Identification of mRNA vaccines and conserved ferroptosis related immune landscape for individual precision treatment in bladder cancer
Background The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine development and selecting suitable patients for precision treatment. Methods Gene expression profiles and clinical information of 1216 BCa patient...
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Published in | Journal of big data Vol. 9; no. 1; p. 88 |
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Main Authors | , , , , , , , , , |
Format | Journal Article |
Language | English |
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Cham
Springer International Publishing
07.07.2022
Springer Nature B.V SpringerOpen |
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Abstract | Background
The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine development and selecting suitable patients for precision treatment.
Methods
Gene expression profiles and clinical information of 1216 BCa patients were extracted from TCGA-BLCA, three GEO databases and IMvigor210 cohort. We comprehensively established the FeME landscape of 1216 BCa samples based on 290 ferroptosis related genes (FRGs), and systematically correlated these regulation patterns with TME cell-infiltrating characteristics. Besides, we identified the patients’ ferroptosis risk index (FRI) to predict the prognosis of BCa for precise treatment.
Results
Six over-expressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in BCa. Furthermore, we demonstrated the evaluation of FeME within individual tumors could predict stages of tumor inflammation, subtypes, genetic variation, and patient prognosis. Then, 5-lncRNA signature was mined to produce the FRI. Low FRI was also linked to increased mutation load, better prognosis and enhanced response to anti-PD-L1 immunotherapy. Besides, an immunotherapy cohort confirmed patients with lower FRI demonstrated significant therapeutic advantages and clinical benefits.
Conclusions
TFRC, SCD, G6PD, FADS2, SQLE, and SLC3A2 are potent antigens for developing anti-BCa mRNA vaccine. Establishment of FRI will contribute to enhancing our cognition of TME infiltration characterization and guiding more effective immunotherapy strategies and selecting appropriate patients for tumor vaccine therapy. |
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AbstractList | BackgroundThe aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine development and selecting suitable patients for precision treatment.MethodsGene expression profiles and clinical information of 1216 BCa patients were extracted from TCGA-BLCA, three GEO databases and IMvigor210 cohort. We comprehensively established the FeME landscape of 1216 BCa samples based on 290 ferroptosis related genes (FRGs), and systematically correlated these regulation patterns with TME cell-infiltrating characteristics. Besides, we identified the patients’ ferroptosis risk index (FRI) to predict the prognosis of BCa for precise treatment.ResultsSix over-expressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in BCa. Furthermore, we demonstrated the evaluation of FeME within individual tumors could predict stages of tumor inflammation, subtypes, genetic variation, and patient prognosis. Then, 5-lncRNA signature was mined to produce the FRI. Low FRI was also linked to increased mutation load, better prognosis and enhanced response to anti-PD-L1 immunotherapy. Besides, an immunotherapy cohort confirmed patients with lower FRI demonstrated significant therapeutic advantages and clinical benefits.ConclusionsTFRC, SCD, G6PD, FADS2, SQLE, and SLC3A2 are potent antigens for developing anti-BCa mRNA vaccine. Establishment of FRI will contribute to enhancing our cognition of TME infiltration characterization and guiding more effective immunotherapy strategies and selecting appropriate patients for tumor vaccine therapy. BackgroundThe aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine development and selecting suitable patients for precision treatment. MethodsGene expression profiles and clinical information of 1216 BCa patients were extracted from TCGA-BLCA, three GEO databases and IMvigor210 cohort. We comprehensively established the FeME landscape of 1216 BCa samples based on 290 ferroptosis related genes (FRGs), and systematically correlated these regulation patterns with TME cell-infiltrating characteristics. Besides, we identified the patients' ferroptosis risk index (FRI) to predict the prognosis of BCa for precise treatment. ResultsSix over-expressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in BCa. Furthermore, we demonstrated the evaluation of FeME within individual tumors could predict stages of tumor inflammation, subtypes, genetic variation, and patient prognosis. Then, 5-lncRNA signature was mined to produce the FRI. Low FRI was also linked to increased mutation load, better prognosis and enhanced