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Schäffer DE, Li W, Elbasir A, Altieri DC, Long Q, Auslander N. Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes. ISME COMMUNICATIONS 2023; 3:128. [PMID: 38049632 PMCID: PMC10696091 DOI: 10.1038/s43705-023-00338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023]
Abstract
Local microbiome shifts are implicated in the development and progression of gastrointestinal cancers, and in particular, esophageal carcinoma (ESCA), which is among the most aggressive malignancies. Short-read RNA sequencing (RNAseq) is currently the leading technology to study gene expression changes in cancer. However, using RNAseq to study microbial gene expression is challenging. Here, we establish a new tool to efficiently detect viral and bacterial expression in human tissues through RNAseq. This approach employs a neural network to predict reads of likely microbial origin, which are targeted for assembly into longer contigs, improving identification of microbial species and genes. This approach is applied to perform a systematic comparison of bacterial expression in ESCA and healthy esophagi. We uncover bacterial genera that are over or underabundant in ESCA vs healthy esophagi both before and after correction for possible covariates, including patient metadata. However, we find that bacterial taxonomies are not significantly associated with clinical outcomes. Strikingly, in contrast, dozens of microbial proteins were significantly associated with poor patient outcomes and in particular, proteins that perform mitochondrial functions and iron-sulfur coordination. We further demonstrate associations between these microbial proteins and dysregulated host pathways in ESCA patients. Overall, these results suggest possible influences of bacteria on the development of ESCA and uncover new prognostic biomarkers based on microbial genes. In addition, this study provides a framework for the analysis of other human malignancies whose development may be driven by pathogens.
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Affiliation(s)
- Daniel E Schäffer
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- The Wistar Institute, Philadelphia, PA, 19104, USA
- Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wenrui Li
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Qi Long
- University of Pennsylvania, Philadelphia, PA, USA
| | - Noam Auslander
- The Wistar Institute, Philadelphia, PA, 19104, USA.
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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2
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Ge Z, Song D. A five ferroptosis-related genes risk score for prognostic prediction of osteosarcoma. Medicine (Baltimore) 2022; 101:e32083. [PMID: 36550843 PMCID: PMC9771194 DOI: 10.1097/md.0000000000032083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Osteosarcoma (OS) is the most common bone cancer in adolescents, and has a high propensity to metastasize. Ferroptosis is a unique modality of cell death, driving the metastasis of cancer cells. Identifying ferroptosis-related genes (FRGs) as prognostic factors will be critical to predict the outcomes of OS. This study aimed to explore the prognostic value of FRGs in OS and build a prognostic model to indirectly improve OS patients' outcomes. METHODS OS data were downloaded from the TARGET database and 2 Gene Expression Omnibus datasets. Univariate Cox regression was conducted to assess FRGs. A risk score model basing on 5 FRGs was constructed via LASSO-Cox regression. Multivariate Cox regression analysis was used to determine the independent prognostic factors. The Nomogram model was built using independent prognostic factors. The relationship between the risk score and the immune cell infiltration was estimated by CIBERSORT, and the correlation between the risk score and immune checkpoints was also analyzed. RESULTS Based on the prognosis-related FRGs, we built a regression model: Risk score = (-0.01382853 × ACSL4) - (0.05371778 × HMOX1) - (0.02434655 × GPX4) - (0.16432810 × PRNP) - (0.15567120 × ATG7). OS patients with high risk score tended to suffer from poor prognosis, validated in 2 Gene Expression Omnibus datasets. The Nomogram model showed the combination of the risk score and the tumour-node-metastasis stage improved predictive effectiveness. The risk score was also related to immune cell infiltration and immune checkpoint expression. CONCLUSION The risk score model based on 5 FRGs was a reliable prognostic predictive indicator for OS patients.
