Theranostics 2021; 11(10):4957-4974. doi:10.7150/thno.55075 This issue

Research Paper

Single-cell transcriptome analysis of the heterogeneous effects of differential expression of tumor PD-L1 on responding TCR-T cells

Renpeng Ding1,2*, Shang Liu1,2*, Shanshan Wang1,2*, Huanyi Chen1, Fei Wang1,2, Qumiao Xu1,3, Linnan Zhu1,5, Xuan Dong1,3, Ying Gu1,4, Xiuqing Zhang1,3, Cheng-Chi Chao1✉, Qianqian Gao1,3,5✉

1. BGI-Shenzhen, Shenzhen 518083, China.
2. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
3. Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics.
4. Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518083, China.
5. Shenzhen Bay Laboratory, Shenzhen 518132, China.
*These authors contributed equally to this work.

This is an open access article distributed under the terms of the Creative Commons Attribution License ( See for full terms and conditions.
Ding R, Liu S, Wang S, Chen H, Wang F, Xu Q, Zhu L, Dong X, Gu Y, Zhang X, Chao CC, Gao Q. Single-cell transcriptome analysis of the heterogeneous effects of differential expression of tumor PD-L1 on responding TCR-T cells. Theranostics 2021; 11(10):4957-4974. doi:10.7150/thno.55075. Available from

File import instruction


Graphic abstract

Rationale: TCR-T cell therapy plays a critical role in the treatment of malignant cancers. However, it is unclear how TCR-T cells are affected by PD-L1 molecule in the tumor environment. We performed an in-depth evaluation on how differential expressions of tumor PD-L1 can affect the functionality of T cells.

Methods: We used MART-1-specific TCR-T cells (TCR-TMART-1), stimulated with MART-127-35 peptide-loaded MEL-526 tumor cells, expressing different proportions of PD-L1, to perform cellular assays and high-throughput single-cell RNA sequencing.

Results: Different clusters of activated or cytotoxic TCR-TMART-1 responded divergently when stimulated with tumor cells expressing different percentages of PD-L1 expression. Compared to control T cells, TCR-TMART-1 were more sensitive to exhaustion, and secreted not only pro-inflammatory cytokines but also anti-inflammatory cytokines with increasing proportions of PD-L1+ tumor cells. The gene profiles of chemokines were modified by increased expression of tumor PD-L1, which concurrently downregulated pro-inflammatory and anti-inflammatory transcription factors. Furthermore, increased expression of tumor PD-L1 showed distinct effects on different inhibitory checkpoint molecules (ICMs). In addition, there was a limited correlation between the enrichment of cell death signaling in tumor cells and T cells and increased tumor PD-L1 expression.

Conclusion: Overall, though the effector functionality of TCR-T cells was suppressed by increased expression percentages of tumor PD-L1 in vitro, scRNA-seq profiles revealed that both the anti-inflammatory and pro-inflammatory responses were triggered by a higher expression of tumor PD-L1. This suggests that the sole blockade of tumor PD-L1 might inhibit not only the anti-inflammatory response but also the pro-inflammatory response in the complicated tumor microenvironment. Thus, the outcome of PD-L1 intervention may depend on the final balance among the highly dynamic and heterogeneous immune regulatory circuits.

Keywords: TCR-T, PD-L1, differential expression, single-cell RNA sequencing, melanoma