Spatial Proteomics and Transcriptomics Reveal Early Immune Cell Organization in Pancreatic Intraepithelial Neoplasia

Background: Pancreatic ductal adenocarcinoma (PDAC) has a poor survival rate largely due to late detection of disease. PDAC arises from precursor microscopic lesions, termed pancreatic intraepithelial neoplasia (PanIN), that develop at least a decade before overt disease progression––this provides an opportunity to intercept PanIN–to–PDAC progression. However, immune interception strategies require a full understanding of PanIN and PDAC cellular architecture. Methods: Surgical specimens containing PanIN and PDAC lesions from a unique cohort of treatment-naïve patients with PDAC were surveyed using spatial-omics (proteomic and transcriptomic). Results: We uncovered, for the first time, the organization of lymphoid cells into tertiary lymphoid structures (TLSs) adjacent to PanIN lesions. These TLSs lack CD21+CD23+ B cells in comparison to more mature TLSs. Mature TLSs were found near the invasive PDAC border, despite patients being treatment-naïve. PanINs harbored mostly CD4+ T cells with fewer Tregs and exhausted T cells than PDAC tumors. Peri-tumoral space was enriched with naïve CD4+ and central memory T cells. Conclusions: These data show that early PanIN lesions recruit effector lymphoid populations capable of organizing into immature TLSs with few immune suppressive T cells relative to PDAC-associated TLS. These results implicate the opportunity to modulate the immune microenvironment in pre–malignant PanINs before immune exclusion and immunosuppression emerge during progression into PDACs. Resected pancreas tissue from 5 treatment-naïve patients with PanIN and chronic pancreatitis in association with pancreatic ductal adenocarcinoma (PDAC) underwent profiling of immune infiltrates surrounding these lesions. Infiltrates surrounding normal pancreatic ducts, PanIN ducts, PDAC tumors, and regions of chronic pancreatitis were profiled and compared by imaging mass cytometry and Visium spatial transcriptomics. Visium spatial transcriptomic data from samples CP04, CP05B, NRL04, PANIN02A, PANIN02B, PANIN04, and PANIN03 are available from GEO accession GSE254829 (GSM8058249 - GSM8058255, respectively). *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. ***************************************************************