Intratumoral Cell Neighborhoods Coordinate Outcomes in Pancreatic Ductal Adenocarcinoma

Background and Aims Pancreatic ductal adenocarcinoma (PDA) is a highly lethal disease characterized by a spatially heterogenous tumor microenvironment (TME). Within the PDA microenvironment, cells organize into communities where cell fate is influenced by neighboring cells of diverse ontogeny and function. However, it remains unclear how cell neighborhoods in the TME evolve with treatment and impact clinical outcomes. Methods Here, using automated chromogenic multiplex immunohistochemistry (mIHC) and unsupervised computational image analysis of human PDA tumors, we investigated cell neighborhoods in surgically resected tumors from patients with chemotherapy-naïve PDA (n = 59) and neoadjuvant chemotherapy-treated PDA (n = 57). Single cells were defined by lineage markers (CD3, CD8, Foxp3, CD68, CK19), proliferation (Ki67) and neighboring cells. Results Distinct intra-tumoral immune and tumor cell subsets defined by neighboring cells. Higher content of stromal-associated macrophages was seen in chemotherapy-naive tumors from long-term survivors (LTS, OS > 3 years) compared to short-term survivors (STS, OS < 1 year), whereas immune-excluded tumor cells were higher in STS. Chemotherapy-treated versus -naïve tumors showed lower content of tumor-associated T cells and macrophages but similar densities of stromal-associated immune cells. However, proliferating tumor cell subsets with immune rich neighborhoods were higher in chemotherapy-treated tumors. In a blinded analysis of tumors from patients treated with neoadjuvant chemotherapy, a composite index comprising lower quantities of immune-excluded tumor cells and higher spatially distinct immune cell subsets associated with prolonged survival. Conclusions: Together, these data provide new insights into discrete cell communities in PDA and show their clinical relevance.