Neoadjuvant immunotherapy promotes the formation of mature tertiary lymphoid structures in a remodeled pancreatic tumor microenvironment

Pancreatic adenocarcinoma (PDAC) is a rapidly progressing cancer that responds poorly to immunotherapies. Intratumoral tertiary lymphoid structures (TLS) have been associated with rare long-term PDAC survivors, but the role of TLS in PDAC and their spatial relationships within the context of the broader tumor microenvironment remain unknown. Here, we report the generation of a spatial multi-omics atlas of PDAC tumors and tumor-adjacent lymph nodes from patients treated with combination neoadjuvant immunotherapies. Using machine learning–enabled hematoxylin and eosin image classification models, imaging mass cytometry, and unsupervised gene expression matrix factorization methods for spatial transcriptomics, we characterized cellular states within and adjacent to TLS spanning across distinct spatial niches and pathologic responses. Unsupervised learning identified TLS-specific spatial gene expression signatures that significantly associated with improved survival in PDAC patients. We identified spatial features of pathologic immune responses, including intratumoral TLS–associated B-cell maturation colocalizing with IgG dissemination and extracellular matrix remodeling. Our findings offer insights into the cellular and molecular landscape of TLS in PDACs during immunotherapy treatment. Spatial transcriptomics with Visium (10x Genomics) was performed on surgical specimens obtained from patients with pancreatic ductal adenocarcinoma. *************************************************************** Submitter states that missing raw data are being made available for controlled access in dbGaP. ***************************************************************

胰腺导管腺癌（Pancreatic adenocarcinoma, PDAC）是一类进展迅速且对免疫治疗应答不佳的恶性肿瘤。瘤内三级淋巴结构（tertiary lymphoid structures, TLS）已被证实与罕见的胰腺导管腺癌长期存活者相关，但TLS在胰腺导管腺癌中的作用及其在更广泛肿瘤微环境中的空间关联仍未明确。本研究构建了接受新辅助联合免疫治疗的胰腺导管腺癌患者的肿瘤及肿瘤旁淋巴结的空间多组学图谱。研究团队借助机器学习辅助的苏木精-伊红图像分类模型、成像质谱流式细胞术，以及用于空间转录组学的无监督基因表达矩阵分解方法，对不同空间微环境及病理应答状态下，三级淋巴结构内部及其周边的细胞状态进行了系统表征。无监督学习方法鉴定出了TLS特异性空间基因表达特征，该特征与胰腺导管腺癌患者的更长生存期显著相关。研究还发现了病理性免疫应答的空间特征，包括瘤内TLS相关的B细胞成熟与IgG扩散及细胞外基质重塑共定位。本研究结果为免疫治疗期间胰腺导管腺癌中TLS的细胞与分子特征图谱提供了新见解。本研究针对胰腺导管腺癌患者的手术标本开展了基于Visium（10x Genomics）平台的空间转录组学检测。
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数据提交者声明，缺失的原始数据将通过dbGaP数据库进行受控访问。
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