Cancer-specific CD8 T cell frequency at baseline in blood correlates with response to PD-1 blockade in Merkel cell carcinoma.. Cancer-specific CD8 T cell frequency at baseline in blood correlates with response to PD-1 blockade in Merkel cell carcinoma.

Understanding immunotherapy resistance is challenging due to difficulty identifying cancer-specific T cells. Merkel cell carcinoma (MCC) is typically driven by Merkel cell polyomavirus (MCPyV), facilitating identification of cancer-specific T cells across patients. We characterized cancer-specific T cells in 35 MCC patients, including participants in a neoadjuvant anti-PD-1 trial. Higher MCPyV-specific CD8 T-cell frequency in pre-treatment blood (but not tumors) correlated with response (p=0.005). Single-cell transcriptomics revealed MCPyV-specific CD8 T cells in blood had increased stem/memory signatures and decreased exhaustion signatures relative to their intratumoral counterparts. While frequency of peripheral cancer-specific T cells was associated with response to initial PD-(L)1 blockade, longitudinal study of acquired resistance revealed immune evasion by tumor-cell MHC-I downregulation despite cancer-specific T cell expansion to 0.5% in blood. Blood thus appears to be an important reservoir of cancer-specific CD8 T cells and adoptive cell therapies may be particularly effective in patients without such cells. Overall design: We used 10x Genomic's Chromium Single Cell 5' Reagent Kits (v1.1 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein and Immune Receptor to identify antigen specific T cell V(D)J sequences. This was performed on tumor and blood specimen taken from 7 pateints. Due to patient privacy concerns, only processed and not raw sequencing reads were deposited. ***raw data were not included due to patient privacy regulations***

由于难以鉴定癌症特异性T细胞，解析免疫治疗耐药性机制颇具挑战。默克尔细胞癌（Merkel cell carcinoma, MCC）通常由默克尔细胞多瘤病毒（Merkel cell polyomavirus, MCPyV）驱动，这使得跨患者群体的癌症特异性T细胞鉴定工作更为便捷。我们对35例默克尔细胞癌患者的癌症特异性T细胞进行了特征分析，其中包含参与新辅助抗PD-1临床试验的受试者。治疗前外周血中MCPyV特异性CD8 T细胞的频率（而非肿瘤组织中）与治疗应答呈显著正相关（p=0.005）。单细胞转录组测序分析显示，相较于肿瘤内的MCPyV特异性CD8 T细胞，外周血中的此类细胞具有更高的干细胞/记忆特征评分与更低的耗竭特征评分。尽管外周癌症特异性T细胞频率与初始PD-(L)1阻断治疗的应答相关，但针对获得性耐药的纵向研究显示，即便外周血中癌症特异性T细胞扩增至0.5%，肿瘤细胞仍可通过下调MHC-I分子实现免疫逃逸。由此可见，外周血是癌症特异性CD8 T细胞的重要储存库，而过继性细胞疗法在缺乏此类细胞的患者中或可展现出更优的治疗效果。

整体实验设计：我们采用10x Genomics的Chromium单细胞5'试剂试剂盒（v1.1化学双索引版本），结合用于细胞表面蛋白与免疫受体检测的特征条形码标记技术，鉴定抗原特异性T细胞的V(D)J序列。该实验针对7例患者的肿瘤与外周血样本开展。出于患者隐私保护考量，本数据集仅上传了处理后的测序读数，未包含原始测序数据。***由于患者隐私相关法规要求，未提交原始数据***