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Cellular and Molecular Biology

Single-cell sequencing reveals VEGFR as a potential target for CAR-T cell therapy in chordoma

British Journal of Cancer (2024)Cite this article

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Abstract

Background

Chordomas are rare osseous neoplasms with a dismal prognosis when they recur. Here we identified cell surface proteins that could potentially serve as novel immunotherapeutic targets in patients with chordoma.

Methods

Fourteen chordoma samples from patients attending Xuanwu Hospital Capital Medical University were subjected to single-cell RNA sequencing. Target molecules were identified on chordoma cells and cancer metastasis-related signalling pathways characterised. VEGFR-targeting CAR-T cells and VEGFR CAR-T cells with an additional TGF-β scFv were synthesised and their in vitro antitumor activities were evaluated, including in a primary chordoma organoid model.

Results

Single-cell transcriptome sequencing identified the chordoma-specific antigen VEGFR and TGF-β as therapeutic targets. VRGFR CAR-T cells and VEGFR/TGF-β scFv CAR-T cells recognised antigen-positive cells and exhibited significant antitumor effects through CAR-T cell activation and cytokine secretion. Furthermore, VEGFR/TGF-β scFv CAR-T cells showed enhanced and sustained cytotoxicity of chordoma cell lines in vitro compared with VRGFR CAR-T cells.

Conclusions

This study provides a comprehensive single-cell landscape of human chordoma and highlights its heterogeneity and the role played by TGF-β in chordoma progression. Our findings substantiate the potential of VEGFR as a target for CAR-T cell therapies in chordoma which, together with modulated TGF-β signalling, may augment the efficacy of CAR-T cells.

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Fig. 1: Single-cell heterogeneity landscape of human chordoma.
Fig. 2: Cell communication network analysis of the chordoma tumour microenvironment.
Fig. 3: Generation and characterisation of VEGFR CAR and VEGFR/TGF-β CAR-T cells.
Fig. 4: VEGFR/TGF-β scFv CAR-T cells enhance anti-tumour cytotoxicity of cells in vitro.
Fig. 5: VEGFR/TGF-β scFv CAR-T cells can manipulate the TME to enhance anti-tumour efficacy.
Fig. 6: The therapeutic efficacy of VEGFR/TGF-β scFv CAR-T cells is superior to VEGFR CAR-T cells when targeting primary chordoma cells.

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Data availability

The datasets generated and analysed during this study are publicly accessible from the NGDC Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa-human/), accession number HRA006471.

Code availability

Additionally, the code utilised in our study is available from a dedicated GitHub repository, accessible at https://github.com/restore1997/chordoma2024.

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Funding

This work was supported by Beijing Natural Science Foundation Grant (L212039), National High Level Hospital Clinical Research Funding (2022-PUMCH-D-004), Beijing Hospitals Authority Clinical Medicine Development of Special Funding Support (XMLX202138), The “Young Talents” Programme, supported by Beijing Municipal Hospital Administration (QML20210801), the Research and Application of Clinical Characteristic Diagnosis and Treatment Programme, Supported by Beijing Municipal Science & Technology Commission (Z221100007422019), and the CAMS Innovation Fund for Medical Sciences (CIFMS #2021-1-I2M-025).

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Author notes

  1. These authors contributed equally: Huantong Wu, Xinqiang Li, Boyan Zhang.

Authors and Affiliations

  1. Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China

    Huantong Wu, Boyan Zhang, Penghao Liu, Maoyang Qi, Yueqi Du, Can Zhang, Wanru Duan & Zan Chen

  2. Lab of Spinal Cord, Injury and Functional Reconstruction, China International Neuroscience Institute (CHINA-INI), Beijing, China

    Huantong Wu, Boyan Zhang, Penghao Liu, Maoyang Qi, Yueqi Du, Can Zhang, Wanru Duan & Zan Chen

  3. Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China

    Xinqiang Li

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Contributions

Zan Chen, Wanru Duan, Huantong Wu, and Xinqiang Li contributed to study’s conception and design. Huantong Wu, Xinqiang Li, Boyan Zhang, Penghao Liu, Maoyang Qi, Yueqi Du, Can Zhang performed the experiments and analysed the data. Zan Chen, Wanru Duan, Huantong Wu, Xinqiang Li, and Boyan Zhang wrote and revised the manuscript. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Wanru Duan or Zan Chen.

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The authors declare no competing interests.

Ethics approval and consent to participate

This study was approved by the Medical Ethics Committee of Xuanwu Hospital, Capital Medical University, Beijing, China (Ethics Committee Approval No: [2021]021). Informed consent was obtained from all individual participants included in the study. The study was performed in accordance with the Declaration of Helsinki.

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Wu, H., Li, X., Zhang, B. et al. Single-cell sequencing reveals VEGFR as a potential target for CAR-T cell therapy in chordoma. Br J Cancer (2024). https://doi.org/10.1038/s41416-024-02635-5

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