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Li W, Yao R, Yu N, Zhang W. Identification of a prognostic signature based on five ferroptosis-related genes for diffuse large B-cell lymphoma. Cancer Biomark 2024:CBM230325. [PMID: 38517778 DOI: 10.3233/cbm-230325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
BACKGROUND Therapies for diffuse large B-cell lymphoma (DLBCL) are limited due to the diverse gene expression profiles and complicated immune microenvironments, making it an aggressive lymphoma. Beyond this, researches have shown that ferroptosis contributes to tumorigenesis, progression, and metastasis. We thus are interested to dissect the connection between ferroptosis and disease status of DLBCL. We aim at generating a valuable prognosis gene signature for predicting the status of patients of DLBCL, with focus on ferroptosis-related genes (FRGs). OBJECTIVE To examine the connection between ferroptosis-related genes (FRGs) and clinical outcomes in DLBCL patients based on public datasets. METHODS An expression profile dataset for DLBCL was downloaded from GSE32918 (https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=gse32918), and a ferroptosis-related gene cluster was obtained from the FerrDb database (http://www. zhounan.org/ferrdb/). A prognostic signature was developed from this gene cluster by applying a least absolute shrinkage and selection operator (LASSO) Cox regression analysis to GSE32918, followed by external validation. Its effectiveness as a biomarker and the prognostic value was determined by a receiver operator characteristic curve mono factor analysis. Finally, functional enrichment was evaluated by the package Cluster Profiler of R. RESULTS Five ferroptosis-related genes (FRGs) (GOP1, GPX2, SLC7A5, ATF4, and CXCL2) associated with DLBCL were obtained by a multivariate analysis. The prognostic power of these five FRGs was verified by TCGA (https://xenabrowser.net/datapages/?dataset=TCGA.DLBC.sampleMap%2FHiSeqV2_PANCAN&host=https%3A%2F%2Ftcga.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A44) and GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse 32918) datasets, with ROC analyses. KEGG and GO analyses revealed that upregulated genes in the high-risk group based on the gene signature were enriched in receptor interactions and other cancer-related pathways, including pathways related to abnormal metabolism and cell differentiation. CONCLUSION The newly developed signature involving GOP1, GPX2, SLC7A5, ATF4, and CXCL2 has the potential to serve as a prognostic biomarker. Furthermore, our results provide additional support for the contribution of ferroptosis to DLBCL.
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Affiliation(s)
- Wuping Li
- Departments of Lymphatic and Hematological Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, China
| | - Ruizhe Yao
- Queen Mrry College of Nan Chang University, Nanchang, Jiangxi, China
| | - Nasha Yu
- Departments of Lymphatic and Hematological Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, China
| | - Weiming Zhang
- Departments of Lymphatic and Hematological Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, China
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Hu R, Shi Z, Yang J, Ren Y, Li X. Anti-Ferroptosis: A Promising Therapeutic Method for Thyroid Cancer. FRONT BIOSCI-LANDMRK 2024; 29:77. [PMID: 38420811 DOI: 10.31083/j.fbl2902077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/31/2023] [Accepted: 12/06/2023] [Indexed: 03/02/2024]
Abstract
At present, many problems remain to be solved in studying the pathogenesis of thyroid cancer. Ferroptosis is a programmed cell death mode discovered in recent years, and many studies have found that ferroptosis plays a significant role in the prognosis and progression of thyroid cancer. The researchers showed that ferroptosis-related genes are essential in diagnosing thyroid cancer. Therefore, this paper summarizes some pathological and clinical characteristics of thyroid cancer and makes a series of combs on the relationship between ferroptosis and the basis and function of thyroid cancer, thus providing specific ideas for the diagnosis and treatment of thyroid cancer.
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Affiliation(s)
- Rongyi Hu
- Head and Neck Surgery, Yunnan Cancer Hospital, 650118 Kunming, Yunnan, China
| | - Zhizhou Shi
- Medical School, Kunming University of Science and Technology, 650500 Kunming, Yunnan, China
| | - Jie Yang
- Head and Neck Surgery, Yunnan Cancer Hospital, 650118 Kunming, Yunnan, China
| | - Yanxin Ren
- Head and Neck Surgery, Yunnan Cancer Hospital, 650118 Kunming, Yunnan, China
| | - Xiaojiang Li
- Head and Neck Surgery, Yunnan Cancer Hospital, 650118 Kunming, Yunnan, China
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Huang Y, Yuan X. Novel ferroptosis gene biomarkers and immune infiltration profiles in diabetic kidney disease via bioinformatics. FASEB J 2024; 38:e23421. [PMID: 38198194 DOI: 10.1096/fj.202301357rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/16/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Diabetic kidney disease (DKD) is the primary cause of end-stage renal disease, exhibiting high disability and mortality rates. Ferroptosis is vital for the progression of DKD, but the exact mechanism remains unclear. This study aimed to explore the potential mechanism of ferroptosis-related genes in DKD and their relationship with the immune and to identify new diagnostic biomarkers to help treat and diagnose DKD. GSE30122 and GSE47185 were obtained from the Gene Expression Omnibus database and were integrated into a merged dataset, followed by functional enrichment analysis. Then potential differentially expressed genes were screened. Ferroptosis-related differentially-expressed genes were identified, followed by gene ontology analysis. Protein-protein interaction networks were constructed and hub genes were screened. The immune cell-infiltrating state in the dataset was assessed using appropriate algorithms. Immune signature subtypes were constructed using the consensus clustering analysis. Hub gene expression was validated using qRT-PCR and immunohistochemistry. A total of Eleven screened ferroptosis-related differentially expressed genes were screened. Six potentially diagnostically favorable ferroptosis-related hub genes were identified. Significantly increased expression of γδT cells, resting mast cells, and macrophages infiltration was observed in the DKD group. Additionally, two distinct immune signature subgroups were identified. Ferroptosis-related hub genes were significantly correlated with differentially infiltrated immune cells. Six hub genes were significantly upregulated in HK-2 cells following high glucose treatment and in human kidney tissues of patients with DKD. Six ferroptosis-related hub genes were identified as potential biomarkers of diabetic kidney disease, but further validation is needed.
