新辅助化疗可以提高边缘性和不可切除的胰腺导管腺癌患者的生存率；然而，对化疗的不均一反应仍然是一个重要的临床挑战。在这里，我们对未接受化疗的患者样本和术后化疗（chemoradiotherapy除外）切除的患者样本进行了RNA测序（n=97）和多重免疫荧光染色（n=122），以定义新辅助化疗的影响。结合高分辨率的整体组织切片映射的转录组分析，确定了GATA6（经典型）、KRT17（基底样型）和细胞色素P450 3A（CYP3A）共表达细胞在术后化疗切除样本中富集。GATA6高表达和KRT17高表达细胞在化疗后仍然存在与mFOLFIRINOX（mFFX）治疗后的生存不良有明显关联，但与吉西他滨（GEM）治疗无关。从未接受化疗和术后化疗样本衍生的器官模型的分析证明，CYP3A表达是化疗反应的预测因子，而CYP3A表达的药物解毒途径可以代谢mFFX的组分伊立替康。这些发现确定了在残余疾病中表达CYP3A的耐药细胞表型，这最终可能为辅助治疗选择提供信息。© 2023。作者（们）。

Neoadjuvant chemotherapy can improve the survival of individuals with borderline and unresectable pancreatic ductal adenocarcinoma; however, heterogeneous responses to chemotherapy remain a significant clinical challenge. Here, we performed RNA sequencing (n = 97) and multiplexed immunofluorescence (n = 122) on chemo-naive and postchemotherapy (post-CTX) resected patient samples (chemoradiotherapy excluded) to define the impact of neoadjuvant chemotherapy. Transcriptome analysis combined with high-resolution mapping of whole-tissue sections identified GATA6 (classical), KRT17 (basal-like) and cytochrome P450 3A (CYP3A) coexpressing cells that were preferentially enriched in post-CTX resected samples. The persistence of GATA6hi and KRT17hi cells post-CTX was significantly associated with poor survival after mFOLFIRINOX (mFFX), but not gemcitabine (GEM), treatment. Analysis of organoid models derived from chemo-naive and post-CTX samples demonstrated that CYP3A expression is a predictor of chemotherapy response and that CYP3A-expressing drug detoxification pathways can metabolize the prodrug irinotecan, a constituent of mFFX. These findings identify CYP3A-expressing drug-tolerant cell phenotypes in residual disease that may ultimately inform adjuvant treatment selection.© 2023. The Author(s).