Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq
Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq
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DOI：
10.1080/2162402x.2020.1737369
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发表时间：
2020-01-01
期刊：
影响因子：
7.2
通讯作者：
Gfeller, David
中科院分区：
文献类型：
--
作者：
Carmona, Santiago J.;Siddiqui, Imran;Gfeller, David
最近的研究提出，肿瘤特异性肿瘤浸润性CD 8（+）T淋巴细胞（CD 8 TIL）可以分为两大类：“耗竭”TIL，其特征在于抑制性受体PD-1和TIM-3的高表达以及转录因子1（Tcf 1）的缺乏;和“记忆样”TIL，具有自我更新能力并且共表达Tcf 1和PD-1。然而，CD 8 TIL中存在的异质性的全面定义尚未明确建立。为了在转录组水平上研究这种异质性，我们对浸润B16小鼠黑色素瘤肿瘤的CD 8 T细胞（包括已知肿瘤特异性的细胞）进行了配对的单细胞RNA和TCR测序。无监督聚类和基因签名分析揭示了四种不同的CD 8 TIL状态-耗尽，记忆样，幼稚和效应记忆样（EM样）-并预测了新的标志物，包括EM样细胞的Ly 6C，通过流式细胞术验证。肿瘤特异性PMEL T细胞主要在耗尽和记忆样状态中发现，但也在EM样状态中发现。此外，T细胞受体测序揭示了耗尽的记忆样和EM样细胞的大量克隆扩增，它们之间具有部分克隆相关性。最后，对公共批量和单细胞RNA-seq数据的荟萃分析表明，抗PD-1治疗诱导了EM样细胞的扩增。我们的鼠CD 8 TILs的转录组学图谱将有助于解释未来的批量和单细胞转录组学研究，并可能指导对治疗干预的CD 8 IL亚群的分析。
Recent studies have proposed that tumor-specific tumor-infiltrating CD8(+) T lymphocytes (CD8 TIL) can be classified into two main groups: "exhausted" TILs, characterized by high expression of the inhibitory receptors PD-1 and TIM-3 and lack of transcription factor 1 (Tcf1); and "memory-like" TILs, with self-renewal capacity and co-expressing Tcf1 and PD-1. However, a comprehensive definition of the heterogeneity existing within CD8 TILs has yet to be clearly established. To investigate this heterogeneity at the transcriptomic level, we performed paired single-cell RNA and TCR sequencing of CD8 T cells infiltrating B16 murine melanoma tumors, including cells of known tumor specificity. Unsupervised clustering and gene-signature analysis revealed four distinct CD8 TIL states - exhausted, memory-like, naive and effector memory-like (EM-like) - and predicted novel markers, including Ly6C for the EM-like cells, that were validated by flow cytometry. Tumor-specific PMEL T cells were predominantly found within the exhausted and memory-like states but also within the EM-like state. Further, T cell receptor sequencing revealed a large clonal expansion of exhausted, memory-like and EM-like cells with partial clonal relatedness between them. Finally, meta-analyses of public bulk and single-cell RNA-seq data suggested that anti-PD-1 treatment induces the expansion of EM-like cells. Our reference map of the transcriptomic landscape of murine CD8 TILs will help interpreting future bulk and single-cell transcriptomic studies and may guide the analysis of CD8IL subpopulations in response to therapeutic interventions.