Single-cell transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinoma

• Published in: Cell research Vol. 30; no. 11; pp. 950 - 965
• Main Authors: Jin, Shanzhao, Li, Ruoyan, Chen, Ming-Yuan, Yu, Chao, Tang, Lin-Quan, Liu, Yan-Min, Li, Jiang-Ping, Liu, Yi-Na, Luo, Yi-Ling, Zhao, Yifan, Zhang, Yu, Xia, Tian-Liang, Liu, Shang-Xin, Liu, Qi, Wang, Guan-Nan, You, Rui, Peng, Jing-Yun, Li, Jiang, Han, Feng, Wang, Jianwei, Chen, Qiu-Yan, Zhang, Li, Mai, Hai-Qiang, Gewurz, Benjamin E., Zhao, Bo, Young, Lawrence S., Zhong, Qian, Bai, Fan, Zeng, Mu-Sheng
• Format: Journal Article
• Language: English
• Published: Singapore Springer Singapore 01-11-2020; Nature Publishing Group
• Subjects: 13/31; 13/51; 38/32; 38/39; 631/67/327; 631/67/69; 64/60; 82/1; Biomedical and Life Sciences; CD8 antigen; Cell Biology; Ecosystems; Epstein-Barr virus; Gene sequencing; Immune system; Interferon; Life Sciences; Lymphocytes; Lymphocytes T; Malignancy; Nasopharyngeal carcinoma; Ribonucleic acid; RNA; Throat cancer; Tumor cells; Tumorigenesis; Tumors; γ-Interferon
• ISSN: 1001-0602; 1748-7838
• DOI: 10.1038/s41422-020-00402-8

Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignancy with a complex tumor ecosystem. How the interplay between tumor cells, EBV, and the microenvironment contributes to NPC progression and immune evasion remains unclear. Here we performed single-cell RNA sequencing on ~104,000 cells from 19 EBV
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NPCs and 7 nonmalignant nasopharyngeal biopsies, simultaneously profiling the transcriptomes of malignant cells, EBV, stromal and immune cells. Overall, we identified global upregulation of interferon responses in the multicellular ecosystem of NPC. Notably, an epithelial–immune dual feature of malignant cells was discovered and associated with poor prognosis. Functional experiments revealed that tumor cells with this dual feature exhibited a higher capacity for tumorigenesis. Further characterization of the cellular components of the tumor microenvironment (TME) and their interactions with tumor cells revealed that the dual feature of tumor cells was positively correlated with the expression of co-inhibitory receptors on CD8
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tumor-infiltrating T cells. In addition, tumor cells with the dual feature were found to repress IFN-γ production by T cells, demonstrating their capacity for immune suppression. Our results provide new insights into the multicellular ecosystem of NPC and offer important clinical implications.