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Single-cell transcriptome profiling reveals intra-tumoral heterogeneity in human chordomas

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Abstract

Chordoma is a rare and aggressive bone tumor. An accurate investigation of tumor heterogeneity is necessary for the development of effective therapeutic strategies. This study aims to assess the poorly understood tumor heterogeneity of chordomas and identify potential therapeutic targets. Single-cell RNA sequencing was performed to delineate the transcriptomic landscape of chordomas. Six tumor samples of chordomas were obtained, and 33,737 cells passed the quality control test and were analyzed. The main cellular populations identified with specific markers were as follows: chordoma cells (16,052 [47.6%]), fibroblasts (6945 [20.6%]), mononuclear phagocytes (4734 [14.0%]), and T/natural killer (NK) cells (3944 [11.7%]). Downstream analysis of each cell type was performed. Six subclusters of chordomas exhibited properties of an epithelial-like extracellular matrix, stem cells, and immunosuppressive activity. Although few immune checkpoints were detected on cytotoxic immune cells such as T and NK cells, a strong immunosuppressive effect was exerted on the Tregs and M2 macrophages. In addition, the cellular interactions were indicative of enhancement of the TGF-β signaling pathway being the main mechanism for tumor progression, invasion, and immunosuppression. These findings, especially from the analysis of molecular targeted therapy and tumor immune microenvironment, may help in the identification of therapeutic targets in chordomas.

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Code availability

All scripts used are available at https://github.com/restore1997/chordoma.

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Acknowledgements

We acknowledge the contributions of specific colleagues, institutions, or agencies that aided the authors' efforts.

Funding

CAMS/PUMC Research Project #201920200501, Human Brain Tissue Bank Platform for Neurological Diseases.

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Authors and Affiliations

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

    Wanru Duan, Boyan Zhang, Shanhang Jia, Zong Xin, Qiang Jian, Fengzeng Jian & Zan Chen

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

    Wanru Duan, Fengzeng Jian & Zan Chen

  3. Department of Liver Transplantation, The Affiliated Hospital of Qingdao University, Qingdao, China

    Xinqiang Li

  4. Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China

    Wei Chen

  5. Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA

    Dean Chou

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  1. Wanru Duan
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Contributions

ZC involved in conception and design; WD and BZ took part in collection and assembly of data; WD and XL involved in data analysis and interpretation; all authors involved in manuscript writing and approval of the manuscript.

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Correspondence to Zan Chen.

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Supplementary Information

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262_2022_3152_MOESM1_ESM.pdf

Fig. S1 Immumohistochemical staining, A Hematoxylin-eosin staining results of chordoma tissues, B Immunohistochemistry of Brachyury staining of chordoma tissues (PDF 891 kb)

262_2022_3152_MOESM2_ESM.pdf

Fig. S2 Quality control process A Violin plots showing cell infiltration using nFeature_RNA, nCount_RNA, and percent_mt, B Dot plots showing the feature-feature relationships (PDF 507 kb)

262_2022_3152_MOESM3_ESM.pdf

Fig. S3 Visualization of all the cells based on sample and site, A UMAP plots of all the cells colored by samples, B UMAP plots of all the cells colored by site, C Bar plots showing the proportion of the identified cell types in various locations (PDF 1186 kb)

262_2022_3152_MOESM4_ESM.pdf

Fig. S4 Supplementary transcriptomic heterogeneity of tumor cells, A UMAP plot of tumor cells colored by samples, B UMAP plot of tumor cells colored by site, C Violin plots showing the expression of the immune checkpoints, D Bar plots showing the functional enrichment analysis of GO terms for each cluster of tumor cells, E Violin plots showing the expression of CDKN2A, F The ordering of tumor cells along pseudotime in a two-dimensional state space (colored by pseudotime), GO, Gene Ontology (PDF 1660 kb)

262_2022_3152_MOESM5_ESM.pdf

Fig. S5 Clustering and subtype analysis of supplementary T and NK cells, A UMAP plots of T and NK cells colored by samples, B UMAP plots of T and NK cells colored by site (PDF 5298 kb)

262_2022_3152_MOESM6_ESM.pdf

Fig. S6 The significant signaling pathways in the interplay between distinct cells, A The alluvial plot showing the outgoing (left) and incoming (right) signaling patterns of distinct cells, B Circle plot showing the significant inferred signaling networks (PDF 3809 kb)

Supplementary file7 (PDF 21 kb)

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Duan, W., Zhang, B., Li, X. et al. Single-cell transcriptome profiling reveals intra-tumoral heterogeneity in human chordomas. Cancer Immunol Immunother 71, 2185–2195 (2022). https://doi.org/10.1007/s00262-022-03152-1

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