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Affiliation(s)
- Yixiong Huang
- Department of Nephrology, The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan, China
| | - Xinke Yuan
- Department of Nephrology, The First Hospital of Changsha, Changsha, Hunan, China
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Chen X, Li C, Wang Y, Geng S, Xiao M, Zeng L, Deng C, Li M, Huang X, Weng J, Du X, Lai P. Diagnostic and prognostic value of ferroptosis-related genes in patients with Myelodysplastic neoplasms. Hematology 2023; 28:2288475. [PMID: 38038045 DOI: 10.1080/16078454.2023.2288475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
This study delves into the emerging role of ferroptosis in Myelodysplastic Neoplasms (MDS) and aims to identify a prognostic ferroptosis-related gene signature for MDS. Utilizing RNA-seq data and clinical information from the Gene Expression Omnibus database, the researchers extracted ferroptosis-related genes from the FerrDb website and conducted differential expression analysis using the 'limma' package in R. Hub ferroptosis-related genes in MDS were screened using the "RandomForest" and "carat" R packages. Kaplan -Meier and Cox regression analyses were employed to assess the prognostic role of three identified hub genes (BNIP3, MDM2, and RRM2). Receiver operator characteristic curve analysis confirmed the diagnostic efficacy of these genes. The study delved further into immune infiltration correlations, ncRNA-transcription factor coregulatory network analysis, and the identification of potential therapeutic drugs targeting hub ferroptosis-related genes in MDS. The researchers constructed a 3-gene signature-based risk score using datasets GSE58831 and GSE19429, demonstrating high accuracy (AUC > 0.75) in both datasets for survival prediction in MDS. A nomogram analysis reinforced the prognostic value of the risk-scoring model. Immunological analysis revealed an association between the risk score and immune infiltration. Quantitative reverse transcription polymerase chain reaction (qPCR) data indicated significant expression differences in MDM2, RRM2, and BNIP3 between MDS and healthy bone marrow samples. Notably, MDM2 and RRM2 showed decreased expression, while BNIP3 exhibited increased expression in MDS samples. This comprehensive study concludes that BNIP3, MDM2, and RRM2 hold diagnostic and prognostic significance in MDS and provide valuable insights into immune cell landscapes and potential therapeutic avenues for this condition.
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Affiliation(s)
- Xiaomei Chen
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Chao Li
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, People's Republic of China
| | - Yulian Wang
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Suxia Geng
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Maozhi Xiao
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Lingji Zeng
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Chengxin Deng
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Minming Li
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Xin Huang
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jianyu Weng
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Xin Du
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Peilong Lai
- Department of Hematology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People's Republic of China
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Chen B, Zhao L, Yang R, Xu T. The recent advancements of ferroptosis in the diagnosis, treatment and prognosis of ovarian cancer. Front Genet 2023; 14:1275154. [PMID: 38028615 PMCID: PMC10665572 DOI: 10.3389/fgene.2023.1275154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Ovarian cancer affects the female reproductive system and is the primary cause of cancer related mortality globally. The imprecise and non-specific nature of ovarian cancer symptoms often results in patients being diagnosed at an advanced stage, with metastatic lesions extending beyond the ovary. This presents a significant clinical challenge and imposes a substantial economic burden on both patients and society. Despite advancements in surgery, chemotherapy, and immunotherapy, the prognosis for most patients with ovarian cancer remains unsatisfactory. Therefore, the development of novel treatment strategies is imperative. Ferroptosis, a distinct form of regulated cell death, characterized by iron-dependent lipid peroxidation, differs from autophagy, apoptosis, and necrosis, and may hold promise as a novel cell death. Numerous studies have demonstrated the involvement of ferroptosis in various conventional signaling pathways and biological processes. Recent investigations have revealed the significant contribution of ferroptosis in the initiation, progression, and metastasis of diverse malignant tumors, including ovarian cancer. Moreover, ferroptosis exhibits a synergistic effect with chemotherapy, radiotherapy, and immunotherapy in restraining the proliferation of ovarian cancer cells. The aforementioned implies that ferroptosis holds considerable importance in the management of ovarian cancer and has the potential to serve as a novel therapeutic target. The present review provides a comprehensive overview of the salient features of ferroptosis, encompassing its underlying mechanisms and functional role in ovarian cancer, along with the associated signaling pathways and genes. Furthermore, the review highlights the prospective utility of ferroptosis in the treatment of ovarian cancer.
