Single-cell transcriptional dissection illuminates an evolution of immunosuppressive microenvironment during pancreatic ductal adenocarcinoma metastasis

How the host immune system loses its surveillance function during the evolution from normal cell to malignancy is still largely unknown. Here, we investigate the dynamics changes of the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment by profiling 132,115 single-cell transcriptomes derived from 51 tissues, including healthy pancreatic tissue, non-metastatic PDAC primary tumors, metastatic primary tumors, and patient-matched liver metastases. The cellular proportion, bio-functional, and interaction between each cell type are carefully characterized. Aberrant copy number variations (CNVs) indicating malignant intensity are identified at chromosomes 7 and 20 of epithelial cells during tumor development. A bio-functional transition of predominant genes from physiology to pancreatic oncogenesis and metastasis is observed. Combinatorial analysis of epithelial cells and immunocytes indicates a gradient loss of immune surveillance during the malignant transformation. By dissecting cellular interaction, we unravel an incremental tumor cell-triggered apoptosis of DCs through molecular pair ANXA1-FPR1/3. Consequently, the activation and infiltration of cytotoxic CD8⁺ T cells are dampened progressively. Remarkably, we unveil a novel subtype of stress-response NK cells (strNK), which are characterized by robust proliferation, diminished cytolytic capabilities, and negative immune regulation. Notably, the presence of strNK cells is associated with poor prognosis of PDAC patients, implying a potential pro-tumor function. Taken together, our results not only shed light on the intricate mechanisms underlying step-wise evasion of immune surveillance during PDAC tumor development, but also provide a potential strategy for holding back malignant transition by reinforcing DCs' function.