Single‐cell transcriptomic analysis reveals a metastasis‐associated PCSK1 + neuroendocrine subpopulation in pancreatic neuroendocrine tumors

Abstract Pancreatic neuroendocrine tumors (PNETs) are uncommon malignancies characterized by significant clinical heterogeneity and a pronounced tendency for liver metastasis. Despite this, the cellular mechanisms driving PNET progression remain inadequately elucidated, especially concerning neuroendocrine subpopulations. We analyzed publicly available single‐cell RNA sequencing (scRNA‐seq) data from 27 samples, including adjacent normal tissues (NT), primary tumors (PT), and hepatic metastases (HM), to explore the heterogeneity of neuroendocrine cells. Our downstream analyses encompassed copy number variation (CNV) inference, pseudotime trajectory modeling using CytoTRACE2 and Monocle3, Single‐Cell Regulatory Network Inference and Clustering (SCENIC), cell–cell communication analysis via CellChat, and external validation with bulk RNA‐seq datasets. We identified a distinct PCSK1 + neuroendocrine cell subpopulation, predominantly found in HM, which exhibited a high CNV burden, low differentiation potential, and significant transcriptional divergence from the NEUROD1 + neuroendocrine cells prevalent in primary tumors. The trajectory analysis delineated a developmental continuum commencing from the NEUROD1 + subpopulation and culminating in the PCSK1 + subpopulation. SCENIC analysis identified ATF6 as a pivotal transcriptional regulator within the PCSK1 + subpopulation, while KEGG enrichment of its target genes indicated involvement in stress‐related signaling pathways. Furthermore, cell–cell communication analysis demonstrated that fibroblasts were the predominant signaling source to the PCSK1 + subpopulation in both primary tumors (PT) and hepatic metastases (HM), with conserved ligand–receptor interactions, including the CD99–CD99 and collagen–integrin axes. Our study identifies a metastasis‐enriched, terminally differentiated PCSK1 + subpopulation and elucidates its potential regulatory and microenvironmental characteristics. These findings enhance our understanding of the cellular states linked to the progression of PNETs and lay the groundwork for subsequent mechanistic investigations.