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Affiliation(s)
| | | | | | - Tianmin Xu
- The Second Hospital of Jilin University, Changchun, China
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Lian X, Tang X. Use of a ferroptosis-related gene signature to construct diagnostic and prognostic models for assessing immune infiltration in metabolic dysfunction-associated fatty liver disease. Front Cell Dev Biol 2023; 11:1199846. [PMID: 37928903 PMCID: PMC10622674 DOI: 10.3389/fcell.2023.1199846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/22/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction: Metabolic dysfunction-associated fatty liver disease (MAFLD), a serious health problem worldwide, can involve ferroptosis. This study aimed to comprehensively analyze the ferroptosis-related genes associated with MAFLD. Methods: Ferroptosis-related differentially expressed genes (FRDEGs) were identified in patients with MAFLD and healthy individuals. Gene ontology functional enrichment analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and gene set enrichment analysis (GSEA) were used to analyze the relevant action pathways of the FRDEGs. The Encyclopedia of RNA Interactomes, CHIPBase, and comparative toxicogenomics databases were used to build mRNA-miRNA, mRNA-transcription factor (TF), and mRNA-drug interaction networks, respectively. A diagnostic model was constructed and bioinformatics analysis methods, such as least absolute shrinkage and selection operator regression analysis, Cox regression analysis, nomogram-based analysis, consensus clustering analysis, and single-sample GSEA, were used to systematically investigate the prognostic values and immunologic characteristics. Results: A total of 13 FRDEGs were obtained and eight were used to construct a diagnostic model and perform a prognostic analysis. Hub genes were also used to construct mRNA-miRNA and mRNA-TF interaction networks and potential drug or molecular compounds. Two MAFLD subtypes were identified: cluster2, which represents an "immunoactive" type, and cluster1, which represents an "immunosuppressive" type; a significant correlation was observed between the immune cell contents and the expression of three FRDEGs (NR4A1, FADS2, and SCD). Conclusion: A ferroptosis-related gene signature was constructed to diagnose MAFLD-associated steatohepatitis, predict the prognosis of MAFLD patients, and analyze the immunologic characteristics of MAFLD. Our findings may provide insights into developing innovative MAFLD treatment techniques.
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Affiliation(s)
- Xin Lian
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Xulei Tang
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
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Liu XW, Xu HW, Yi YY, Zhang SB, Wang SJ. Role of ferroptosis and immune infiltration in intervertebral disc degeneration: novel insights from bioinformatics analyses. Front Cell Dev Biol 2023; 11:1170758. [PMID: 37736497 PMCID: PMC10509768 DOI: 10.3389/fcell.2023.1170758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
Background: Intervertebral disc degeneration (IVDD), which contributes to stenosis of the spinal segment, commonly causes lower back pain. The process of IVDD degradation entails gradual structural adjustments accompanied by extreme transformations in metabolic homeostasis. However, the molecular and cellular mechanisms associated with IVDD are poorly understood. Methods: The RNA-sequencing datasets GSE34095 and GSE56081 were obtained from the Gene Expression Omnibus (GEO) database. Ferroptosis-related differentially expressed genes (DEGs) were identified from these gene sets. The protein-protein interaction (PPI) network was established and visualized using the STRING database and Cytoscape software, and the key functional modules of ferroptosis-related genes were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DEGs. Weighted gene co-expression network analysis (WGCNA), immune infiltration analysis in the GEO database, and other GSE series were used as validation datasets. The xCELL algorithm was performed to investigate the immune cell infiltration differences between the degenerated IVDD and control groups. Results: The major genes involved in nucleus pulposus tissue immune infiltration and ferroptosis-related genes were mined by bioinformatics analysis. A total of 3,056 DEGs were obtained between the IVDD tissue and control groups. The DEGs were enriched in the cell cycle; apoptosis; necroptosis; and the PI3K-Akt, Hippo, and HIF-1 signaling pathways. PCR and Western blot techniques were utilized to confirm the differential ferroptosis-related genes. The results indicated that the protein expression levels of NCOA4 and PCBP1 were elevated, while the protein expression level of GPX4 was reduced in NPCs following IL-1β treatment. Our study has found that severe disc tissue degeneration leads to a noteworthy increase in the expression of CD8A in naive T cells, CCR7 in memory CD4+ cells, GZMB in natural killer (NK) cells, and CD163 and CD45 in macrophages. Conclusion: Our data demonstrate that ferroptosis occurs in IVDD, suggesting that ferroptosis may also increase IVDD improvement by triggering immune infiltration. This work was conducted to further understand IVDD pathogenesis and identify new treatment strategies.
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Affiliation(s)
- Xiao-Wei Liu
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hao-Wei Xu
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yu-Yang Yi
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shu-Bao Zhang
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shan-Jin Wang
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Orthopedic, East Hospital, Ji’an Hospital, Jinggangshan University School of Medicine, Jiangxi, China
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Guo B, Li M, Wu P, Chen Y. Identification of ferroptosis-related genes as potential diagnostic biomarkers for diabetic nephropathy based on bioinformatics. Front Mol Biosci 2023; 10:1183530. [PMID: 37593129 PMCID: PMC10428009 DOI: 10.3389/fmolb.2023.1183530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
Objective: This study investigated to probe ferroptosis-related diagnostic biomarkers and underlying molecular mechanisms in Diabetic nephropathy (DN). Methods: GSE30122 and GSE1009 from GEO database were used as training and verification sets, respectively, to screen differentially expressed ferroptosis-related genes (FRGs). These genes were further analyzed using GO, KEGG, and GSEA methods, and screened with PPI, LASSO, and SVM-RFE to identify ferroptosis-related diagnostic biomarkers for DN. A diagnostic model was established using the Glm function and verified with ROC curve. The relationship between these biomarkers and immune cell was analyzed, and qRT-PCR and Western blot were used to detect the expression of these biomarkers in kidney tissues and identify the effect of TP53 on DN development. Results: Fifty one differentially expressed FRGs were enriched in bioprocesses such as p53 signaling pathway, oxidative stress and chemical stress response, and mTOR signaling pathway. TP53, RB1, NF2, RRM2, PRDX1, and CDC25A were identified as ferroptosis-related diagnostic biomarkers for DN. TP53 showed the most differential expression. ROC analysis showed that AUC values of TP53, RB1, NF2, RRM2, PRDX1, and CDC25A were 0.751, 0.705, 0.725, 0.882, 0.691, and 0.675, respectively. The AUC value of DN diagnosis model was 0.939 in training set and 1.000 in verification set. qRT-PCR results confirmed significant differences in these six biomarkers between DN and normal kidney tissue (p < 0.05), and correlation analysis showed that five biomarkers were significantly correlated with infiltrating immune cells (p < 0.05). Furthermore, western blots showed that TP53 promotes apoptosis through PI3K-AKT signaling in DN. Conclusion: TP53, RB1, NF2, RRM2, PRDX1, and CDC25A have potential as diagnostic biomarkers for DN. The diagnostic model containing the above six biomarkers performs well in the diagnosis of DN. Five of the six biomarkers are strongly associated with several infiltrating immune cells. TP53 may play an essential role in the development of DN.
