AUTHOR=Pedrosa L. , Araujo I. K. , Cuatrecasas M. , Soy G. , López S. , Maurel J. , Sánchez-Montes C. , Montironi C. , Saurí T. , Sendino O. , Pérez F. M. , Ausania F. , Fernández-Esparrach G. , Espósito F. M. , Vaquero E. C. , Ginès A.
TITLE=Targeted transcriptomic analysis of pancreatic adenocarcinoma in EUS-FNA samples by NanoString technology
JOURNAL=Frontiers in Molecular Biosciences
VOLUME=10
YEAR=2023
URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2023.1161893
DOI=10.3389/fmolb.2023.1161893
ISSN=2296-889X
ABSTRACT=Background: Integration of transcriptomic testing into EUS-FNA samples is a growing need for precision oncology in pancreatic ductal adenocarcinoma (PDAC). The NanoString platform is suitable for transcriptome profiling in low yield RNA samples.
Methods: Inclusion of patients that underwent EUS-FNA cytological diagnosis of pancreatic ductal adenocarcinoma using 19G and/or 22G needles and subsequent surgical resection. Formalin-fixed, paraffin-embedded (FFPE) cytological and surgical samples underwent RNA extraction and transcriptomic analysis using a custom 52-gene NanoString panel of stromal PDAC features. Cell type abundance was quantified in FFPE specimens and correlated.
Results: 18 PDAC patients were included. Mean EUS-FNA passes was 2 + 0.7. All FFPE passed the RNA quality control for genomic analysis. Hierarchical clustering on the global gene expression data showed that genes were differentially expressed between EUS and surgical samples. A more enriched cancer-associated fibroblasts and epithelial-mesenchymal transition transcriptomic profile was observed across surgical specimens whereas immunological biomarkers were more represented in EUS-FNA samples. Cytological examination confirmed a scanty representation of CAF and more immunological cell abundance in cytological samples in comparison to surgical specimens.
Conclusion: Targeted transcriptomic NanoString profiling of PDAC samples obtained by EUS-FNA is a feasible approach for pre-surgical molecular analysis although stromal CAF/EMT mRNA biomarkers are underrepresented.