developed a ferroptosis-related gene-based prognostic model that provides novel insights into the prediction of ESCC prognosis and identifies the relevance of the immune microenvironment for patient outcomes.
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Affiliation(s)
- Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Ran Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Qi Li
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin 150081, China
| | - Jia-Ying Zhao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Bo Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Han Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Ji-da Guo
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Sheng-Qiang Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Hua-Wei Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Jun Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Lin-You Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
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540
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Tang Y, Li C, Zhang YJ, Wu ZH. Ferroptosis-Related Long Non-Coding RNA signature predicts the prognosis of Head and neck squamous cell carcinoma. Int J Biol Sci 2021; 17:702-711. [PMID: 33767582 PMCID: PMC7975700 DOI: 10.7150/ijbs.55552] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/12/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) are head and neck cancers. On the other hand, ferroptosis is a novel iron-dependent and ROS reliant type of cell death observed various disease conditions. Method: We constructed a prognostic multilncRNA signature based on ferroptosis-related differentially expressed lncRNAs in HNSCC. Results: We identified 25 differently expressed lncRNAs associated with prognosis of HNSCC. Kaplan-Meier analyses revealed the high-risk lncRNAs signature associated with poor prognosis of HNSCC. Moreover, the AUC of the lncRNAs signature was 0.782, underscoring their utility in prediction HNSCC prognosis. Indeed, our risk assessment model was superior to traditional clinicopathological features in predicting HNSCC prognosis. GSEA revealed the immune and tumor-related pathways in the low risk group individuals. Moreover, TCGA revealed T cell functions including cytolytic activity, HLA, regulation of inflammationp, co-stimulation, co-inhibition and coordination of type II INF response were significantly different between the low-risk and high-risk groups. Immune checkpoints such as PDCD-1 (PD-1), CTLA4 and LAG3, were also expressed differently between the two risk groups. Conclusion: A novel ferroptosis-related lncRNAs signature impacts on the prognosis of HNSCC.
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Affiliation(s)
- Yun Tang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Cheng Li
- Department of Otolaryngology Head and Neck Surgery, The Central Hospital of Wuhan, Tongji Medical College Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - You-Jing Zhang
- School of Public Health, Tongji Medical College, Huazhong University of Science and technology, Wuhan, China
| | - Zeng-Hong Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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541
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Zhou N, Bao J, Ning Y. H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection. BMC Bioinformatics 2021; 22:18. [PMID: 33413085 PMCID: PMC7789886 DOI: 10.1186/s12859-020-03935-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/15/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The ongoing global COVID-19 pandemic is caused by SARS-CoV-2, a novel coronavirus first discovered at the end of 2019. It has led to more than 50 million confirmed cases and more than 1 million deaths across 219 countries as of 11 November 2020, according to WHO statistics. SARS-CoV-2, SARS-CoV, and MERS-CoV are similar. They are highly pathogenic and threaten public health, impair the economy, and inflict long-term impacts on society. No drug or vaccine has been approved as a treatment for these viruses. Efforts to develop antiviral measures have been hampered by the insufficient understanding of how the human body responds to viral infections at the cellular and molecular levels. RESULTS In this study, journal articles and transcriptomic and proteomic data surveying coronavirus infections were collected. Response genes and proteins were then identified by differential analyses comparing gene/protein levels between infected and control samples. Finally, the H2V database was created to contain the human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection. CONCLUSIONS H2V provides molecular information about the human response to infection. It can be a powerful tool to discover cellular pathways and processes relevant for viral pathogenesis to identify potential drug targets. It is expected to accelerate the process of antiviral agent development and to inform preparations for potential future coronavirus-related emergencies. The database is available at: http://www.zhounan.org/h2v .
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Affiliation(s)
- Nan Zhou
- Affiliated Brain Hospital of Guangzhou Medical University, 36 Mingxin Rd, Guangzhou, 510370, China
- Guangzhou Huiai Hospital, 36 Mingxin Rd, Guangzhou, 510370, China
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, 36 Mingxin Rd, Guangzhou, 510370, China
| | - Jinku Bao
- College of Life Sciences, Sichuan University, 29 Wangjiang Rd, Chengdu, 610064, China.
| | - Yuping Ning
- Affiliated Brain Hospital of Guangzhou Medical University, 36 Mingxin Rd, Guangzhou, 510370, China.
- Guangzhou Huiai Hospital, 36 Mingxin Rd, Guangzhou, 510370, China.
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, 36 Mingxin Rd, Guangzhou, 510370, China.