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Affiliation(s)
- Binbin Guo
- International Special Medical Department, Shengli Oilfield Central Hospital, Dongying, Shandong, China
| | - Minhui Li
- Department of Pediatrics Internal Medicine, Dongying Municipal Children’s Hospital, Dongying, Shandong, China
| | - Peipei Wu
- International Special Medical Department, Shengli Oilfield Central Hospital, Dongying, Shandong, China
| | - Yan Chen
- International Special Medical Department, Shengli Oilfield Central Hospital, Dongying, Shandong, China
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Chen Y, Liu A, Liu H, Cai G, Lu N, Chen J. Identification and validation of the diagnostic signature associated with immune microenvironment of acute kidney injury based on ferroptosis-related genes through integrated bioinformatics analysis and machine learning. Front Cell Dev Biol 2023; 11:1210714. [PMID: 37576602 PMCID: PMC10413118 DOI: 10.3389/fcell.2023.1210714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
Background: Acute kidney injury (AKI) is a common and severe disease, which poses a global health burden with high morbidity and mortality. In recent years, ferroptosis has been recognized as being deeply related to Acute kidney injury. Our aim is to develop a diagnostic signature for Acute kidney injury based on ferroptosis-related genes (FRGs) through integrated bioinformatics analysis and machine learning. Methods: Our previously uploaded mouse Acute kidney injury dataset GSE192883 and another dataset, GSE153625, were downloaded to identify commonly expressed differentially expressed genes (coDEGs) through bioinformatic analysis. The FRGs were then overlapped with the coDEGs to identify differentially expressed FRGs (deFRGs). Immune cell infiltration was used to investigate immune cell dysregulation in Acute kidney injury. Functional enrichment analysis and protein-protein interaction network analysis were applied to identify candidate hub genes for Acute kidney injury. Then, receiver operator characteristic curve analysis and machine learning analysis (Lasso) were used to screen for diagnostic markers in two human datasets. Finally, these potential biomarkers were validated by quantitative real-time PCR in an Acute kidney injury model and across multiple datasets. Results: A total of 885 coDEGs and 33 deFRGs were commonly identified as differentially expressed in both GSE192883 and GSE153625 datasets. In cluster 1 of the coDEGs PPI network, we found a group of 20 genes clustered together with deFRGs, resulting in a total of 48 upregulated hub genes being identified. After ROC analysis, we discovered that 25 hub genes had an area under the curve (AUC) greater than 0.7; Lcn2, Plin2, and Atf3 all had AUCs over than this threshold in both human datasets GSE217427 and GSE139061. Through Lasso analysis, four hub genes (Lcn2, Atf3, Pir, and Mcm3) were screened for building a nomogram and evaluating diagnostic value. Finally, the expression of these four genes was validated in Acute kidney injury datasets and laboratory investigations, revealing that they may serve as ideal ferroptosis markers for Acute kidney injury. Conclusion: Four hub genes (Lcn2, Atf3, Pir, and Mcm3) were identified. After verification, the signature's versatility was confirmed and a nomogram model based on these four genes effectively distinguished Acute kidney injury samples. Our findings provide critical insight into the progression of Acute kidney injury and can guide individualized diagnosis and treatment.
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Affiliation(s)
- Yalei Chen
- Department of Critical Care Medicine, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Anqi Liu
- Department of Critical Care Medicine, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Hunan Liu
- Department of Critical Care Medicine, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Guangyan Cai
- State Key Laboratory of Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Department of Nephrology, First Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Kidney Diseases, Nephrology Institute of the Chinese People’s Liberation Army, Beijing, China
| | - Nianfang Lu
- Department of Critical Care Medicine, Capital Medical University Electric Power Teaching Hospital/State Grid Beijing Electric Power Hospital, Beijing, China
| | - Jianwen Chen
- State Key Laboratory of Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Department of Nephrology, First Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Kidney Diseases, Nephrology Institute of the Chinese People’s Liberation Army, Beijing, China
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Cheng Z, Chen Y, Huang H. Identification and Validation of a Novel Prognostic Signature Based on Ferroptosis-Related Genes in Ovarian Cancer. Vaccines (Basel) 2023; 11:vaccines11020205. [PMID: 36851083 PMCID: PMC9962729 DOI: 10.3390/vaccines11020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Ovarian cancer is the most lethal gynecological tumor, with a poor prognosis due to the lack of early symptoms, resistance to chemotherapy, and recurrence. Ferroptosis belongs to the regulated cell death family, and is characterized by iron-dependent processes. Here, comprehensive bioinformatics analysis was applied to explore a valuable prognostic model based on ferroptosis-related genes, which was further validated in clinical OC samples. METHODS mRNA data of normal and ovarian tumor samples were obtained separately from the GTEx and TCGA databases. The least absolute shrinkage and selection operator (LASSO) cox regression was applied to construct the prognostic model based on ferroptosis-associated genes. Expression of ALOX12 in OC cell lines, as well as cell functions, including proliferation and migration, were examined. Finally, the prognostic efficiency of the model was assessed in the clinical tissues of OC patients. RESULTS A gene signature consisting of ALOX12, RB1, DNAJB6, STEAP3, and SELENOS was constructed. The signature divided TCGA, ICGC, and GEO cohorts into high-risk and low-risk groups separately. Receiver operating characteristic (ROC) curves and independent prognostic factor analysis were carried out, and the prognostic efficacy was validated. The expression levels of ALOX12 in cell lines were examined. Inhibition of ALOX12 attenuated cell proliferation and migration in HEY cells. Moreover, the prognostic value of ALOX12 expression was examined in clinical samples of OC patients. CONCLUSION This work constructed a novel ferroptosis-associated gene model. Furthermore, the clinical predictive role of ALOX12 was identified in OC patients, suggesting that ALOX12 might act as a potential prognostic tool and therapeutic target for OC patients.
