DEDICATED DIGITAL MRNA DETECTION METHOD WITH EUS FNA SAMPLES FOR STABLISHING PANCREATIC ADENOCARCINOMA (PDAC) GENE EXPRESSION PROFILE SIGNATURE

Aims To evaluate the adequacy of EUS FNA samples for performing gene expression analysis with digital mRNA and to investigate their correlation with gene expression profile (genEP) of the corresponding resected specimen.

Methods 22G/19G needles (both n=9) (EUS-3 Cook^R/Olympus EZ-shot^R, respectively) were used. Number of passes was decided with rapid on site evaluation with an extrapass to ensure enough sample for molecular analysis. RNA was extracted from both HistoGel-embeded cytological specimens and from their corresponding formalin fixed paraffin embedded surgical specimens. The NanoString nCounter gene expression system (NanoString Technologies; Seattle, WA) was used for genEP, with a custom nCounter CodeSet (Integrated DNA Technologies, BVBA, Belgium) checking a panel of 52 genes (cancer associated fibroblasts, immune/myeloid-monocytic cells and checkpoint blockade and epithelial-mesenchymal transition). Heatmaps were developed using agglomerative clustering to compare genEP

Results Eighteen PDAC patients (11 females and 4 men) were included. Mean number of passes was 1.7+0.7. All 36 samples (cellular blocks and resected specimens) passed the RNA quality control test for genomic analysis with Nanostring. A different pattern of genEP was found between cytologies and the surgically resected specimens. Enriched expression of more specific fibroblasts’genes was seen in samples from surgical specimens whereas samples from EUS FNA were enriched with immunological cells.

Conclusions Targeted mRNA expression in EUS FNA samples is feasible. EUS FNA samples might be an optimal approach for tumour immunophenotyping but not to identify fibroblast targets in PDAC

Publication History

Article published online:
14 April 2022