Exploratory single‐nucleus multiomics analysis of myeloid cell states associated with neoadjuvant chemotherapy response in pancreatic ductal adenocarcinoma

Abstract

Abstract Background Pancreatic ductal adenocarcinoma (PDAC) continues to be one of the most lethal human malignancies, with the vast majority of patients ineligible for immunotherapy. Tumour‐associated macrophages (TAMs) are key regulators of the PDAC tumour microenvironment (TME), yet their transcriptional and epigenomic heterogeneity in the context of chemotherapy response is poorly understood. Therefore, we performed an exploratory single nucleus multiomics analysis of PDAC tumors stratified by histopathologic response to neoadjuvant chemotherapy. Methods Surgical resection specimens from PDAC patients were classified as responders or non‐responders using the American College of Pathologists (CAP) histopathologic criteria. Frozen tissue underwent simultaneous snRNA‐seq and snATAC‐seq on the 10x Genomics Chromium Single Cell Multiome platform, followed by downstream analyses such as differential gene expression, GO and hallmark pathway enrichment, pseudotime trajectory inference and ChromVAR transcription factor motif analysis. Results Multiomics profiling of 30 840 high‐quality nuclei revealed a myeloid compartment that differed in composition and transcriptional state between CAP‐defined responders and non‐responders in this small cohort. We observed a trend toward higher LAM‐like state proportions in the responders than non‐responders (38.4% vs. 26.7%), although this disparity did not achieve statistical significance. The transcriptional programs of the responder myeloid cells are associated with phagocytosis and lipid handling. Chromatin accessibility analysis further suggested candidate response‐associated transcription factor motif accessibility patterns. Conclusions Neoadjuvant‐treated PDAC tumours from CAP‐defined responders in this cohort myeloid landscape with apparent enrichment of LAM‐like states and immune‐activating transcriptional/epigenetic programs. However, these findings are preliminary and hypothesis‐generating because of the small cohort size, heterogeneous treatment regimens, absence of matched pre‐treatment biopsies, and lack of knockout validation. Larger treatment cohorts and functional/mechanistic studies are needed to determine whether LAM‐like myeloid programs contribute to chemotherapy response or reflect a consequence of chemotherapy treatment.