Single-cell RNA sequencing via endoscopic ultrasound-guided fine-needle biopsy for pancreatic tumors uncovered an aggressive subclone with a poor prognosis.

BACKGROUNDSingle-cell RNA sequencing (scRNA-seq) is a powerful tool which can unveil regulatory connections between genes and cells. However, due to the high demand for tissue quality, most scRNA-seq for pancreatic cancer is carried out by surgical specimen. This study (NCT05767697) aims to gain practical experience in carrying out scRNA-seq using endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB).

MATERIALS AND METHODSWith a within-subjects design, two punctures from the same lesion, with a negative pressure of 5 ml (suction group) and without applying suction (non-suction group), were evaluated. Each biopsy sample was separated into three parts: white tissue, red material, and buffer for living cell counting. scRNA-seq was carried out according to the manufacturer's protocol. The pancreatic adenocarcinoma dataset in The Cancer Genome Atlas (TCGA) was used as external validation.

RESULTSA total of 20 patients with 40 specimens were enrolled. The suction group achieved a success rate of 80% (16/20), which was significantly higher than the 10% (2/20) success rate in the non-suction group (P < 0.001). scRNA-seq data were generated for four patients, including two early stage and two late stage. Overall, 15 major cell subtypes, including 4 cancer subclones, were identified across early and late stages. Analysis of differentially expressed genes identified an aggressive subclone highlighted by ubiquitin-conjugating enzyme E2 C (UBE2C) high expression, commonly in late stage. The TCGA dataset also demonstrated that UBE2C high-expression pancreatic cancer had a poor prognosis.

CONCLUSIONSEUS-FNB with a negative pressure of 5 ml is feasible for scRNA-seq in clinical practice. A UBE2C high-expression subclone correlates with a poor prognosis, potentially becoming a new therapeutic target in future studies.