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Affiliation(s)
- Zhe Cheng
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Huichao Huang
- Department of Infectious Disease, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence:
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Zhao M, Zhang Y, Zhao H. Identification of ferroptosis-related genes and predicted overall survival in patients with burns. Front Surg 2023; 9:1060036. [PMID: 36700031 PMCID: PMC9869674 DOI: 10.3389/fsurg.2022.1060036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/29/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction Burns are a common trauma associated with considerable mortality and morbidity. Although a lot is known regarding burns' pathogenesis, the involvement of ferroptosis is uncertain. Here, we aimed to explore vital ferroptosis-related genes and molecules in burns, through bioinformatics analysis, to uncover new effective therapeutic targets. Methods The FerrDb database was used to acquire ferroptosis-related genes and GSE19743 was downloaded from Gene Expression Omnibus (GEO), a dataset with analysis of control and burned individuals. Hub genes were selected with Cytoscape software, and Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Cox proportional hazard function and Kaplan-Meier survival analyses were implemented to screen prognosis-related genes. Additionally, the miRWalk database was used to acquire the miRNAs relevant to our hub genes function and analyzed for enrichment. Result We identified 64 differentially expressed genes and through the intersection with ferroptosis-related genes, 10 were selected as hub genes. GO analysis revealed that the hub genes' most enriched activities were response to oxidative stress, pyridine-containing compound metabolic processes, and reactive oxygen species metabolic processes. KEGG pathways' analysis showed that these overlapped genes were enriched in several pathways, namely, in VEGF signaling. Furthermore, the molecular miRNA functions significantly enriched were signal transduction and cell communication, namely, the biological pathways of the glypican pathway and the ErbB receptor signaling network. SLC40A1 and GPT2 genes were found to be associated with overall survival, suggesting an important role in burn prognosis. Discussion This study may improve our understanding of the underlying burn mechanisms and provide a new direction for the prevention of poor outcomes, advances in burns treatment, and drug development.
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Affiliation(s)
- Mingjian Zhao
- Graduate School, Dalian Medical University, Dalian, China
| | - Yetong Zhang
- Graduate School, Dalian Medical University, Dalian, China
| | - Hongliang Zhao
- Department of Burns and Plastic Surgery, Miyun Hospital, Capital Medical University, Beijing, China,Correspondence: Hongliang Zhao
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Li J, Wu F, Xiao X, Su L, Guo X, Yao J, Zhu H. A novel ferroptosis-related gene signature to predict overall survival in patients with osteosarcoma. Am J Transl Res 2022; 14:6082-6094. [PMID: 36247280 PMCID: PMC9556449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVES Ferroptosis plays vital roles in the pathogenesis of various malignant tumors. However, knowledge on roles of ferroptosis in osteosarcoma remains scarce. In the present study, a comprehensive bioinformatics analysis was performed aiming to identify ferroptosis-related genes (FRGs), construct a FRGs-based model predicting overall survival (OS), and assess the impact of these FRGs on the migration and invasion of osteosarcoma cells. METHODS Initially, data regarding differentially expressed FRGs were obtained from the GSE160881 dataset. Prognostic significance and possible biological functions of these differentially expressed FRGs were comprehensively and systematically explored adopting a series of bioinformatics methods. The impact of cystathionine β-synthase (CBS) on migration and invasion of osteosarcoma cells were assessed using transwell assays. RESULTS A total of 50 FRGs were differentially expressed. Four FRGs including G6PD, VEGFA, CBS, and HMOX1 were used to construct a model predicting OS in osteosarcoma patients. In the training cohort, patients with high risk had significantly poorer OS than those with low risk, which was also demonstrated in validation cohorts (GSE16091 and GSE39058). Furthermore, we established a clinically useful nomogram predicting OS using the four FRGs mentioned above. Risk scores were significantly associated with the proportion of tumor-infiltrating immune cells. Additionally, we used the Cytoscape software to identify hub FRGs, and found that TP53, HMOX1, SLC7A11, HRAS, VEGFA, and TXNRD1 were hub FRGs. By performing in vitro cell culture experiments, we demonstrated that invasion and migration capability of Saos2 and HOS cells were significantly weakened after CBS knock down. CONCLUSIONS In conclusion, gene signatures based on four FRGs were reliable in predicting OS in patients with osteosarcoma. Findings from this study will enable a better understanding of the prognostic significance of FRGs and tumor immunity in osteosarcoma.
