Introduction
Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal malignancy with marked biological heterogeneity and limited tools for individualized prognostic stratification and treatment selection. Molecular biomarkers capable of predicting survival and chemotherapy response are still lacking in routine clinical practice. Transcriptomic profiling has identified two main PDAC subtypes—classical and basal-like—associated with distinct tumor biology, prognosis, and chemosensitivity patterns. However, most available evidence derives from surgical specimens, while data obtained from minimally invasive samples, such as endoscopic ultrasound-guided fine-needle aspiration/biopsy (EUS-FNA/FNB), are scarce and not yet fully validated. This represents a major limitation, as the majority of PDAC patients are diagnosed at an unresectable stage and rely on small biopsy samples for molecular characterization. Moreover, the potential evolution of transcriptomic profiles under chemotherapy pressure remains poorly understood.
Aims & Methods
We aimed to characterize transcriptomic subtypes and biomarker expression in baseline EUS-FNA/FNB samples, assess their association with prognosis and chemotherapy response, and explore dynamic molecular changes through EUS-based tumor re-sampling after first-line therapy (first results of the PACEUT trial). 240 PDAC patients undergoing diagnostic EUS were prospectively enrolled, and FNA samples underwent RNA sequencing. PURIST was applied to classify subtypes. Outcomes included overall survival (OS) and progression-free survival (PFS), adjusted for age and stage. A subgroup of 25 patients underwent paired tumor sampling before and after chemotherapy.
Results
RNA-seq succeeded in 239/240 basaline samples (99,6%). Among those, 16 (6,7%) were basal-like and 223 (93,3%) classical. Basal-like patients had shorter OS (11 vs 15 months; p=0,04) and PFS (7 vs 9 months; p=0,02) and were older (mean age 72,3 vs 66,9 years; p=0,02). Current follow-up comprehends 51% of patients deceased and mean follow-up of 17,4 months. A basal subtype was associated with an increased risk of progression probability (aHR 1,91; 95% CI 1,05-3,49; p=0,03) Purist score inversely correlated with OS (r = –0,21; p=0,001) and PFS (r= -0,21; p=0,0009). and was associated with increased mortality risk (aHR 1,23; 95%CI 1,03-1,47; p=0,02), and progression risk (aHR 1,31; 95%CI 1,12-1,54; p=0,0009), in particular for patient receiving FOLFIRINOX (aHR 1,47; 95%CI 1,10-1,95; p=0,008), as also classical patients responded best to FOLFIRINOX compared to other regimes (aHR 0,78; 95% CI 0,62 – 0,98; p=0,004). In the 25 PACEUT samples (RNA-seq success rate 100%), 0,4% were basal-like before chemotherapy, 0,8% afterwards. Purist score increased in 8(32%) patients (towards a more basal-profile), remained stable in 9(36%) patients, and decreased in 8(32%) patients (towards a more classical-profile). Increased Purist score after chemotherapy associated with increased mortality risk (HR 4,48; 95%CI 1,45-13,0; p=0,0097).
Conclusion
This is the largest study evaluating transcriptomics at diagnosis on EUS-acquired tissue and it is the first study to evaluate tumor molecular features after chemotherapy. Transcriptome profiling of EUS-Acquired samples enabled prognostic stratification in PDAC both at diagnosis and after first line chemotherapy.