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Integrated transcriptome study of the tumor microenvironment for treatment response prediction in male predominant hypopharyngeal carcinoma

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  • Yang Zhang

    (Beijing Tongren Hospital, Capital Medical University, Key Laboratory of Otolaryngology Head and Neck Surgery (Capital Medical University), Ministry of Education)

  • Gan Liu

    (Tsinghua University
    Tsinghua University)

  • Minzhen Tao

    (Tsinghua University)

  • Hui Ning

    (Tsinghua University)

  • Wei Guo

    (Beijing Tongren Hospital, Capital Medical University, Key Laboratory of Otolaryngology Head and Neck Surgery (Capital Medical University), Ministry of Education)

  • Gaofei Yin

    (Beijing Tongren Hospital, Capital Medical University, Key Laboratory of Otolaryngology Head and Neck Surgery (Capital Medical University), Ministry of Education)

  • Wen Gao

    (Beijing Tongren Hospital, Capital Medical University, Key Laboratory of Otolaryngology Head and Neck Surgery (Capital Medical University), Ministry of Education)

  • Lifei Feng

    (Beijing Tongren Hospital, Capital Medical University, Key Laboratory of Otolaryngology Head and Neck Surgery (Capital Medical University), Ministry of Education)

  • Jin Gu

    (Tsinghua University)

  • Zhen Xie

    (Tsinghua University)

  • Zhigang Huang

    (Beijing Tongren Hospital, Capital Medical University, Key Laboratory of Otolaryngology Head and Neck Surgery (Capital Medical University), Ministry of Education)

Abstract

The efficacy of the first-line treatment for hypopharyngeal carcinoma (HPC), a predominantly male cancer, at advanced stage is only about 50% without reliable molecular indicators for its prognosis. In this study, HPC biopsy samples collected before and after the first-line treatment are classified into different groups according to treatment responses. We analyze the changes of HPC tumor microenvironment (TME) at the single-cell level in response to the treatment and identify three gene modules associated with advanced HPC prognosis. We estimate cell constitutions based on bulk RNA-seq of our HPC samples and build a binary classifier model based on non-malignant cell subtype abundance in TME, which can be used to accurately identify treatment-resistant advanced HPC patients in time and enlarge the possibility to preserve their laryngeal function. In summary, we provide a useful approach to identify gene modules and a classifier model as reliable indicators to predict treatment responses in HPC.

Suggested Citation

  • Yang Zhang & Gan Liu & Minzhen Tao & Hui Ning & Wei Guo & Gaofei Yin & Wen Gao & Lifei Feng & Jin Gu & Zhen Xie & Zhigang Huang, 2023. "Integrated transcriptome study of the tumor microenvironment for treatment response prediction in male predominant hypopharyngeal carcinoma," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37159-8
    DOI: 10.1038/s41467-023-37159-8
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    1. Nayoung Kim & Hong Kwan Kim & Kyungjong Lee & Yourae Hong & Jong Ho Cho & Jung Won Choi & Jung-Il Lee & Yeon-Lim Suh & Bo Mi Ku & Hye Hyeon Eum & Soyean Choi & Yoon-La Choi & Je-Gun Joung & Woong-Yang, 2020. "Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    2. Roser Vento-Tormo & Mirjana Efremova & Rachel A. Botting & Margherita Y. Turco & Miquel Vento-Tormo & Kerstin B. Meyer & Jong-Eun Park & Emily Stephenson & Krzysztof Polański & Angela Goncalves & Lucy, 2018. "Single-cell reconstruction of the early maternal–fetal interface in humans," Nature, Nature, vol. 563(7731), pages 347-353, November.
    3. Yang Liu & Shuai He & Xi-Liang Wang & Wan Peng & Qiu-Yan Chen & Dong-Mei Chi & Jie-Rong Chen & Bo-Wei Han & Guo-Wang Lin & Yi-Qi Li & Qian-Yu Wang & Rou-Jun Peng & Pan-Pan Wei & Xiang Guo & Bo Li & Xi, 2021. "Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    4. Yingyao Zhou & Bin Zhou & Lars Pache & Max Chang & Alireza Hadj Khodabakhshi & Olga Tanaseichuk & Christopher Benner & Sumit K. Chanda, 2019. "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
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    1. Aleksandr Ianevski & Kristen Nader & Kyriaki Driva & Wojciech Senkowski & Daria Bulanova & Lidia Moyano-Galceran & Tanja Ruokoranta & Heikki Kuusanmäki & Nemo Ikonen & Philipp Sergeev & Markus Vähä-Ko, 2024. "Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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