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Affiliation(s)
- Junqing Li
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital)Zhengzhou 450016, China
| | - Feiran Wu
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital)Zhengzhou 450016, China
| | - Xing Xiao
- Scientific Research Center, Seventh Affiliated Hospital, Sun Yat-sen UniversityShenzhen 518000, China
| | - Li Su
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital)Zhengzhou 450016, China
| | - Xinjun Guo
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital)Zhengzhou 450016, China
| | - Jie Yao
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital)Zhengzhou 450016, China
| | - Huimin Zhu
- Minimally Invasive Spinal Surgery Center, Luoyang Orthopedic-Traumatological Hospital of Henan Province (Henan Provincial Orthopedic Hospital)Zhengzhou 450016, China
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Yin J, Fu J, Zhao Y, Xu J, Chen C, Zheng L, Wang B. Comprehensive Analysis of the Significance of Ferroptosis-Related Genes in the Prognosis and Immunotherapy of Oral Squamous Cell Carcinoma. Bioinform Biol Insights 2022; 16:11779322221115548. [PMID: 35966810 PMCID: PMC9373167 DOI: 10.1177/11779322221115548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/26/2022] [Indexed: 12/09/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a life-threatening disease, associated
with poor prognosis and the absence of specific biomarkers. Studies have shown
that the ferroptosis-related genes (FRGs) can be used as tumor prognostic
markers. However, FRGs’ prognostic value in OSCC needs further exploration. In
our study, gene expression profile and clinical data of OSCC patients were
collected from a public domain. We performed univariate and multivariate Cox
regression analyses to construct a multigene signature. The Kaplan-Meier and
receiver operating characteristic (ROC) methods were used to test the
effectiveness of the signature, followed by the expression analysis of human
leukocyte antigen (HLA) and immune checkpoints. The Cox regression analysis
identified 4 hubs from 103 FRGs expressed in OSCC that were associated with
overall survival (OS). A risk model based on the 4 FRGs was established to
classify patients into high-risk and low-risk groups. Compared with the low-risk
group, the survival time of the high-risk group was significantly reduced.
According to the multivariate Cox regression analysis, the risk score acted as
an independent predictor for OS. The accuracy of the 4 FRGs risk predictive
model was confirmed by ROC curve analysis. Moreover, the low-risk group had the
characteristics of higher expression of HLA and immune checkpoints, a lower
tumor purity, and a higher immune infiltration, indicating a more sensitive
response to immunotherapy. The novel FRGs-OSCC risk score system can be used to
predict the prognosis of OSCC patients and their response to immunotherapy.
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Affiliation(s)
- Junhao Yin
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.,National Center for Stomatology, Shanghai, China.,National Clinical Research Center for Oral Disease, Shanghai, China.,Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiayao Fu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.,National Center for Stomatology, Shanghai, China.,National Clinical Research Center for Oral Disease, Shanghai, China.,Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yijie Zhao
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Jiabao Xu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.,National Center for Stomatology, Shanghai, China.,National Clinical Research Center for Oral Disease, Shanghai, China.,Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Changyu Chen
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.,National Center for Stomatology, Shanghai, China.,National Clinical Research Center for Oral Disease, Shanghai, China.,Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Lingyan Zheng
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.,National Center for Stomatology, Shanghai, China.,National Clinical Research Center for Oral Disease, Shanghai, China.,Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Baoli Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.,National Center for Stomatology, Shanghai, China.,National Clinical Research Center for Oral Disease, Shanghai, China.,Shanghai Key Laboratory of Stomatology, Shanghai, China
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14
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Miao TW, Yang DQ, Chen FY, Zhu Q, Chen X. A Ferroptosis-Related Gene Signature for Overall Survival Prediction and Immune Infiltration in Lung Squamous Cell Carcinoma. Biosci Rep 2022:BSR20212835. [PMID: 35866375 DOI: 10.1042/BSR20212835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 02/05/2023] Open
Abstract
Background: Ferroptosis is associated with cancer initiation and progression. However, the molecular mechanism and prognostic value of ferroptosis-related genes in lung squamous cell carcinoma (LUSC) are poorly understood. Methods: The mRNA expression profiles, methylation data, and clinical information of patients with LUSC were downloaded from TCGA and GEO database. Ferroptosis-related differentially expressed genes (DEGs) were identified between cancerous and non-cancerous tissues, and their prognostic value was systemically investigated by bioinformatic analyses. Results: A ferroptosis-related gene signature (ALOX5, TFRC, PHKG2, FADS2, NOX1) was constructed using multivariate Cox regression analysis and represented as a risk score. Overall survival (OS) probability was significantly lower in the high-risk group than in the low-risk group (P<0.001), and receiver operating characteristic curve showed a good predictive capacity (AUC = 0.739). The risk score was an independent prognostic factor for LUSC. A nomogram was constructed to predict the OS probabilities at 1, 3, and 5 years. High-risk score was associated with increased immune infiltration, lower methylation levels, higher immune checkpoint genes expression levels, and better chemotherapy response. Cell adhesion molecules, focal adhesion, and extracellular matrix receptor interaction were the main pathways in the high-risk group. The signature was validated using the TCGA test cohort, entire TCGA cohort, GSE30219, GSE157010, GSE73403, and GSE4573 datasets. The gene disorders in patients with LUSC were validated using real-time PCR and single-cell RNA sequencing analysis. Conclusions: A ferroptosis-related gene signature was constructed to predict OS probability in LUSC. This could facilitate novel therapeutic methods and guide individualized therapy.
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Sun L, Li B, Wang B, Li J, Li J. Construction of a Risk Model to Predict the Prognosis and Immunotherapy of Low-Grade Glioma Ground on 7 Ferroptosis-Related Genes. Int J Gen Med 2022; 15:4697-4716. [PMID: 35548585 PMCID: PMC9085428 DOI: 10.2147/ijgm.s352773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/16/2022] [Indexed: 12/27/2022] Open
Abstract
Purpose Ferroptosis is closely associated with tumors. The purpose of this study was to investigate the correlation between ferroptosis and prognosis of low grade glioma (LGG) via construction and verification of a risk model. Patients and Methods The data of LGG were downloaded from public databases. Through LASSO analysis of characteristic genes, a gene signature was constructed. Patients into were divided two groups based on risk score. Subsequently, survival, clinical phenotype, functional enrichment, immune cell infiltration and somatic mutation analysis were performed. In addition, whether ferroptosis-related genes (FRGs) signature can predict the patient's response to anti-PD-1/PD-L1 immunotherapy was also investigated. Results FRGs signature had strong prognostic assessment ability, and high risk score was associated with poor overall survival (OS) of LGG. The high risk score group had higher degree of immune cell infiltration, stronger stromal activity, higher immune score, and high expression of immune checkpoint. In low risk score group anti-PD-1/PD-L1 immunotherapy has significant therapeutic advantages and clinical response. Genes and frequency of somatic mutations and clinical phenotypes in the high and low risk score groups were significantly different. Conclusion A prognostic model based on 7 FRGs can be used to predict the prognosis and immunotherapeutic response of LGG.
