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Xu W, Tao J, Zhu W, Liu W, Anwaier A, Tian X, Su J, Shi G, Huang H, Wei G, Li C, Qu Y, Zhang H, Ye D. Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma. Front Immunol 2021; 12:734646. [PMID: 34795663 PMCID: PMC8593147 DOI: 10.3389/fimmu.2021.734646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/11/2021] [Indexed: 12/09/2022] Open
Abstract
Interferon-gamma (IFN-γ) has a complex role in modulating the tumor microenvironment (TME) during renal cell carcinoma (RCC) development. To define the role of IFN-γ response genes in RCC progression, we characterized the differential gene expression, prognostic implications, and DNA variation profiles of selected IFN-γ response signatures, which exhibited a significant hazard ratio for the overall survival (OS) and progression-free survival (PFS) of papillary, chromophobia, and clear cell RCC (ccRCC) patients (n = 944). Prognostic nomograms were constructed to predict the outcomes for ccRCC patients, highlighting the prognostic implications of RANBP2-type and C3HC4-type zinc finger containing 1 (RBCK1). Interestingly, large-scale pan-cancer samples (n = 12,521) and three single-cell RNA datasets revealed that RBCK1 showed markedly differential expression between cancer and normal tissues and significantly correlated with tumor-infiltrating immune cells, tumor purity, and immune checkpoint molecules, such as PD-L1, CTLA-4, LAG-3, and TIGIT in pan-cancer samples. Notably, the TIDE score was significantly higher in the RBCK1high group compared with the RBCK1low group in both ccRCC and RCC cohorts. Besides, immunohistochemistry staining showed significantly elevated RBCK1 expression in tumors (n = 50) compared with kidney samples (n = 40) from a real-world cohort, Fudan University Shanghai Cancer Center (FUSCC, Shanghai). After RBCK1 expression was confirmed in ccRCC, we found a significantly decreased number of infiltrating CD4+ T cells, CD4+ FOXP3+ Treg cells, M1 macrophages, and CD56bight/dim NK cells in the immune-cold RBCK1high group. In addition to the distinct heterogeneous immune microenvironment, the increased expression of RBCK1 predicted a prominently worse prognosis than the RBCK1low group for 232 ccRCC patients in the FUSCC proteomic cohort. Furthermore, after transfected with siRNA in human ccRCC cells, extraordinarily decreased cell proliferation, migration capacities, and prominently elevated apoptosis tumor cell proportion were found in the siRNA groups compared with the negative control group. In conclusion, this study identified IFN-γ response clusters, which might be used to improve the prognostic accuracy of immune contexture in the ccRCC microenvironment. Immune-cold RBCK1high patients have pro-tumorigenic immune infiltration and significantly worse outcomes than RBCK1low patients based on results from multi-omics to real-world data. Our discovery of novel independent prognostic indicators for RCC highlights the association between tumor alterations and immune phenotype.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/enzymology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/therapy
- Cell Line, Tumor
- Databases, Genetic
- Decision Support Techniques
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Genomics
- Humans
- Interferon-gamma/genetics
- Interferon-gamma/metabolism
- Kidney Neoplasms/enzymology
- Kidney Neoplasms/genetics
- Kidney Neoplasms/immunology
- Kidney Neoplasms/therapy
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Nomograms
- Phenotype
- Progression-Free Survival
- Protein Interaction Maps
- Proteome
- Proteomics
- RNA-Seq
- Signal Transduction
- Single-Cell Analysis
- Time Factors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptome
- Tumor Microenvironment
- Tumor-Associated Macrophages/immunology
- Tumor-Associated Macrophages/metabolism
- Ubiquitin-Protein Ligases/genetics
- Ubiquitin-Protein Ligases/metabolism
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Juli Tao
- Department of Hematology and Rheumatology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wenkai Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | | | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Haineng Huang
- Department of Hematology and Rheumatology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Gaomeng Wei
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Chuanyu Li
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
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Mutations in the Mitochondrial ND1 Gene Are Associated with Postoperative Prognosis of Localized Renal Cell Carcinoma. Int J Mol Sci 2016; 17:ijms17122049. [PMID: 27941608 PMCID: PMC5187849 DOI: 10.3390/ijms17122049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 01/20/2023] Open
Abstract
We analyzed mutations in the mitochondrial ND1 gene to determine their association with clinicopathological parameters and postoperative recurrence of renal cell carcinoma (RCC) in Japanese patients. Among 62 RCC cases for which tumor pathology was confirmed by histopathology, ND1 sequencing revealed the presence of 30 mutation sites in 19 cases. Most mutations were heteroplasmic, with 16 of 19 cases harboring one or more heteroplasmic sites. Additionally, 12 sites had amino acid mutations, which were frequent in 10 of the cases. The 5-year recurrence-free survival (RFS) rate was significantly worse in patients with tumors >40 mm in diameter (p = 0.0091), pathological T (pT) stage ≥3 (p = 0.0122), Fuhrman nuclear atypia grade ≥III (p = 0.0070), and ND1 mutations (p = 0.0006). Multivariate analysis using these factors revealed that mutations in ND1 were significantly associated with the 5-year RFS rate (p = 0.0044). These results suggest a strong correlation between the presence of ND1 mutations in cancer tissue and postoperative recurrence of localized RCC in Japanese patients.
