Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma

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 profi...

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Autores principales: Xu, Wenhao, Tao, Juli, Zhu, Wenkai, Liu, Wangrui, Anwaier, Aihetaimujiang, Tian, Xi, Su, Jiaqi, Shi, Guohai, Huang, Haineng, Wei, Gaomeng, Li, Chuanyu, Qu, Yuanyuan, Zhang, Hailiang, Ye, Dingwei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8593147/
https://www.ncbi.nlm.nih.gov/pubmed/34795663
http://dx.doi.org/10.3389/fimmu.2021.734646
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author Xu, Wenhao
Tao, Juli
Zhu, Wenkai
Liu, Wangrui
Anwaier, Aihetaimujiang
Tian, Xi
Su, Jiaqi
Shi, Guohai
Huang, Haineng
Wei, Gaomeng
Li, Chuanyu
Qu, Yuanyuan
Zhang, Hailiang
Ye, Dingwei
author_facet Xu, Wenhao
Tao, Juli
Zhu, Wenkai
Liu, Wangrui
Anwaier, Aihetaimujiang
Tian, Xi
Su, Jiaqi
Shi, Guohai
Huang, Haineng
Wei, Gaomeng
Li, Chuanyu
Qu, Yuanyuan
Zhang, Hailiang
Ye, Dingwei
author_sort Xu, Wenhao
collection PubMed
description 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 RBCK1(high) group compared with the RBCK1(low) 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 CD56(bight/dim) NK cells in the immune-cold RBCK1(high) group. In addition to the distinct heterogeneous immune microenvironment, the increased expression of RBCK1 predicted a prominently worse prognosis than the RBCK1(low) 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 RBCK1(high) patients have pro-tumorigenic immune infiltration and significantly worse outcomes than RBCK1(low) 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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spelling pubmed-85931472021-11-17 Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma Xu, Wenhao Tao, Juli Zhu, Wenkai Liu, Wangrui Anwaier, Aihetaimujiang Tian, Xi Su, Jiaqi Shi, Guohai Huang, Haineng Wei, Gaomeng Li, Chuanyu Qu, Yuanyuan Zhang, Hailiang Ye, Dingwei Front Immunol Immunology 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 RBCK1(high) group compared with the RBCK1(low) 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 CD56(bight/dim) NK cells in the immune-cold RBCK1(high) group. In addition to the distinct heterogeneous immune microenvironment, the increased expression of RBCK1 predicted a prominently worse prognosis than the RBCK1(low) 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 RBCK1(high) patients have pro-tumorigenic immune infiltration and significantly worse outcomes than RBCK1(low) 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. Frontiers Media S.A. 2021-11-02 /pmc/articles/PMC8593147/ /pubmed/34795663 http://dx.doi.org/10.3389/fimmu.2021.734646 Text en Copyright © 2021 Xu, Tao, Zhu, Liu, Anwaier, Tian, Su, Shi, Huang, Wei, Li, Qu, Zhang and Ye https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Immunology
Xu, Wenhao
Tao, Juli
Zhu, Wenkai
Liu, Wangrui
Anwaier, Aihetaimujiang
Tian, Xi
Su, Jiaqi
Shi, Guohai
Huang, Haineng
Wei, Gaomeng
Li, Chuanyu
Qu, Yuanyuan
Zhang, Hailiang
Ye, Dingwei
Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma
title Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma
title_full Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma
title_fullStr Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma
title_full_unstemmed Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma
title_short Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma
title_sort comprehensive multi-omics identification of interferon-γ response characteristics reveals that rbck1 regulates the immunosuppressive microenvironment of renal cell carcinoma
topic Immunology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8593147/
https://www.ncbi.nlm.nih.gov/pubmed/34795663
http://dx.doi.org/10.3389/fimmu.2021.734646
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