Protocol for identifying immune checkpoint on circulating tumor cells of human pancreatic ductal adenocarcinoma by single-cell RNA sequencing

Circulating tumor cells (CTCs) are regarded as the "seeds" of tumor metastasis. Identifying immune checkpoints on CTCs is essential for establishing efficient immunotherapies to prevent tumor metastasis. Here, we present a protocol for isolating CTCs and obtaining single-cell suspensions from pancreatic ductal adenocarcinoma liver metastatic patients. We describe steps for biospecimen acquisition, CTC isolation, and tissue dissociation. We then detail procedures for performing single-cell RNA-seq, annotating cell types, and identifying immune checkpoints on CTCs. For complete details on the use and execution of this protocol, please refer to Liu et al. (2023).1