response to anti-PD-L1 immunotherapy. Besides, an immunotherapy cohort confirmed patients with lower FRI demonstrated significant therapeutic advantages and clinical benefits. ConclusionsTFRC, SCD, G6PD, FADS2, SQLE, and SLC3A2 are potent antigens for developing anti-BCa mRNA vaccine. Establishment of FRI will contribute to enhancing our cognition of TME infiltration characterization and guiding more effective immunotherapy strategies and selecting appropriate patients for tumor vaccine therapy. Supplementary InformationThe online version contains supplementary material available at 10.1186/s40537-022-00641-z. Background The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine development and selecting suitable patients for precision treatment. Methods Gene expression profiles and clinical information of 1216 BCa patients were extracted from TCGA-BLCA, three GEO databases and IMvigor210 cohort. We comprehensively established the FeME landscape of 1216 BCa samples based on 290 ferroptosis related genes (FRGs), and systematically correlated these regulation patterns with TME cell-infiltrating characteristics. Besides, we identified the patients’ ferroptosis risk index (FRI) to predict the prognosis of BCa for precise treatment. Results Six over-expressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in BCa. Furthermore, we demonstrated the evaluation of FeME within individual tumors could predict stages of tumor inflammation, subtypes, genetic variation, and patient prognosis. Then, 5-lncRNA signature was mined to produce the FRI. Low FRI was also linked to increased mutation load, better prognosis and enhanced response to anti-PD-L1 immunotherapy. Besides, an immunotherapy cohort confirmed patients with lower FRI demonstrated significant therapeutic advantages and clinical benefits. Conclusions TFRC, SCD, G6PD, FADS2, SQLE, and SLC3A2 are potent antigens for developing anti-BCa mRNA vaccine. Establishment of FRI will contribute to enhancing our cognition of TME infiltration characterization and guiding more effective immunotherapy strategies and selecting appropriate patients for tumor vaccine therapy. Abstract Background The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine development and selecting suitable patients for precision treatment. Methods Gene expression profiles and clinical information of 1216 BCa patients were extracted from TCGA-BLCA, three GEO databases and IMvigor210 cohort. We comprehensively established the FeME landscape of 1216 BCa samples based on 290 ferroptosis related genes (FRGs), and systematically correlated these regulation patterns with TME cell-infiltrating characteristics. Besides, we identified the patients’ ferroptosis risk index (FRI) to predict the prognosis of BCa for precise treatment. Results Six over-expressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in BCa. Furthermore, we demonstrated the evaluation of FeME within individual tumors could predict stages of tumor inflammation, subtypes, genetic variation, and patient prognosis. Then, 5-lncRNA signature was mined to produce the FRI. Low FRI was also linked to increased mutation load, better prognosis and enhanced response to anti-PD-L1 immunotherapy. Besides, an immunotherapy cohort confirmed patients with lower FRI demonstrated significant therapeutic advantages and clinical benefits. Conclusions TFRC, SCD, G6PD, FADS2, SQLE, and SLC3A2 are potent antigens for developing anti-BCa mRNA vaccine. Establishment of FRI will contribute to enhancing our cognition of TME infiltration characterization and guiding more effective immunotherapy strategies and selecting appropriate patients for tumor vaccine therapy. Abstract Background The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine development and selecting suitable patients for precision treatment. Methods Gene expression profiles and clinical information of 1216 BCa patients were extracted from TCGA-BLCA, three GEO databases and IMvigor210 cohort. We comprehensively established the FeME landscape of 1216 BCa samples based on 290 ferroptosis related genes (FRGs), and systematically correlated these regulation patterns with TME cell-infiltrating characteristics. Besides, we identified the patients’ ferroptosis risk index (FRI) to predict the prognosis of BCa for precise treatment. Results Six over-expressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in BCa. Furthermore, we demonstrated the evaluation of FeME within individual tumors could predict stages of tumor inflammation, subtypes, genetic variation, and patient prognosis. Then, 5-lncRNA signature was mined to produce the FRI. Low FRI was also linked to increased mutation load, better prognosis and enhanced response to anti-PD-L1 immunotherapy. Besides, an immunotherapy cohort confirmed patients with lower FRI demonstrated significant therapeutic advantages and clinical benefits. Conclusions TFRC, SCD, G6PD, FADS2, SQLE, and SLC3A2 are potent antigens for developing anti-BCa mRNA vaccine. Establishment of FRI will contribute to enhancing our cognition of TME infiltration characterization and guiding more effective immunotherapy strategies and selecting appropriate patients for tumor vaccine therapy. |
