Spatial proteomics and transcriptomics reveal early immune cell organization in pancreatic intraepithelial neoplasia

JCI Insight. 2025 Jun 26;10(15):e191595. doi: 10.1172/jci.insight.191595. eCollection 2025 Aug 8.

Abstract

Pancreatic ductal adenocarcinoma (PDAC) has a poor survival rate due to late detection. PDAC arises from precursor microscopic lesions, termed pancreatic intraepithelial neoplasia (PanIN), that develop at least a decade before overt disease; this provides an opportunity to intercept PanIN-to-PDAC progression. However, immune interception strategies require full understanding of PanIN and PDAC cellular architecture. Surgical specimens containing PanIN and PDAC lesions from a unique cohort of 5 treatment-naive patients with PDAC were surveyed using spatial omics (proteomic and transcriptomic). Findings were corroborated by spatial proteomics of PanIN and PDAC from tamoxifen-inducible KPC mice. We uncovered the organization of lymphoid cells into tertiary lymphoid structures (TLSs) adjacent to PanIN lesions. These TLSs lacked CD21+CD23+ B cells compared with more mature TLSs near the PDAC border. PanINs harbored mostly CD4+ T cells, with fewer Tregs and exhausted T cells than PDAC. Peritumoral space was enriched with naive CD4+ and central memory T cells. These observations highlight the opportunity to modulate the immune microenvironment in PanINs before immune exclusion and immunosuppression emerge during progression into PDAC.

Keywords: Adaptive immunity; Cancer immunotherapy; Gastric cancer; Immunology; Inflammation; Oncology.

MeSH terms

  • Animals
  • Carcinoma in Situ* / genetics
  • Carcinoma in Situ* / immunology
  • Carcinoma in Situ* / pathology
  • Carcinoma, Pancreatic Ductal* / genetics
  • Carcinoma, Pancreatic Ductal* / immunology
  • Carcinoma, Pancreatic Ductal* / pathology
  • Disease Progression
  • Female
  • Humans
  • Male
  • Mice
  • Middle Aged
  • Pancreatic Neoplasms* / genetics
  • Pancreatic Neoplasms* / immunology
  • Pancreatic Neoplasms* / pathology
  • Proteomics / methods
  • Tertiary Lymphoid Structures / immunology
  • Tertiary Lymphoid Structures / pathology
  • Transcriptome
  • Tumor Microenvironment / immunology