Spatial Proteomics Uncovers Immune Cell Neighborhoods and Tumor-Immune Interfaces in Pancreatic Ductal Adenocarcinoma
Year: 2026
Type: article
Study design: Observational Study
Abstract: Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies with dismal prognosis and limited treatment options. The complex interplay between tumor cells and their microenvironment contributes significantly to treatment resistance, yet technological challenges have hindered comprehensive spatial characterization of immune components in PDAC tissues. Here, we performed high-dimensional spatial proteomics using multiplexed ion beam imaging (MIBI) to quantify 27 protein markers across tissues from twelve treatment-naïve PDAC patients who subsequently underwent adjuvant chemotherapy. We achieved confident single-cell phenotypic mapping of the PDAC ecosystem through deep-learning based segmentation and expert-validated phenotypic annotation. Our analysis revealed significant enrichment of immunosuppressive myeloid populations in patients who eventually experienced disease relapse. Conversely, cytotoxic CD8+ T cells were depleted in these relapse-prone tumors. Using spatial probabilistic topic modeling, we identified eight distinct cellular neighborhoods with unique compositions and functional states, including the enrichment of an immune suppressive neighborhood in relapsed patients. While immunogenic cell neighborhoods were present in both patient populations, analysis of the tumor-immune neighborhoods demonstrated altered functional marker expression profiles, suggesting distinct immune activation in patients who relapsed versus those who did not. Our findings provide a high-resolution spatial atlas of the PDAC immune landscape and identify prognostic microenvironmental signatures that may inform the development of novel immunotherapeutic strategies for this recalcitrant disease.
Source: Molecular & Cellular Proteomics
Institutions: Beth Israel Deaconess Medical Center, Harvard University, Broad Institute, The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Agency for Science, Technology and Research, Singapore Immunology Network, Erasmus MC, Essen University Hospital, RWTH Aachen University, University of Oxford, Kennedy Institute of Rheumatology, Bristol-Myers Squibb (United States), Stanford University, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, University of Birmingham, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Massachusetts Institute of Technology
Language: English
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $3,430
OpenAlex ID: W7223839289