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Comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers

Author

Listed:
  • Ryosuke Jikuya

    (Yokohama City University Graduate School of Medicine, Department of Urology
    RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics)

  • Todd A. Johnson

    (RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics)

  • Erika Muraoka

    (Yokohama City University Graduate School of Medicine, Department of Molecular Pathology)

  • Go Noguchi

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Shigekatsu Maekawa

    (Iwate Medical University, Department of Urology, School of Medicine)

  • Wataru Obara

    (Iwate Medical University, Department of Urology, School of Medicine)

  • Kazuyuki Numakura

    (Akita University Graduate School of Medicine, Department of Urology)

  • Tomonori Habuchi

    (Akita University Graduate School of Medicine, Department of Urology)

  • Kazuhiro Maejima

    (RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics)

  • Shota Sasagawa

    (RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics)

  • Yuki Kanazashi

    (RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics)

  • Hwajin Lee

    (Kyung Hee University, Department of Biomedical Science
    Kyung Hee University, Department of Precision Medicine
    Kyung Hee University, Department of Biochemistry and Molecular Biology)

  • Woo Jeung Song

    (Kyung Hee University, Department of Biomedical Science)

  • Hajime Sasagawa

    (RIKEN Center for Integrative Medical Sciences, Laboratory for Genotyping Development)

  • Taku Mitome

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Shinji Ohtake

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Sachi Kawaura

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Yasuhiro Iribe

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Kota Aomori

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Hirotaka Nagasaka

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Tomoyuki Tatenuma

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Daiki Ueno

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Mitsuru Komeya

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Hiroki Ito

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Yusuke Ito

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Kentaro Muraoka

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Takashi Kawahara

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Mitsuko Furuya

    (Hokkaido University Hospital, Department of Surgical Pathology)

  • Ikuma Kato

    (Yokohama City University Graduate School of Medicine, Department of Molecular Pathology)

  • Haruka Hamanoue

    (Yokohama City University Graduate School of Medicine, Clinical Genetics Department)

  • Akira Nishiyama

    (Yokohama City University Graduate School of Medicine, Department of Immunology
    Yokohama City University Graduate School of Medicine, Advanced Medical Research Center)

  • Tomohiko Tamura

    (Yokohama City University Graduate School of Medicine, Department of Immunology
    Yokohama City University Graduate School of Medicine, Advanced Medical Research Center)

  • Masaya Baba

    (Kumamoto University, Laboratory of Cancer Metabolism, International Research Center for Medical Sciences)

  • Toshio Suda

    (Kumamoto University, Laboratory of Cancer Metabolism, International Research Center for Medical Sciences)

  • Tatsuhiko Kodama

    (University of Tokyo, Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology)

  • Takehiko Ogawa

    (Yokohama City University, Department of Regenerative Medicine)

  • Hiroji Uemura

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Masahiro Yao

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Toyonori Tsuzuki

    (Aichi Medical University Hospital, Department of Surgical Pathology)

  • Yoji Nagashima

    (Tokyo Women’s Medical University, Department of Surgical Pathology)

  • Yuji Miura

    (The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Department of Medical Oncology)

  • Go Kimura

    (Nippon Medical School, Department of Urology)

  • Seiya Imoto

    (University of Tokyo, Human Genome Center, Institute of Medical Science)

  • Yukihide Momozawa

    (RIKEN Center for Integrative Medical Sciences, Laboratory for Genotyping Development)

  • Satoshi Fujii

    (Yokohama City University Graduate School of Medicine, Department of Molecular Pathology)

  • Kazuhide Makiyama

    (Yokohama City University Graduate School of Medicine, Department of Urology)

  • Takanori Hasegawa

    (Institute of Science Tokyo, M&D Data Science Center, Institute of Integrated Research)

  • Brian M. Shuch

    (UCLA School of Medicine, Institute of Urologic Oncology)

  • Christopher J. Ricketts

    (National Institutes of Health, Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute)

  • Laura S. Schmidt

    (National Institutes of Health, Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute
    Frederick National Laboratory for Cancer Research, Basic Science Program)

  • W. Marston Linehan

    (National Institutes of Health, Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute)

  • Hidewaki Nakagawa

    (RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics)

  • Hisashi Hasumi

    (Yokohama City University Graduate School of Medicine, Department of Urology)

Abstract

There is a great unmet medical need for development of molecularly characterizing modalities to assist in the complex classification of rare kidney cancers, some of which are diagnosed as unclassified renal cell carcinoma (unclassified RCC) due to complex histology. Here we show utility of the comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers. Whereas whole genome sequencing (WGS) of 52 rare kidney cancers identifies very few clinically significant variants in a subset of cases, unsupervised clustering results of RNA-seq data from 219 renal tumors including 140 rare kidney cancers are largely consistent with the histological classification based on WHO2022 classification. Additionally, the comparative transcriptome atlas may provide an opportunity to define the molecular characteristics of unclassified RCC and might predict patient outcome. These findings support the comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers.

Suggested Citation

  • Ryosuke Jikuya & Todd A. Johnson & Erika Muraoka & Go Noguchi & Shigekatsu Maekawa & Wataru Obara & Kazuyuki Numakura & Tomonori Habuchi & Kazuhiro Maejima & Shota Sasagawa & Yuki Kanazashi & Hwajin L, 2025. "Comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-65303-z
    DOI: 10.1038/s41467-025-65303-z
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