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Affiliation(s)
- Zhanyong Ge
- Department of Orthopaedic, Tianjin Jinnan Hospital, Tianjin, P.R. China
| | - Delei Song
- Department of West Hospital Orthopaedic Trauma, ZiBo Central Hospital, Zibo, P.R. China
- * Correspondence: Delei Song, Department of West Hospital Orthopaedic Trauma, ZiBo Central Hospital, No. 54 Gongqingtuan West Road, Zhangdian District, Zibo, Shandong 255020, P.R. China (e-mail: )
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3
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Pan S, Meng H, Fan T, Hao B, Song C, Li D, Li N, Geng Q. Comprehensive Analysis of Programmed Cell Death Signature in the Prognosis, Tumor Microenvironment and Drug Sensitivity in Lung Adenocarcinoma. Front Genet 2022; 13:900159. [PMID: 35664309 PMCID: PMC9157820 DOI: 10.3389/fgene.2022.900159] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/26/2022] [Indexed: 12/14/2022] Open
Abstract
Programmed cell death (PCD) is a process that regulates the homeostasis of cells in the body, and it plays an important role in tumor immunity. However, the expression profile and clinical characteristics of PCD-related genes remain unclear. In this study, we comprehensively analysed the PCD genes with the tumor microenvironment (TME), drug sensitivity, immunothearapy response, and evaluated their prognostic value through systematic bioinformatics methods.We identified 125 PCD-related regulatory factors, which were expressed differently in lung adenocarcinoma (LUAD) and normal lung tissues. 32 PCD related prognostic genes associated with LUAD were identified by univariate Cox analysis. 23 PCD-related gene signature was constructed, and all LUAD patients in the Cancer Genome Atlas (TCGA) dataset were stratified as low-risk or high-risk groups according to the risk score. This signature had a powerful prognostic value, which was validated in three independent data sets and clinical subtypes. Additionally, it has unique properties in TME. Further analysis showed that different risk groups have different immune cell infiltration, immune inflammation profile, immune pathways, and immune subtypes. In addition, the low-risk group had a better immunotherapy response with higher levels of multiple immune checkpoints and lower Tumor immune dysfunction and exclusion (TIDE) score, while the high-risk group was sensitive to multiple chemotherapeutic drugs because of its lower IC50. In short, this is the first model to predict the prognosis and immunological status of LUAD patients based on PCD-related genes. It may be used as a predictor of immunotherapy response to achieve customized treatment of LUAD.
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Affiliation(s)
- Shize Pan
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Heng Meng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tao Fan
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bo Hao
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Donghang Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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Song X, Wu L, Wang G, Liu B, Zhu W. Construction of a Novel Ferroptosis-Related Gene Signature for Predicting Survival of Patients With Lung Adenocarcinoma. Front Oncol 2022; 12:810526. [PMID: 35311093 PMCID: PMC8928751 DOI: 10.3389/fonc.2022.810526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most diagnosed subtype of lung cancer; ferroptosis is widely involved in the pathological cell death associated with various cancers, including lung cancer. However, the comprehensive relationship between ferroptosis and LUAD is little known in molecular levels until now. In the present study, 513 LUAD patients could be aggregated into three clusters by consensus clustering based on RNA sequencing data of 291 ferroptosis-related genes (FRGs) in The Cancer Genome Atlas (TCGA) database; cluster2 had significant survival advantage compared to the other two clusters. A novel prognostic model of 8 differential FRGs was constructed to effectively divide LUAD patients into high- or low-risk group according to the risk scores by the Cox and LASSO regression analyses. The overall survival of LUAD patients in the high-risk group was significantly worse in the TCGA and GEO cohorts. Moreover, patients with radiation therapy or high clinical stage had obviously higher risk scores. We validated the differential mRNA and protein expression of four FRGs in paired tumor and normal samples from our clinical cohort. Our study constructed a novel FRG signature to predict the prognosis of LUAD patients, which might provide a new prognostic tool and potential therapeutic targets for LUAD.