ArticleNumber | 88 |
Author | Gui, Cheng-Peng Zhang, Li-zhen Li, Jia-Ying Wu, Rong-Pei Tang, Yi-Ming Luo, Cheng-Gong Luo, Jun-Hang Zhang, Chi Shu, Guan-nan Fu, Liang-Min |
Author_xml | – sequence: 1 givenname: Cheng-Peng surname: Gui fullname: Gui, Cheng-Peng email: dogluckya@gmail.com organization: Department of Urology, First Affiliated Hospital, Sun Yat-Sen University, Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-Sen University – sequence: 2 givenname: Jia-Ying surname: Li fullname: Li, Jia-Ying organization: Department of Urology, First Affiliated Hospital, Sun Yat-Sen University – sequence: 3 givenname: Liang-Min surname: Fu fullname: Fu, Liang-Min organization: Department of Urology, First Affiliated Hospital, Sun Yat-Sen University – sequence: 4 givenname: Cheng-Gong surname: Luo fullname: Luo, Cheng-Gong organization: Department of Urology, First Affiliated Hospital, Sun Yat-Sen University – sequence: 5 givenname: Chi surname: Zhang fullname: Zhang, Chi organization: Department of Urology, Third Affiliated Hospital, Sun Yat-Sen University – sequence: 6 givenname: Yi-Ming surname: Tang fullname: Tang, Yi-Ming organization: Department of Urology, Second Affiliated Hospital, Guangzhou Medical University – sequence: 7 givenname: Li-zhen surname: Zhang fullname: Zhang, Li-zhen organization: Department of Urology, First Affiliated Hospital, Sun Yat-Sen University – sequence: 8 givenname: Guan-nan surname: Shu fullname: Shu, Guan-nan organization: Department of Urology, First Affiliated Hospital, Sun Yat-Sen University – sequence: 9 givenname: Rong-Pei surname: Wu fullname: Wu, Rong-Pei email: pacemaker_wrp@163.com organization: Department of Urology, First Affiliated Hospital, Sun Yat-Sen University – sequence: 10 givenname: Jun-Hang surname: Luo fullname: Luo, Jun-Hang email: luojunh@mail.sysu.edu.cn organization: Department of Urology, First Affiliated Hospital, Sun Yat-Sen University, Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-Sen University |
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CitedBy_id | crossref_primary_10_1615_CritRevEukaryotGeneExpr_2023048536 crossref_primary_10_2147_PGPM_S449230 crossref_primary_10_1186_s40537_023_00803_7 crossref_primary_10_1007_s12672_023_00853_6 crossref_primary_10_1016_j_canlet_2024_216867 crossref_primary_10_3390_cancers15020459 crossref_primary_10_1016_j_biopha_2022_113897 crossref_primary_10_1093_toxres_tfae010 crossref_primary_10_1007_s11010_023_04694_3 crossref_primary_10_32948_auo_2023_01_20 crossref_primary_10_3389_fimmu_2022_1014638 crossref_primary_10_3389_fphar_2022_1043283 crossref_primary_10_1038_s41419_024_06584_y crossref_primary_10_18632_aging_205089 |
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Keywords | Ferroptosis Tumor immune microenvironment Bladder cancer Immunotherapy Precise treatment mRNA vaccine |
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14 P Langfelder (641_CR25) 2008; 9 H Salmon (641_CR34) 2012; 122 ME Timmerman (641_CR19) 2013; 45 HH Jabara (641_CR43) 2016; 48 SJ Turley (641_CR30) 2015; 15 Y Jiang (641_CR49) 2017; 7 JA Joyce (641_CR33) 2015; 348 TF Gajewski (641_CR32) 2015; 42 TF Gajewski (641_CR31) 2013; 25 E Dai (641_CR11) 2020; 16 H Xu (641_CR50) 2020; 1874 N Li (641_CR36) 2020; 24 P Jiang (641_CR27) 2018; 24 Y Chen (641_CR37) 2021; 40 AB Apolo (641_CR3) 2017; 35 C Qian (641_CR28) 2018; 35 Y Vivas-Garcia (641_CR46) 2020; 77 C Mao (641_CR13) 2018; 78 |
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Snippet | Background
The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine... Abstract Background The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA... BackgroundThe aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine... Abstract Background The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA... |
SourceID | doaj pubmedcentral proquest crossref springer |
SourceType | Open Website Open Access Repository Aggregation Database Publisher |
StartPage | 88 |
SubjectTerms | Antigens Big Data Bladder Bladder cancer Cancer Cognition Communications Engineering Computational Science and Engineering Computer Science Data Mining and Knowledge Discovery Database Management Ferroptosis Gene expression Immunotherapy Infiltration Information Storage and Retrieval Mathematical Applications in Computer Science mRNA vaccine mRNA vaccines Mutation Networks Precise treatment Prognosis Tumor immune microenvironment Tumors Vaccines |
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Title | Identification of mRNA vaccines and conserved ferroptosis related immune landscape for individual precision treatment in bladder cancer |
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