Exploring the prognostic value of circular RNAs in pancreatic ductal adenocarcinoma using genome-wide expression profiling

• Published in: Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.] Vol. 24; no. 5; pp. 706 - 718
• Main Authors: Ørbeck, Siri Vreim, Jakobsen, Theresa, García-Rodríguez, Juan Luis, Burton, Mark, Rasmussen, Lukas Gammelgaard, Ewald, Jesper Dupont, Fristrup, Claus Wilki, Pfeiffer, Per, Mortensen, Michael Bau, Kristensen, Lasse Sommer, Detlefsen, Sönke
• Format: Journal Article
• Language: English
• Published: Switzerland Elsevier B.V 01.08.2024
• Subjects: Aged; Biomarkers, Tumor - genetics; Carcinoma, Pancreatic Ductal - genetics; Carcinoma, Pancreatic Ductal - pathology; circRNA; Female; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Humans; Male; Middle Aged; Pancreatic ductal adenocarcinoma; Pancreatic Neoplasms - diagnosis; Pancreatic Neoplasms - genetics; Pancreatic Neoplasms - pathology; Prognosis; RNA sequencing; RNA, Circular - genetics; Survival; RNA sequencing; Prognosis; circRNA; Survival; Pancreatic ductal adenocarcinoma
• ISSN: 1424-3903; 1424-3911; 1424-3911
• DOI: 10.1016/j.pan.2024.04.004

Median survival of pancreatic ductal adenocarcinoma (PDAC) is around eight months and new prognostic tools are needed. Circular RNAs (circRNAs) have gained interest in different types of cancer. However, only a few studies have evaluated their potential in PDAC. We aimed to identify the most differentially expressed circRNAs in PDAC compared to controls and to explore their potential as prognostic markers. Using frozen specimens with PDAC and controls, we performed RNA sequencing and identified 20,440 unique circRNAs. A custom code set of capture- and reporter probes for NanoString nCounter analysis was designed to target 152 circRNAs, based on abundancy, differential expression and a literature study. Expression of these 152 circRNAs was examined in 108 formalin-fixed and paraffin-embedded surgical PDAC specimens and controls. The spatial expression of one of the most promising candidates, ciRS-7 (hsa_circ_0001946), was evaluated by chromogenic in situ hybridization (CISH) using multi-punch tissue microarrays (TMAs) and digital imaging analysis. Based on circRNA expression profiles, we identified different PDAC subclusters. The 30 most differentially expressed circRNAs showed log2 fold changes from −3.43 to 0.94, where circNRIP1 (hsa_circ_0004771), circMBOAT2 (hsa_circ_0007334) and circRUNX1 (hsa_circ_0002360) held significant prognostic value in multivariate analysis. CiRS-7 was absent in PDAC cells but highly expressed in the tumor microenvironment. We identified several new circRNAs with biomarker potential in surgically treated PDAC, three of which showed an independent prognostic value. We also found that ciRS-7 is absent in cancer cells but abundant in tumor microenvironment and may hold potential as marker of activated stroma.