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Affiliation(s)
- Liwei Sun
- Department of Intervention, Tianjin Huanhu Hospital, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Disease, Tianjin Neurosurgical Institute, Tianjin, People’s Republic of China
| | - Bing Li
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin, People’s Republic of China
| | - Bin Wang
- Department of Intervention, Tianjin Huanhu Hospital, Tianjin, People’s Republic of China
| | - Jinduo Li
- Department of Intervention, Tianjin Huanhu Hospital, Tianjin, People’s Republic of China
| | - Jing Li
- Department of Intervention, Tianjin Huanhu Hospital, Tianjin, People’s Republic of China
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Wang H, Cheng Q, Chang K, Bao L, Yi X. Integrated Analysis of Ferroptosis-Related Biomarker Signatures to Improve the Diagnosis and Prognosis Prediction of Ovarian Cancer. Front Cell Dev Biol 2022; 9:807862. [PMID: 35071242 PMCID: PMC8766510 DOI: 10.3389/fcell.2021.807862] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
Ovarian cancer remains the most lethal gynecological malignancy. Ferroptosis, a specialized form of iron-dependent, nonapoptotic cell death, plays a crucial role in various cancers. However, the contribution of ferroptosis to ovarian cancer is poorly understood. Here, we characterized the diagnostic, prognostic, and therapeutic value of ferroptosis-related genes in ovarian cancer by analyzing transcriptomic data from The Cancer Genome Atlas and Gene Expression Omnibus databases. A reliable 10-gene ferroptosis signature (HIC1, ACSF2, MUC1, etc.) for the diagnosis of ovarian cancer was identified. Notably, we constructed and validated a novel prognostic signature including three FRGs: HIC1, LPCAT3, and DUOX1. We also further developed a risk score model based on these three genes which divided ovarian cancer patients into two risk groups. Functional analysis revealed that immune response and immune-related pathways were enriched in the high-risk group. Meanwhile, the tumor microenvironment was distinct between the two groups, with more M2 Macrophage infiltration and higher expression of key immune checkpoint molecules in the high-risk group than in the other group. Low-risk patients exhibited more favorable immunotherapy and chemotherapy responses. We conclude that crosstalk between ferroptosis and immunity may contribute to the worse prognosis of patients in the high-risk group. In particular, HIC1 showed both diagnostic and prognostic value in ovarian cancer. In vitro experiments demonstrated that inhibition of HIC1 improved drug sensitivity of chemotherapy and immunotherapy agents by inducing ferroptosis. Our findings provide new insights into the potential role of FRGs in the early detection, prognostic prediction, and individualized treatment decision-making for ovarian cancer patients.
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Affiliation(s)
- Huan Wang
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Department of Gynecology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Qi Cheng
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Kaikai Chang
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Lingjie Bao
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Xiaofang Yi
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
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Ren X, Du H, Cheng W, Wang Y, Xu Y, Yan S, Gao Y. Construction of a ferroptosis-related eight gene signature for predicting the prognosis and immune infiltration of thyroid cancer. Front Endocrinol (Lausanne) 2022; 13:997873. [PMID: 36407322 PMCID: PMC9672669 DOI: 10.3389/fendo.2022.997873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Thyroid cancer is the most common malignant tumor of the endocrine system. Most patients with thyroid cancer have a good prognosis, although a small proportion experience recurrence and metastasis and have a poor prognosis. Ferroptosis is a novel form of regulated cell death (RCD); previous studies have confirmed that ferroptosis was associated with thyroid cancer. The purpose of this study was to investigate the key ferroptosis-related genes in thyroid cancer and their relationship with prognosis and immune cell infiltration. METHODS In this study, 497 thyroid cancer RNA expression datasets were downloaded from the cancer genome atlas (TCGA) cohort and a prognostic risk model for eight ferroptosis-related genes (FRGs) was constructed by Lasso-Cox regression. The prognostic value of the risk model and the correlation of prognostic features with immune scores and tumor immune cell infiltration were systematically analyzed. RESULTS The prognostic risk model for eight FRGs (DPP4, TYRO3, TIMP1, CDKN2A, SNCA, NR4A1, IL-6 and FABP4) were constructed and validated in training and testing cohorts. Kaplan-Meier curve and receiver operating characteristic (ROC) curve analysis confirmed that that the ferroptosis-related eight gene signature had good predictive value for the prognosis of thyroid cancer (THCA) patients. Multivariate regression analysis further showed that the risk score of the prognostic model could be used as an independent prognostic factor for THCA patients. Functional enrichment analysis showed that DEGs in high risk and low risk groups were involved in immune-related biological processes and that there were significant differences in immune cell infiltration between the two risk groups. CONCLUSION We identified eight key genes related to ferroptosis in THCA patients. Further studies are now needed to investigate the mechanisms involved; these genes may represent clinical diagnostic and prognostic biomarkers.