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Affiliation(s)
- Xiaojie Song
- Department of Respiratory Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Liqun Wu
- Department of Respiratory Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Guangqiang Wang
- Department of Respiratory Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Baoyi Liu
- Department of Respiratory Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Wenyong Zhu
- Department of Thoracic Surgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- *Correspondence: Wenyong Zhu,
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Yi L, Huang P, Gu Y, Wu G, Zou X, Guo L, Wen C, Zhu J, Zhao D. Clinical Significance and Immune Landscape of Recurrence-Associated Ferroptosis Signature in Early-Stage Lung Adenocarcinoma. Front Oncol 2022; 12:794293. [PMID: 35155238 PMCID: PMC8828635 DOI: 10.3389/fonc.2022.794293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/04/2022] [Indexed: 12/02/2022] Open
Abstract
Background The prevalence of patients newly diagnosed with early-stage lung adenocarcinoma (LUAD) is growing alongside significant advances in screening approaches. This study aimed to construct ferroptosis-related gene score (FRGscore) for predicting recurrence, explore immune-molecular characteristics, and determine the benefit of immunotherapy in distinct ferroptosis-based patterns and FRGscore-defined subgroups. Methods A total of 1,085 early-stage LUAD patients from four independent cohorts were included. Consensus clustering analysis was performed using 217 co-expressed FRGs to explore different ferroptosis-mediated patterns. An FRG scoring system was established to predict relapse, quantify ferroptosis-mediated patterns, and evaluate the response to immunotherapy in individual patients based on Lasso-penalized and stepwise Cox regression analyses. Immune landscape involving multiple parameters was further evaluated, stratified by cluster subtypes and FRGscore subgroups. Results Two ferroptosis-mediated patterns were identified and verified, which were characterized by significantly distinct prognosis and immune profiles. Analyses of immune characteristics showed that identified ferroptosis patterns were characterized as immune-inflamed phenotype and immune-exhausted phenotype. The FRG scoring model based on 11 FRG-derived signatures panel classified patients into the FRGscore-high and FRGscore-low subgroups. Significantly longer recurrence-free survival (RFS) and overall survival (OS) were observed in the FRGscore-low subgroup. FRGscore-low patients were characterized by higher tumor mutational burden (TMB), immunoscore, immunophenoscore, and PD-L1 expression level and were associated with lower Tumor Immune Dysfunction and Exclusion (TIDE) score, whereas the opposite was observed in FRGscore-high patients. Immune-active pathways were remarkably enriched in the FRGscore-low subgroup. This scoring model remained highly predictive of prognosis across different clinical, molecular, and immune subgroups. Further analysis indicated that FRGscore-low patients exhibited higher response to anti-PD-1/PD-L1 immunotherapy and better clinical benefits based on two independent immunotherapy cohorts. Conclusion The proposed FRGscore could highly distinguish the recurrence patterns and molecular and immune characteristics and could predict immunotherapy prognosis, potentially representing a powerful prognostic tool for further optimization of individuated treatment and management strategies in early-stage LUAD.
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Affiliation(s)
- Lilan Yi
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Ping Huang
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Yinfang Gu
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Guowu Wu
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Xiaofang Zou
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Longhua Guo
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Chunling Wen
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Junlin Zhu
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
| | - Dongdong Zhao
- Department of Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, China
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6
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Ferroptosis Markers Predict the Survival, Immune Infiltration, and Ibrutinib Resistance of Diffuse Large B cell Lymphoma. Inflammation 2022; 45:1146-1161. [DOI: 10.1007/s10753-021-01609-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 12/17/2022]
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7
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Yang J, Wei X, Hu F, Dong W, Sun L. Development and validation of a novel 3-gene prognostic model for pancreatic adenocarcinoma based on ferroptosis-related genes. Cancer Cell Int 2022; 22:21. [PMID: 35033072 PMCID: PMC8760727 DOI: 10.1186/s12935-021-02431-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/25/2021] [Indexed: 12/24/2022] Open
Abstract
Background Molecular markers play an important role in predicting clinical outcomes in pancreatic adenocarcinoma (PAAD) patients. Analysis of the ferroptosis-related genes may provide novel potential targets for the prognosis and treatment of PAAD. Methods RNA-sequence and clinical data of PAAD was downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public databases. The PAAD samples were clustered by a non-negative matrix factorization (NMF) algorithm. The differentially expressed genes (DEGs) between different subtypes were used by “limma_3.42.2” package. The R software package clusterProfiler was used for functional enrichment analysis. Then, a multivariate Cox proportional and LASSO regression were used to develop a ferroptosis-related gene signature for pancreatic adenocarcinoma. A nomogram and corrected curves were constructed. Finally, the expression and function of these signature genes were explored by qRT-PCR, immunohistochemistry (IHC) and proliferation, migration and invasion assays. Results The 173 samples were divided into 3 categories (C1, C2, and C3) and a 3-gene signature model (ALOX5, ALOX12, and CISD1) was constructed. The prognostic model showed good independent prognostic ability in PAAD. In the GSE62452 external validation set, the molecular model also showed good risk prediction. KM-curve analysis showed that there were significant differences between the high and low-risk groups, samples with a high-risk score had a worse prognosis. The predictive efficiency of the 3-gene signature-based nomogram was significantly better than that of traditional clinical features. For comparison with other models, that our model, with a reasonable number of genes, yields a more effective result. The results obtained with qPCR and IHC assays showed that ALOX5 was highly expressed, whether ALOX12 and CISD1 were expressed at low levels in tissue samples. Finally, function assays results suggested that ALOX5 may be an oncogene and ALOX12 and CISD1 may be tumor suppressor genes. Conclusions We present a novel prognostic molecular model for PAAD based on ferroptosis-related genes, which serves as a potentially effective tool for prognostic differentiation in pancreatic cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02431-8.
