Biomarker Discovery with Oxford Nanopore Sequencing and Phage Display

Abstract

Pancreatic cancer is often diagnosed at an advanced stage due to the lack of effective biomarkers for early detection. Extracellular vesicles released by tumor cells represent a promising source of cancer-associated biomarkers because they reflect the molecular composition of their cells of origin. The aim of this pilot study was to develop a high throughput phage display and Oxford Nanopore-based approach for discovering a novel biomarker from pancreatic cancer-associated extracellular vesicle populations. Pancreatic cancer cell lines were cultured for extracellular vesicles. Extracellular vesicle surface markers from cancer cell culture medium and plasma samples of pre-diagnostic cohort were analyzed using immunoassays to identify suitable immobilization targets for phage display. Enriched phage libraries were sequenced using Oxford Nanopore technology, and sequencing data were analyzed using a bioinformatic workflow. Sequencing analysis revealed progressive enrichment of specific phage populations in samples collected closer to the time of pancreatic cancer diagnosis. After quality filtering and removal of negative controls, 49 candidate sequences were identified as enriched in late pre-diagnostic samples. These findings highlight the broader applicability of Nanopore sequencing in biomarker discovery.