Multi-omics analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 antibody. Multi-omics analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 antibody

Successful pancreatic ductal adenocarcinoma (PDAC) immunotherapy necessitates optimization and maintenance of activated effector T cells (Teffs). We prospectively collected and applied multi-omics analysis to paired, pre- and post-treatment PDAC specimens collected in a platform neoadjuvant study of GVAX vaccine +/- nivolumab (anti-PD-1) to uncover sensitivity and resistance mechanisms. We show that GVAX-induced tertiary lymphoid aggregates become immune-regulatory sites in response to GVAX+nivolumab. Higher densities of tumor-associated neutrophils (TANs) following GVAX+nivolumab portend poorer overall survival (OS). Increased T cells expressing CD137 associated with cytotoxic Teff signatures and correlated with increased OS. Bulk and single-cell RNA-sequencing found that nivolumab alters CD4+ T cell chemotaxis signaling in association with CD11b+ neutrophil degranulation, and CD8+ T cell expression of CD137 required for optimal T cell activation. These findings provide new insights into PD-1-regulated immune pathways in PDAC that should inform more effective therapeutic combinations that include TAN regulators and T cell activators. Overall design: Examination of patients participating in the studied clinical trial (NCT02451982). Read counts used in Cancer Cell available as GSE197613_NewGeneCounts.txt.gz and used for the normalization in JEM as GSE197613_JEM_counts_combined_TIIC-RNA-seq.txt.gz and GSE197613_JEM_gene_logtpm_filtered_TMM_qn_normalized_nivo_select_TIIC-RNA-seq.txt.gz. **RAW data will be submitted to dbGAP**

胰腺导管腺癌（pancreatic ductal adenocarcinoma, PDAC）的免疫治疗成功实施，有赖于优化并维持活化效应T细胞（activated effector T cells, Teffs）的状态。本研究针对一项采用GVAX疫苗联合/不联合纳武利尤单抗（anti-PD-1）的新辅助平台临床试验，前瞻性采集了配对的PDAC治疗前后标本，并通过多组学分析揭示该疗法的敏感性与耐药机制。研究发现，GVAX诱导的三级淋巴结构在接受GVAX联合纳武利尤单抗治疗后，会转变为免疫调节位点。GVAX联合纳武利尤单抗治疗后，肿瘤相关中性粒细胞（tumor-associated neutrophils, TANs）的浸润密度越高，预示患者总生存期（overall survival, OS）越差。表达CD137的T细胞增多与细胞毒性Teffs特征相关，且与更长的总生存期呈正相关。批量RNA测序与单细胞RNA测序结果显示，纳武利尤单抗可改变CD4+T细胞的趋化信号通路，该改变与CD11b阳性中性粒细胞脱颗粒相关；同时，CD8+T细胞的CD137表达是实现最佳T细胞活化的必要条件。本研究结果为PDAC中PD-1调控的免疫通路提供了全新见解，可为开发包含肿瘤相关中性粒细胞调节剂与T细胞活化剂的更高效治疗联合方案提供指导。

实验设计概述：本研究纳入参与目标临床试验（注册号NCT02451982）的患者样本进行分析。刊载于《Cancer Cell》的读段计数数据以GSE197613_NewGeneCounts.txt.gz文件形式公开；用于《实验医学杂志》（Journal of Experimental Medicine, JEM）标准化分析的数据分别为GSE197613_JEM_counts_combined_TIIC-RNA-seq.txt.gz与GSE197613_JEM_gene_logtpm_filtered_TMM_qn_normalized_nivo_select_TIIC-RNA-seq.txt.gz。
**原始数据将提交至dbGAP数据库**