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

Author

Listed:
  • 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
    Zhejiang 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)

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.

Suggested Citation

  • 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 & B, 2021. "Integrated exome and RNA sequencing of TFE3-translocation renal cell carcinoma," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25618-z
    DOI: 10.1038/s41467-021-25618-z
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    Cited by:

    1. Lei Guo & Rongjie Zhao & Yi-Tsang Lee & Junhua Huang & James Wengler & Logan Rivera & Tingting Hong & Tianlu Wang & Kunjal Rathod & Ashley Suris & Yitian Wu & Xiaoli Cai & Rui Wang & Yubin Zhou & Yun , 2025. "RNA-mediated condensation of TFE3 oncofusions facilitates transcriptional hub formation to promote translocation renal cell carcinoma," Nature Communications, Nature, vol. 16(1), pages 1-22, December.
    2. Akihiko Fukagawa & Natsuko Hama & Yasushi Totoki & Hiromi Nakamura & Yasuhito Arai & Mihoko Saito-Adachi & Akiko Maeshima & Yoshiyuki Matsui & Shinichi Yachida & Tetsuo Ushiku & Tatsuhiro Shibata, 2023. "Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Kaushal Asrani & Adrianna Amaral & Juhyung Woo & Sanaz Nourmohammadi Abadchi & Thiago Vidotto & Eddie Imada & Alyza Skaist & Kewen Feng & Hans B. Liu & Mithila Kasbe & Yorifumi Satou & Masaya Baba & Y, 2025. "SFPQ-TFE3 reciprocally regulates mTORC1 and induces lineage plasticity in a mouse model of renal tumorigenesis," Nature Communications, Nature, vol. 16(1), pages 1-23, December.
    4. Xingming Zhang & Junjie Zhao & Xiaoxue Yin & Jiayu Liang & Yongquan Wang & Linmao Zheng & Ping Tan & Yifei Lin & Nanwei Xu & Sha Zhu & Junru Chen & Jinge Zhao & Xu Hu & Xiuyi Pan & Ling Nie & Mengni Z, 2025. "Comprehensive molecular profiling of FH-deficient renal cell carcinoma identifies molecular subtypes and potential therapeutic targets," Nature Communications, Nature, vol. 16(1), pages 1-19, December.

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