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542
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Jiao H, Yang H, Yan Z, Chen J, Xu M, Jiang Y, Liu Y, Xue Z, Ma Q, Li X, Chen J. Traditional Chinese Formula Xiaoyaosan Alleviates Depressive-Like Behavior in CUMS Mice by Regulating PEBP1-GPX4-Mediated Ferroptosis in the Hippocampus. Neuropsychiatr Dis Treat 2021; 17:1001-1019. [PMID: 33854318 PMCID: PMC8039849 DOI: 10.2147/ndt.s302443] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/15/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND At present, the pathogenesis of depression is not fully understood, and nearly half of depression patients experience no obvious effects during treatment. This study aimed to establish a depression mouse model to explore the possible role of ferroptosis in the pathogenesis of depression, and observe the effects of Xiaoyaosan on PEBP1-GPX4-mediated ferroptosis in the hippocampus. METHODS Forty-eight male C57BL/6 mice were randomly divided into a control group, CUMS group, Xiaoyaosan group and fluoxetine group, and the model was established by chronic unpredictable mild stress (CUMS) for a successive 6 weeks. The medication procedure was performed from the 4th to the 6th week of modeling. The behavioral evaluations were measured to evaluate depressive-like behaviors. The expressions of GPX4, FTH1, ACSL4 and COX2 were detected as ferroptosis-related indicators. Then, the total iron and ferrous content in the hippocampus were measured. The levels of PEBP1 and ERK1/2 were observed, and the expressions of GFAP and IBA1 were also detected to measure the functions of astrocytes and microglia in the hippocampus. RESULTS Eight herbs of Xiaoyaosan had 133 active ingredients which could regulate the 43 ferroptosis-related genes in depression. After 6 weeks of modeling, the data showed that mice in the CUMS group had obvious depressive-like behaviors, and medication with Xiaoyaosan or fluoxetine could significantly improve the behavioral changes. The expressions of GPX4, FTH1, ACSL4, COX2, PEBP1, ERK1/2, GFAP and IBA1 changed in the CUMS group mice, while the total iron and ferrous content also changed. Xiaoyaosan and fluoxetine had obvious curative effects that could significantly alleviate the above changes in the hippocampus. CONCLUSION Our results revealed that the activation of ferroptosis might exist in the hippocampi of CUMS-induced mice. The PEBP1-GPX4-mediated ferroptosis could be involved in the antidepressant mechanism of Xiaoyaosan. It also implied that ferroptosis could become a new target for research into the depression mechanism and antidepressant drugs.
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Affiliation(s)
- Haiyan Jiao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Hongjun Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Zhiyi Yan
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Jianbei Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Mengbai Xu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Youming Jiang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Yueyun Liu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Zhe Xue
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Qingyu Ma
- Formula-Pattern Research center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, 510632, Guangdong, People's Republic of China
| | - Xiaojuan Li
- Formula-Pattern Research center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, 510632, Guangdong, People's Republic of China
| | - Jiaxu Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China.,Formula-Pattern Research center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, 510632, Guangdong, People's Republic of China
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543
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Yang H, Zhao L, Gao Y, Yao F, Marti TM, Schmid RA, Peng RW. Pharmacotranscriptomic Analysis Reveals Novel Drugs and Gene Networks Regulating Ferroptosis in Cancer. Cancers (Basel) 2020; 12:cancers12113273. [PMID: 33167414 PMCID: PMC7694346 DOI: 10.3390/cancers12113273] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
(1) Background: Ferroptosis is an apoptosis-independent cell death program implicated in many diseases including cancer. Emerging evidence suggests ferroptosis as a promising avenue for cancer therapy, but the paucity of mechanistic understanding of ferroptosis regulation and lack of biomarkers for sensitivity to ferroptosis inducers have significantly hampered the utility of ferroptosis-based therapy. (2) Methods: We performed integrated dataset analysis by correlating the sensitivity of small-molecule compounds (n = 481) against the transcriptomes of solid cancer cell lines (n = 659) to identify drug candidates with the potential to induce ferroptosis. Generalizable gene signatures of ferroptosis sensitivity and resistance are defined by interrogating drug effects of ferroptosis inducers (n = 7) with transcriptomic data of pan-solid cancer cells. (3) Results: We report, for the first time, the comprehensive identification of drug compounds that induce ferroptosis and the delineation of generalizable gene signatures of pro- and anti-ferroptosis in pan-cancer. We further reveal that small cell lung cancer (SCLC) and isocitrate dehydrogenase (IDH1/2)-mutant brain tumors show enrichment of pro-ferroptosis gene signature, suggesting a unique vulnerability of SCLC and IDH-mutant tumors to ferroptosis inducers. Finally, we demonstrate that targeting class I histone deacetylase (HDAC) significantly enhances ferroptotic cell death caused by Erastin, an ferroptosis inducer, in lung cancer cells, revealing a previously underappreciated role for HDAC in ferroptosis regulation. (4) Conclusions: Our work reveals novel drug compounds and gene networks that regulate ferroptosis in cancer, which sheds light on the mechanisms of ferroptosis and may facilitate biomarker-guided stratification for ferroptosis-based therapy.
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Affiliation(s)
- Haitang Yang
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland; (H.Y.); (L.Z.); (Y.G.); (T.M.M.)
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China;
| | - Liang Zhao
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland; (H.Y.); (L.Z.); (Y.G.); (T.M.M.)
| | - Yanyun Gao
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland; (H.Y.); (L.Z.); (Y.G.); (T.M.M.)
| | - Feng Yao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China;
| | - Thomas M. Marti
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland; (H.Y.); (L.Z.); (Y.G.); (T.M.M.)
| | - Ralph A. Schmid
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland; (H.Y.); (L.Z.); (Y.G.); (T.M.M.)
- Correspondence: (R.A.S.); (R.-W.P.)
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland; (H.Y.); (L.Z.); (Y.G.); (T.M.M.)
- Correspondence: (R.A.S.); (R.-W.P.)
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