Integrated exome and RNA sequencing of TFE3-translocation renal cell carcinoma

Guangxi Sun, Junru Chen, Jiayu Liang, Xiaoxue Yin, Mengni Zhang, Jin Yao, Ning He, Cameron M. Armstrong, Linmao Zheng, Xingming Zhang, Sha Zhu, Xiaomeng Sun, Xiaoxia Yang, Wanbin Zhao, Banghua Liao, Xiuyi Pan, Ling Nie, Ling Yang, Yuntian Chen, Jinge Zhao, Haoran Zhang, Jindong Dai, Yali Shen, Jiyan Liu, Rui Huang, Jiandong Liu, Zhipeng Wang, Yuchao Ni, Qiang Wei, Xiang Li, Qiao Zhou, Haojie Huang, Zhenhua Liu (), Pengfei Shen (), Ni Chen () and Hao Zeng ()
Additional contact information
Guangxi Sun: Sichuan University
Junru Chen: Sichuan University
Jiayu Liang: Sichuan University
Xiaoxue Yin: Sichuan University
Mengni Zhang: Sichuan University
Jin Yao: Sichuan University
Ning He: GloriousMed Clinical Laboratory (Shanghai) Co., Ltd
Cameron M. Armstrong: University of California Davis
Linmao Zheng: Sichuan University
Xingming Zhang: Sichuan University
Sha Zhu: Sichuan University
Xiaomeng Sun: GloriousMed Clinical Laboratory (Shanghai) Co., Ltd
Xiaoxia Yang: GloriousMed Clinical Laboratory (Shanghai) Co., Ltd
Wanbin Zhao: GloriousMed Clinical Laboratory (Shanghai) Co., Ltd
Banghua Liao: Sichuan University
Xiuyi Pan: Sichuan University
Ling Nie: Sichuan University
Ling Yang: Sichuan University
Yuntian Chen: Sichuan University
Jinge Zhao: Sichuan University
Haoran Zhang: Sichuan University
Jindong Dai: Sichuan University
Yali Shen: Sichuan University
Jiyan Liu: Sichuan University
Rui Huang: Sichuan University
Jiandong Liu: Sichuan University
Zhipeng Wang: Sichuan University
Yuchao Ni: Sichuan University
Qiang Wei: Sichuan University
Xiang Li: Sichuan University
Qiao Zhou: Sichuan University
Haojie Huang: Mayo Clinic College of Medicine and Science
Zhenhua Liu: Sichuan University
Pengfei Shen: Sichuan University
Ni Chen: Sichuan University
Hao Zeng: Sichuan University

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract TFE3-translocation renal cell carcinoma (TFE3-tRCC) is a rare and heterogeneous subtype of kidney cancer with no standard treatment for advanced disease. We describe comprehensive molecular characteristics of 63 untreated primary TFE3-tRCCs based on whole-exome and RNA sequencing. TFE3-tRCC is highly heterogeneous, both clinicopathologically and genotypically. ASPSCR1-TFE3 fusion and several somatic copy number alterations, including the loss of 22q, are associated with aggressive features and poor outcomes. Apart from tumors with MED15-TFE3 fusion, most TFE3-tRCCs exhibit low PD-L1 expression and low T-cell infiltration. Unsupervised transcriptomic analysis reveals five molecular clusters with distinct angiogenesis, stroma, proliferation and KRAS down signatures, which show association with fusion patterns and prognosis. In line with the aggressive nature, the high angiogenesis/stroma/proliferation cluster exclusively consists of tumors with ASPSCR1-TFE3 fusion. Here, we describe the genomic and transcriptomic features of TFE3-tRCC and provide insights into precision medicine for this disease.

Date: 2021
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DOI: 10.1038/s41467-021-25618-z

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