RARRES1 marks an immune-cold, chemoresistance-associated malignant epithelial subpopulation enriched in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma is characterized by therapy resistance and an immunosuppressive microenvironment. This study investigated the cellular mechanisms underlying chemotherapy resistance and immune evasion in PDAC, focusing on identifying key malignant epithelial subpopulations and their molecular drivers. We analyzed scRNA-seq data from 27 samples, including treatment-naive and chemotherapy-exposed primary tumors and liver metastasis. Analysis included CNV inference, gene set enrichment, cell-cell communication, NMF analysis and drug sensitivity prediction. Validation employed gemcitabine-resistant cells, western blotting and pan-cancer survival analysis of TCGA/ICGC data. We identified a malignant epithelial subcluster enriched in progressive disease samples and liver metastasis. This subcluster exhibited an immune-cold phenotype, characterized by disrupted communication with immune cells, increased immunosuppressive regulatory T cells and exclusion of anti-tumor effector cells. Further, it was associated with activated oncogenic and chemoresistance pathways, multi-drug resistance to standard therapies, higher tumor mutational burden and increased KRAS mutation frequency. RARRES1 was nominated as a core upregulated gene in this subpopulation. Functional studies confirmed RARRES1 overexpression in gemcitabine-resistant cells, and pan-cancer analysis established RARRES1 as a new biomarker for poor prognosis across multiple cancer types. Our work defines a chemotherapy-resistant and metastasis-enriched malignant epithelial subpopulation in PDAC that drives disease progression through an immune-cold niche. We identify RARRES1 as a pivotal regulator of this process, contributing to both therapy resistance and immune exclusion, and propose it as a novel pan-cancer prognostic biomarker. These findings reveal a targetable cellular mechanism underlying poor treatment response in PDAC.