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Affiliation(s)
- Jihua Yang
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - XiaoHong Wei
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - Fang Hu
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - Wei Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China.
| | - Liao Sun
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China.
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Tabnak P, HajiEsmailPoor Z, Soraneh S. Ferroptosis in Lung Cancer: From Molecular Mechanisms to Prognostic and Therapeutic Opportunities. Front Oncol 2021; 11:792827. [PMID: 34926310 PMCID: PMC8674733 DOI: 10.3389/fonc.2021.792827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is the second commonly diagnosed malignancy worldwide and has the highest mortality rate among all cancers. Tremendous efforts have been made to develop novel strategies against lung cancer; however, the overall survival of patients still is low. Uncovering underlying molecular mechanisms of this disease can open up new horizons for its treatment. Ferroptosis is a newly discovered type of programmed cell death that, in an iron-dependent manner, peroxidizes unsaturated phospholipids and results in the accumulation of radical oxygen species. Subsequent oxidative damage caused by ferroptosis contributes to cell death in tumor cells. Therefore, understanding its molecular mechanisms in lung cancer appears as a promising strategy to induce ferroptosis selectively. According to evidence published up to now, significant numbers of research have been done to identify ferroptosis regulators in lung cancer. Therefore, this review aims to provide a comprehensive standpoint of molecular mechanisms of ferroptosis in lung cancer and address these molecules’ prognostic and therapeutic values, hoping that the road for future studies in this field will be paved more efficiently.
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Affiliation(s)
- Peyman Tabnak
- Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Soroush Soraneh
- Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
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Gong M, Liu X, Yang W, Song H, Zhao X, Ai X, Wang S, Wang H. Identification of a Lipid Metabolism-Associated Gene Signature Predicting Survival in Breast Cancer. Int J Gen Med 2021; 14:9503-9513. [PMID: 34916832 PMCID: PMC8668231 DOI: 10.2147/ijgm.s343426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Background Cancer metabolism and specifically lipid metabolism play an important role in breast cancer (BC) progression and metastasis. However, the role of lipid metabolism-associated genes (LMGs) in the prognosis of breast cancer remains unknown. Methods The expression profiles and clinical follow-up information of 1053 BC were downloaded from The Cancer Genome Atlas (TCGA), and metabolic genes were downloaded from the Gene Set Enrichment Analysis (GSEA) dataset. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were performed on the differentially expressed metabolism-related genes. Then, the formula of the metabolism-related risk model was composed, and the risk score of each patient was calculated. The breast cancer patients were divided into high-risk and low-risk groups with a cutoff of the median expression value of the risk score, and the prognostic analysis was also used to analyze the survival time between these two groups. Finally, we analyzed the expression, interaction and correlation among the lipid metabolism-associated genes risk model. Results The results from the prognostic analysis indicated that the survival was significantly poorer in the high-risk group than in the low-risk group in TCGA, and single-sample gene set enrichment analysis (ssGSEA) shows it is plausible that lipid metabolism is highly correlated with tumor immunity. Conclusion Lipid metabolism-associated genes may become a new prognostic indicator predicting the survival of BC patients. The prognostic genes (n = 16) may help provide new strategies for tumor therapy.