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Affiliation(s)
- Xiaoying Ren
- Department of Endocrinology and Metabolism, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huijun Du
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Weilun Cheng
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yujing Wang
- Department of Endocrinology and Metabolism, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuanxin Xu
- Department of Endocrinology and Metabolism, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuang Yan
- Department of Endocrinology and Metabolism, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Shuang Yan, ; Yunan Gao,
| | - Yunan Gao
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Shuang Yan, ; Yunan Gao,
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Li C, Wang X, Qin R, Zhong Z, Sun C. Identification of a Ferroptosis Gene Set That Mediates the Prognosis of Squamous Cell Carcinoma of the Head and Neck. Front Genet 2021; 12:698040. [PMID: 34539737 PMCID: PMC8446460 DOI: 10.3389/fgene.2021.698040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/18/2021] [Indexed: 01/23/2023] Open
Abstract
Squamous cell carcinoma of the head and neck (HNSCC) is one of the six most common malignancies. HNSCC has both a high incidence and poor prognosis, and its prognostic factors remain unclear. Ferroptosis is a newly discovered form of programmed cell death that is iron-dependent. Increasing evidence indicates that targeting ferroptosis may present a new form of anti-tumor treatment. However, the prognostic value of ferroptosis-related genes (FRGs) in HNSCC is unclear. This study was designed to identify molecular markers associated with ferroptosis that influence prognosis in patients with HNSCC. We used HNSCC tumor and normal data from The Cancer Genome Atlas (TCGA) to identify prognosis-related FRGs. An FRG-based prognostic risk score was constructed, and its prognostic value for patients with HNSCC was evaluated using receiver operating characteristic curve (ROC) and nomogram analyses. The model was validated using the Gene Expression Omnibus (GEO) database. Univariate Cox regression analysis in patients with HNSCC revealed 11 FRGs that were significantly associated with overall survival (OS). We constructed a ferroptosis risk score model based on five genes and divided the patients into different risk groups based on its median value. Kaplan-Meier curve analysis showed that patients with a higher ferroptosis risk score had shorter OS (TCGA training set: P < 0.001, TCGA validation set: P < 0.05,GEO validation set: P < 0.001), and Gene Expression Profiling Interactive Analysis (GEPIA) further verified the relationships between these five genes and prognosis in patients with HNSCC. Multivariate Cox regression analysis showed that the risk score remained an independent predictor of OS after the exclusion of clinical confounders (HR > 1, P < 0.01). Significant differences in gene function enrichment analysis and immune cell infiltration status were identified between the two groups. The prognostic model can be used to predict the prognosis of patients with HNSCC. Moreover, the five FRGs may affect ferroptosis in HNSCC and thereby represent potential treatment targets. These results provide new directions for HNSCC treatment.
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Affiliation(s)
- Chunyan Li
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, China
| | - Xuemin Wang
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, China
| | - Rujia Qin
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, China
| | - Zhaoming Zhong
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, China.,Department of Medical Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chuanzheng Sun
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, China
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Zhu J, Kong W, Xie Z. Expression and Prognostic Characteristics of Ferroptosis-Related Genes in Colon Cancer. Int J Mol Sci 2021; 22:ijms22115652. [PMID: 34073365 PMCID: PMC8199073 DOI: 10.3390/ijms22115652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
Ferroptosis is a new type of programmed cell death, which occurs with iron dependence. Previous studies have showed that ferroptosis plays an important regulatory role in the occurrence and development of tumors. Colon cancer is one of the major morbidities and causes of mortality in the world. This study used RNA-seq and colon cancer clinical data to explore the relationship between ferroptosis-related genes and colon cancer. Based on the fifteen prognostic ferroptosis-related genes, two molecular subgroups of colon cancer were identified. Surprisingly, we also found cluster2 was characterized by lower mutation burden and expression of checkpoint genes, better survival, and higher expression of NOX1. Moreover, cluster2 has fewer BRAF mutations. We also found the expression of NOX1 is related to the status of BRAF. Finally, using 15 ferroptosis-related genes from The Cancer Genome Atlas cohort, we constructed a prognosis model, and this model may be used to predict the prognosis of patients in clinics.
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Affiliation(s)
- Jie Zhu
- Department of Pharmacology and International Cancer Institute, School of Basic Medical Sciences, Peking University, Beijing 100191, China;
| | - Weikaixin Kong
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing 100191, China;
| | - Zhengwei Xie
- Department of Pharmacology and International Cancer Institute, School of Basic Medical Sciences, Peking University, Beijing 100191, China;
- Correspondence:
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Zhu G, Huang H, Xu S, Shi R, Gao Z, Lei X, Zhu S, Zhou N, Zu L, Mello RAD, Chen J, Xu S. Prognostic value of ferroptosis-related genes in patients with lung adenocarcinoma. Thorac Cancer 2021; 12:1890-1899. [PMID: 33979897 PMCID: PMC8201541 DOI: 10.1111/1759-7714.13998] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/19/2022] Open
Abstract
Background The prevalence of lung adenocarcinomas (LUADs) has dramatically increased in recent decades. Ferroptosis is a process of iron‐dependent regulatory cell death. It is still unclear whether the expression of ferroptosis‐related genes (FRGs) is involved in the pathogenesis and survival of patients with LUAD. Methods We retrieved LUAD data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and used LASSO Cox regression analysis to select the gene signature suitable for modeling. The risk score was calculated according to the model, and the patients were divided into high‐ and low‐risk groups according to the median risk score. Functional enrichment analysis was carried out by this group, and a model for predicting clinical prognosis was established by combining this group with clinical factors. Results Gene set enrichment analysis (GSEA) and single‐sample gene set enrichment analysis (ssGSEA) analysis showed that there were several immune‐related pathways and immune infiltration differences between high‐ and low‐risk groups. A prognostic model integrating 10 ferroptosis‐related genes (FR‐DEGs), and clinical factors were constructed and validated in an external cohort. Conclusions The FR‐DEGs signature was related to immune infiltration, and a model based on FR‐DEGs and clinical factors was established to predict the prognosis of patients with LUAD.
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Affiliation(s)
- Guangsheng Zhu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Hua Huang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Songlin Xu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Ruifeng Shi
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | | | - Xi Lei
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Shuai Zhu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Ning Zhou
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Lingling Zu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Ramon A De Mello
- Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Jun Chen
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Song Xu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
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