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Xie Z, Wu L, Hua S, Zhang Y, Shi F, Chen M, Zhao S, Liu Z, Liu M, Jiang J. External Validation of the Prognostic Value of an Immune-Associated Gene Panel for Clear Cell Renal Cell Carcinomas. Front Cell Dev Biol 2022; 9:794840. [PMID: 35004689 PMCID: PMC8733896 DOI: 10.3389/fcell.2021.794840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/14/2021] [Accepted: 12/07/2021] [Indexed: 12/25/2022] Open
Abstract
Clear cell renal cell carcinomas (ccRCCs) are highly immune infiltrates, and many of them respond to immunotherapy with checkpoint inhibitors including anti-PD-L1 or anti-PD1 agents. However, the effect of immune genes on clinical outcomes in ccRCCs has not been fully studied. Here, we show in this study that an immune-associated gene panel has a prognostic value for clear cell renal cell carcinomas. We performed single-sample gene set enrichment analysis (ssGSEA) and cell type identification by estimating subsets of RNA transcripts (CIBERSORT) algorithms on patient-matched normal renal and RCC tissues to characterize two immunophenotypes and immunological characteristic subpopulations. Furthermore, LASSO Cox regression was applied to develop a novel prognosis-associated model for ccRCC patients based on an immune-gene panel. The results were verified by the Gene Expression Omnibus (GEO) dataset and coordinated with the clinicopathological characteristics of ccRCCs, along with genomic signatures. Finally, based on the above perspectives, we generated a nomogram with a high prognostic efficiency for ccRCC patients. Overall, this study offers a unique perspective that can contribute to improving the accuracy of prognosis prediction and treatment with immunotherapy.
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Affiliation(s)
- Zhiwen Xie
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Wu
- Department of Urology, Shanghai General Hospital of Nanjing Medical University, Shanghai, China
| | - Shan Hua
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongqing Zhang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Shi
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sheng Zhao
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhihong Liu
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meng Liu
- Department of Urology, The Fifth People's Hospital of Zunyi, Guizhou, China
| | - Juntao Jiang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Urology, Shanghai General Hospital of Nanjing Medical University, Shanghai, China
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Park JS, Pierorazio PM, Lee JH, Lee HJ, Lim YS, Jang WS, Kim J, Lee SH, Rha KH, Cho NH, Ham WS. Gene Expression Analysis of Aggressive Clinical T1 Stage Clear Cell Renal Cell Carcinoma for Identifying Potential Diagnostic and Prognostic Biomarkers. Cancers (Basel) 2020; 12:cancers12010222. [PMID: 31963294 PMCID: PMC7017065 DOI: 10.3390/cancers12010222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 12/23/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
The molecular characteristics of early-stage clear cell renal cell carcinomas (ccRCCs) measuring ≤7 cm associated with poor clinical outcomes remain poorly understood. Here, we sought to validate genes associated with ccRCC progression and identify candidate genes to predict ccRCC aggressiveness. From among 1069 nephrectomies performed on patients, RNA sequencing was performed for 12 ccRCC patients with aggressive characteristics and matched pairs of 12 ccRCC patients without aggressive characteristics. Using a prospective cohort (ClinicalTrials.gov Identifier: NCT03694912), the expression levels of nine genes (PBRM1, BAP1, SETD2, KDM5C, FOXC2, CLIP4, AQP1, DDX11, and BAIAP2L1) were measured by reverse-transcription polymerase chain reaction from frozen tissues, and their relation to Fuhrman grade was investigated in 70 patients with small ccRCC (≤4 cm). In total, 251 genes were differentially expressed and presented fold changes with p-values < 0.05; moreover, 10 genes with the greatest upregulation or downregulation in aggressive ccRCC remained significant even after adjustment. We validated previously identified genes that were associated with ccRCC progression and identified new candidate genes that reflected the aggressiveness of ccRCC. Our study provides new insight into the tumor biology of ccRCC and will help stratify patients with early-stage ccRCC by molecular subtyping.
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Affiliation(s)
- Jee Soo Park
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (H.J.L.); (Y.S.L.); (W.S.J.); (J.K.); (S.H.L.); (K.H.R.)
| | - Phillip M. Pierorazio
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Park 213, Baltimore, MD 21287, USA;
- Department of Oncology, Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University of Medicine, Baltimore, MD 21287, USA
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea;
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul 02447, Korea
| | - Hyo Jung Lee
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (H.J.L.); (Y.S.L.); (W.S.J.); (J.K.); (S.H.L.); (K.H.R.)
| | - Young Soun Lim
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (H.J.L.); (Y.S.L.); (W.S.J.); (J.K.); (S.H.L.); (K.H.R.)
| | - Won Sik Jang
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (H.J.L.); (Y.S.L.); (W.S.J.); (J.K.); (S.H.L.); (K.H.R.)
| | - Jongchan Kim
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (H.J.L.); (Y.S.L.); (W.S.J.); (J.K.); (S.H.L.); (K.H.R.)
| | - Seung Hwan Lee
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (H.J.L.); (Y.S.L.); (W.S.J.); (J.K.); (S.H.L.); (K.H.R.)
| | - Koon Ho Rha
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (H.J.L.); (Y.S.L.); (W.S.J.); (J.K.); (S.H.L.); (K.H.R.)
| | - Nam Hoon Cho
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Won Sik Ham
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (H.J.L.); (Y.S.L.); (W.S.J.); (J.K.); (S.H.L.); (K.H.R.)
- Correspondence: ; Tel.: +82-10-6242-7938
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