High-Dimensional Protein Analysis Uncovers Distinct Immunological and Stromal Features in Primary and Metastatic Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumor type with poor patient outcomes. Most patients present with metastatic disease, which generally has reduced immune infiltration compared to primary tumors. Further work to elucidate the specific cellular features of metastatic PDAC is needed to guide the development of future immunotherapy strategies. Here, we investigated the hypothesis that PDAC tumors harbor distinct immunologic and stromal features depending on their anatomical site. Multiplex immunohistochemistry (mIHC), spatial analysis, and single-cell mass cytometry (CyTOF) uncovered dominant immune and stromal cell populations in tumors derived from 27 primary and 26 liver metastases. Metastatic liver tumors from PDAC patients contained reduced T cell infiltration, fibroblast populations, and collagen accumulation than primary lesions, while CD68+ cells, often co-expressing CCR2, were more abundant. Spatial analyses revealed distinct immune cell communities in primary and metastatic PDAC, whereby CK19+ cells clustered differentially with α-SMA+, CD3+, and CD68+ cells, depending on the tumor site. When comparing tumor-associated regions, the proportion of peritumoral CK19- cells remained consistent, but their composition varied by disease site. CD8+ T cells were significantly less frequent in metastatic tumors, while both CD4+ and CD8+ T cells present in primary tumors expressed more transcription factors (TFs) associated with suppressive properties, including FoxP3 and RORγt. CyTOF revealed that T cells co-expressed multiple inhibitory checkpoint receptors, most notably LAG-3 and PD-1. This report reveals that primary and metastatic tumors from PDAC patients harbor vastly distinct immunologic and stromal features at the protein level.