Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Korea.
Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Korea.
Genome Med. 2020 Feb 28;12(1):22. doi: 10.1186/s13073-020-00722-9.
T cells exhibit heterogeneous functional states in the tumor microenvironment. Immune checkpoint inhibitors (ICIs) can reinvigorate only the stem cell-like progenitor exhausted T cells, which suggests that inhibiting the exhaustion progress will improve the efficacy of immunotherapy. Thus, regulatory factors promoting T cell exhaustion could serve as potential targets for delaying the process and improving ICI efficacy.
We analyzed the single-cell transcriptome data derived from human melanoma and non-small cell lung cancer (NSCLC) samples and classified the tumor-infiltrating (TI) CD8 T cell population based on PDCD1 (PD-1) levels, i.e., PDCD1-high and PDCD1-low cells. Additionally, we identified differentially expressed genes as candidate factors regulating intra-tumoral T cell exhaustion. The co-expression of candidate genes with immune checkpoint (IC) molecules in the TI CD8 T cells was confirmed by single-cell trajectory and flow cytometry analyses. The loss-of-function effect of the candidate regulator was examined by a cell-based knockdown assay. The clinical effect of the candidate regulator was evaluated based on the overall survival and anti-PD-1 responses.
We retrieved many known factors for regulating T cell exhaustion among the differentially expressed genes between PDCD1-high and PDCD1-low subsets of the TI CD8 T cells in human melanoma and NSCLC. TOX was the only transcription factor (TF) predicted in both tumor types. TOX levels tend to increase as CD8 T cells become more exhausted. Flow cytometry analysis revealed a correlation between TOX expression and severity of intra-tumoral T cell exhaustion. TOX knockdown in the human TI CD8 T cells resulted in downregulation of PD-1, TIM-3, TIGIT, and CTLA-4, which suggests that TOX promotes intra-tumoral T cell exhaustion by upregulating IC proteins in cancer. Finally, the TOX level in the TI T cells was found to be highly predictive of overall survival and anti-PD-1 efficacy in melanoma and NSCLC.
We predicted the regulatory factors involved in T cell exhaustion using single-cell transcriptome profiles of human TI lymphocytes. TOX promoted intra-tumoral CD8 T cell exhaustion via upregulation of IC molecules. This suggested that TOX inhibition can potentially impede T cell exhaustion and improve ICI efficacy. Additionally, TOX expression in the TI T cells can be used for patient stratification during anti-tumor treatments, including anti-PD-1 immunotherapy.
T 细胞在肿瘤微环境中表现出异质性的功能状态。免疫检查点抑制剂（ICIs）只能重新激活干细胞样祖细胞耗竭的 T 细胞，这表明抑制耗竭进程将提高免疫疗法的疗效。因此，促进 T 细胞耗竭的调节因子可以作为延迟该过程和提高 ICI 疗效的潜在靶点。
我们分析了来自人类黑色素瘤和非小细胞肺癌（NSCLC）样本的单细胞转录组数据，并根据 PDCD1（PD-1）水平对肿瘤浸润（TI）CD8 T 细胞群体进行分类，即 PDCD1-高和 PDCD1-低细胞。此外，我们鉴定了差异表达的基因作为调节肿瘤内 T 细胞耗竭的候选因子。通过单细胞轨迹和流式细胞术分析，证实了候选基因与 TI CD8 T 细胞中免疫检查点（IC）分子的共表达。通过基于细胞的敲低测定来检验候选调节剂的功能丧失效应。根据总生存期和抗 PD-1 反应评估候选调节剂的临床效果。
我们从人类黑色素瘤和 NSCLC 的 TI CD8 T 细胞的 PDCD1-高和 PDCD1-低亚群之间的差异表达基因中检索到许多已知的调节 T 细胞耗竭的因子。TOX 是在两种肿瘤类型中均预测到的唯一转录因子（TF）。随着 CD8 T 细胞变得更加耗竭，TOX 水平趋于增加。流式细胞术分析显示，TOX 表达与肿瘤内 T 细胞耗竭的严重程度之间存在相关性。TOX 在人 TI CD8 T 细胞中的敲低导致 PD-1、TIM-3、TIGIT 和 CTLA-4 的下调，这表明 TOX 通过上调癌症中的 IC 蛋白促进肿瘤内 T 细胞耗竭。最后，发现 TI T 细胞中的 TOX 水平高度预测黑色素瘤和 NSCLC 的总生存期和抗 PD-1 疗效。
我们使用人类 TI 淋巴细胞的单细胞转录组图谱预测了参与 T 细胞耗竭的调节因子。TOX 通过上调 IC 分子促进肿瘤内 CD8 T 细胞耗竭。这表明 TOX 抑制可能阻碍 T 细胞耗竭并提高 ICI 疗效。此外，在抗肿瘤治疗（包括抗 PD-1 免疫治疗）期间，TI T 细胞中的 TOX 表达可用于患者分层。
