High-Dimensional Protein Analysis Uncovers Distinct Immunological and Stromal Signatures Between Primary and Metastatic Pancreatic Ductal Adenocarcinoma

Abstract

Our understanding of the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME) primarily stems from murine models or primary patient tumors. While metastatic tumors have generally less immune infiltration compared to primary tumors, the specific cellular features of metastatic PDAC remain understudied. This knowledge gap is impactful as most patients present with metastatic disease and are most often enrolled in clinical trials. We hypothesized PDAC tumors harbor distinct immunologic and stromal features depending on their anatomical site. Using multiplex immunohistochemistry (mIHC), spatial analysis, and single-cell mass cytometry (CyTOF), we uncover dominant immune and stromal cell populations in tumors derived from 27 primary and 26 liver metastases. Metastatic liver tumors from PDAC patients contained fewer T cells and alpha-smooth muscle actin (-SMA+) activated fibroblasts than primary lesions, while CD68+ cells were more abundant. Spatial analyses revealed distinct immune cell communities in primary and metastatic PDAC, whereby CK19+ cells clustered differentially with -SMA+, CD3+, and CD68+ cells, depending on 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 ROR{gamma}t. CyTOF revealed that T cells co-expressed multiple inhibitory checkpoint receptors, with LAG-3 and PD-1 predominating. This report reveals that primary and metastatic tumors from PDAC patients harbor vastly distinct immunologic and stromal features at the protein level. Statement of SignificanceProtein level analysis reveals distinct immunological and stromal features between primary and metastatic PDAC tumors, offering a rationale for immunotherapies that target myeloid cells and increase T cell abundance in metastatic disease.