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Artaç M, Çoşkun HŞ, Korkmaz L, Koçer M, Turhal NS, Engin H, Dede İ, Paydaş S, Öksüzoğlu B, Bozcuk H, Demirkazık A. Using Interferon Alfa Before Tyrosine Kinase Inhibitors May Increase Survival in Patients With Metastatic Renal Cell Carcinoma: A Turkish Oncology Group (TOG) Study. Clin Genitourin Cancer 2016; 14:e347-53. [PMID: 27236771 DOI: 10.1016/j.clgc.2016.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 04/20/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND We aimed to investigate the outcomes of interferon alfa and sequencing tyrosine kinase inhibitors (TKIs) in patients with metastatic renal cell carcinoma. PATIENTS AND METHODS This multicenter study assessing the efficacy of TKIs after interferon alfa therapy in the first-line setting in patients with metastatic renal cell carcinoma. Patients (n = 104) from 8 centers in Turkey, who had been treated with interferon alfa in the first-line setting, were included in the study. Prognostic factors were evaluated for progression-free survival (PFS). RESULTS The median age of the patients was 57 years. The median PFS of the patients treated with interferon alfa in the first-line was 3.6 months. A total of 61 patients received TKIs (sunitinib, n = 58; sorafenib, n = 3) after progression while on interferon alfa. The median PFS among the TKI-treated patients was 13.2 months. In the univariate analysis for interferon alfa treatment, neutrophil and hemoglobin level, platelet count, and Karnofsky performance status were the significant factors associated with PFS. In the univariate analysis for TKI treatment, neutrophil and hemoglobin levels were the significant factors for PFS. The median total PFS of the patients who had been treated with first-line interferon alfa and second-line TKIs was 24.9 months. CONCLUSION This study showed that first-line interferon alfa treatment before TKIs may improve the total PFS in patients with metastatic renal cell carcinoma.
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Affiliation(s)
- Mehmet Artaç
- Department of Medical Oncology, Necmettin Erbakan University Meram Medical Faculty, Konya, Turkey.
| | - Hasan Şenol Çoşkun
- Department of Medical Oncology, Akdeniz University Medical Faculty, Antalya, Turkey
| | - Levent Korkmaz
- Department of Medical Oncology, Necmettin Erbakan University Meram Medical Faculty, Konya, Turkey
| | - Murat Koçer
- Department of Medical Oncology, Süleyman Demirel University Medical Faculty, Isparta, Turkey
| | - Nazım Serdar Turhal
- Department of Medical Oncology, Marmara University Medical Faculty, Istanbul, Turkey
| | - Hüseyin Engin
- Department of Medical Oncology, Bülent Ecevit University Medical Faculty, Zonguldak, Turkey
| | - İsa Dede
- Department of Medical Oncology, Ankara University Medical Faculty, Ankara, Turkey
| | - Semra Paydaş
- Department of Medical Oncology, Cukurova University Medical Faculty, Adana, Turkey
| | - Berna Öksüzoğlu
- Department of Medical Oncology, Ankara Oncology Training and Research Hospital, Ankara, Turkey
| | - Hakan Bozcuk
- Department of Medical Oncology, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Ahmet Demirkazık
- Department of Medical Oncology, Ankara University Medical Faculty, Ankara, Turkey
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