Defining the comprehensive genomic landscapes of pancreatic ductal adenocarcinoma using real world endoscopic aspiration samples

Background Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis despite progress in clinically relevant molecular subtyping. Most patients are diagnosed with advanced disease at which point tumors are mostly unresectable. This leaves core biopsy or endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) as the sole source of tumor tissue for molecular characterization. Currently, these small tissue fragments are not considered suitable for genomic analysis, which is why this precious snapshot usually remains unexplored.

Material and methods Applying an EpCAM-enrichment strategy in 31 patients, we show the feasibility and reproducibility of in-depth, molecular-barcoded, whole-exome sequencing (WES) analysis in real-world small biopsies.

Results EpCAM-enrichment resulted in a significant increase of KRAS mutant allele frequency (MAF) level (p = 0.02). Validation experiments showed an excellent correlation between digital-droplet PCR and sequencing based MAF for KRAS and GNAS as well as for MYC amplification levels. Genomic landscape of EUS-FNA samples resembles previous pattern of high-quality tissue sources. Potentially actionable mutations were present in 30% of patients and might be used for trial inclusion. Additionally, a high tumor mutational burden (TMB) - defined as TMB >10 mutations/Mb - correlated with single-nucleotide variants in DNA damage repair genes (p <  0.001) and showed prognostic significance. Correspondingly, high aneuploidy increased with tumor stage (p = 0.03) and had prognostic implications (p = 0.012). To identify predictive biomarkers for first line chemotherapy, we developed a complexity score (CS) based on SCNAs that correlates with response to platinum-based regimens. As a proof of concept, sequential biopsies taken before treatment and at the time of progression revealed molecular alterations associated with acquired resistance to immunotherapy.

Conclusion Collectively, these results emphasize the value, feasibility and reproducibility of real-world small biopsies for molecular characterization of PDAC.

Publication History

Article published online:
08 September 2020