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Affiliation(s)
- Mingkai Gong
- Center of Diagnosis and Treatment of Breast Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Xiangping Liu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Wu Yang
- Department of International Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Hongming Song
- Center of Diagnosis and Treatment of Breast Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Xian Zhao
- Center of Diagnosis and Treatment of Breast Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Xiancheng Ai
- Center of Diagnosis and Treatment of Breast Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Shuo Wang
- Center of Diagnosis and Treatment of Breast Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Haibo Wang
- Center of Diagnosis and Treatment of Breast Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
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Fei X, Hu C, Wang X, Lu C, Chen H, Sun B, Li C. Construction of a Ferroptosis-Related Long Non-coding RNA Prognostic Signature and Competing Endogenous RNA Network in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:751490. [PMID: 34820377 PMCID: PMC8606539 DOI: 10.3389/fcell.2021.751490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Ferroptosis-related genes play an important role in the progression of lung adenocarcinoma (LUAD). However, the potential function of ferroptosis-related lncRNAs in LUAD has not been fully elucidated. Thus, to explore the potential role of ferroptosis-related lncRNAs in LUAD, the transcriptome RNA-seq data and corresponding clinical data of LUAD were downloaded from the TCGA dataset. Pearson correlation was used to mine ferroptosis-related lncRNAs. Differential expression and univariate Cox analysis were performed to screen prognosis related lncRNAs. A ferroptosis-related lncRNA prognostic signature (FLPS), which included six ferroptosis-related lncRNAs, was constructed by the least absolute shrinkage and selection operator (LASSO) Cox regression. Patients were divided into a high risk-score group and low risk-score group by the median risk score. Receiver operating characteristic (ROC) curves, principal component analysis (PCA), and univariate and multivariate Cox regression were performed to confirm the validity of FLPS. Enrichment analysis showed that the biological processes, pathways and markers associated with malignant tumors were more common in high-risk subgroups. There were significant differences in immune microenvironment and immune cells between high- and low-risk groups. Then, a nomogram was constructed. We further investigated the relationship between six ferroptosis-related lncRNAs and tumor microenvironment and tumor stemness. A competing endogenous RNA (ceRNA) network was established based on the six ferroptosis-related lncRNAs. Finally, we detected the expression levels of ferroptosis-related lncRNAs in clinical samples through quantitative real-time polymerase chain reaction assay (qRT-PCR). In conclusion, we identified the prognostic ferroptosis-related lncRNAs in LUAD and constructed a prognostic signature which provided a new strategy for the evaluation and prediction of prognosis in LUAD.
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Affiliation(s)
- Xiang Fei
- Department of Thoracic Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Congli Hu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Xinyu Wang
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaojing Lu
- Department of Thoracic Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Hezhong Chen
- Department of Thoracic Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Bin Sun
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital & National Center for Liver Cancer, Navy Military Medical University, Shanghai, China
| | - Chunguang Li
- Department of Thoracic Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
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Geldenhuys WJ, Piktel D, Moore JC, Rellick SL, Meadows E, Pinti MV, Hollander JM, Ammer AG, Martin KH, Gibson LF. Loss of the redox mitochondrial protein mitoNEET leads to mitochondrial dysfunction in B-cell acute lymphoblastic leukemia. Free Radic Biol Med 2021; 175:226-235. [PMID: 34496224 PMCID: PMC8478879 DOI: 10.1016/j.freeradbiomed.2021.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/28/2021] [Accepted: 09/04/2021] [Indexed: 01/12/2023]
Abstract
B-cell acute lymphoblastic leukemia (ALL) affects both pediatric and adult patients. Chemotherapy resistant tumor cells that contribute to minimal residual disease (MRD) underlie relapse and poor clinical outcomes in a sub-set of patients. Targeting mitochondrial oxidative phosphorylation (OXPHOS) in the treatment of refractory leukemic cells is a potential novel approach to sensitizing tumor cells to existing standard of care therapeutic agents. In the current study, we have expanded our previous investigation of the mitoNEET ligand NL-1 in the treatment of ALL to interrogate the functional role of the mitochondrial outer membrane protein mitoNEET in B-cell ALL. Knockout (KO) of mitoNEET (gene: CISD1) in REH leukemic cells led to changes in mitochondrial ultra-structure and function. REH cells have significantly reduced OXPHOS capacity in the KO cells coincident with reduction in electron flow and increased reactive oxygen species. In addition, we found a decrease in lipid content in KO cells, as compared to the vector control cells was observed. Lastly, the KO of mitoNEET was associated with decreased proliferation as compared to control cells when exposed to the standard of care agent cytarabine (Ara-C). Taken together, these observations suggest that mitoNEET is essential for optimal function of mitochondria in B-cell ALL and may represent a novel anti-leukemic drug target for treatment of minimal residual disease.
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Affiliation(s)
- Werner J Geldenhuys
- Department of Pharmaceutical Sciences, West Virginia University School of Pharmacy, Morgantown, WV, USA; Mitochondria Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Debbie Piktel
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA; West Virginia University Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, USA
| | - Javohn C Moore
- West Virginia University Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, USA
| | - Stephanie L Rellick
- West Virginia University Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, USA
| | - Ethan Meadows
- Department of Human Performance, West Virginia University School of Medicine, Morgantown, WV, USA; Mitochondria Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Mark V Pinti
- Department of Human Performance, West Virginia University School of Medicine, Morgantown, WV, USA; Mitochondria Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - John M Hollander
- Department of Human Performance, West Virginia University School of Medicine, Morgantown, WV, USA; Mitochondria Metabolism and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Amanda G Ammer
- West Virginia University Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, USA
| | - Karen H Martin
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA; West Virginia University Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, USA
| | - Laura F Gibson
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA; West Virginia University Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, USA.
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Zhang Z, Ma Y, Guo X, Du Y, Zhu Q, Wang X, Duan C. FDX1 can Impact the Prognosis and Mediate the Metabolism of Lung Adenocarcinoma. Front Pharmacol 2021; 12:749134. [PMID: 34690780 PMCID: PMC8531531 DOI: 10.3389/fphar.2021.749134] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/08/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Lung cancer has emerged as one of the most common cancers in recent years. The mitochondrial electron transport chain (ETC) is closely connected with metabolic pathways and inflammatory response. However, the influence of ETC-associated genes on the tumor immune response and the pathogenesis of lung cancer is not clear and needs further exploration. Methods: The RNA-sequencing transcriptome and clinical characteristic data of LUAD were downloaded from the Cancer Genome Atlas (TCGA) database. The LASSO algorithm was used to build the risk signature, and the prediction model was evaluated by the survival analysis and receiver operating characteristic curve. We explored the function of FDX1 through flow cytometry, molecular biological methods, and liquid chromatography–tandem mass spectrometry/mass spectrometry (LC–MS/MS). Results: 12 genes (FDX1, FDX2, LOXL2, ASPH, GLRX2, ALDH2, CYCS, AKR1A1, MAOB, RDH16, CYBB, and CYB5A) were selected to build the risk signature, and the risk score was calculated with the coefficients from the LASSO algorithm. The 1-year, 3-year, and 5-year area under the curve (AUC) of ROC curves of the dataset were 0.7, 0.674, and 0.692, respectively. Univariate Cox analysis and multivariate Cox regression analysis indicated that the risk signature is an independent risk factor for LUAD patients. Among these genes, we focused on the FDX1 gene, and we found that knockdown of FDX1 neither inhibited tumor cell growth nor did it induce apoptosis or abnormal cell cycle distribution. But FDX1 could promote the ATP production. Furthermore, our study showed that FDX1 was closely related to the glucose metabolism, fatty acid oxidation, and amino acid metabolism. Conclusion: Collectively, this study provides new clues about carcinogenesis induced by ETC-associated genes in LUAD and paves the way for finding potential targets of LUAD.
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Affiliation(s)
- Zeyu Zhang
- Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, China
| | - Yarui Ma
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | | | - Yingxi Du
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qing Zhu
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiaobing Wang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Changzhu Duan
- Department of Cell Biology and Genetics, Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
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