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

Y.-Y. Su , M.-Y. Lin , S.M. Cheng , W.-L. Chang , C.-W. Hsu , C.-M. Yeh , C.-C. Yu , Y.-C. Hou , C.-J. Huang , Y.-S. Liu , Y.-J. Chao , D.-Y. Hwang , Y.S. Shan , L.-T. Chen
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Abstract

Background

Single-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 methods

With 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.

Results

A 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.

Conclusions

EUS-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.
单细胞RNA测序通过内镜超声引导细针活检胰腺肿瘤发现侵袭性亚克隆与预后不良
单细胞RNA测序(scRNA-seq)是揭示基因与细胞之间调控联系的有力工具。然而,由于对组织质量的高要求,大多数胰腺癌的scRNA-seq都是通过手术标本进行的。本研究(NCT05767697)旨在获得使用内镜超声引导细针活检(EUS-FNB)进行scRNA-seq的实践经验。材料和方法采用受试者内设计,对同一病灶进行两次穿刺,负压5ml(吸引组)和不使用吸引(非吸引组)进行评估。每个活检样本被分成三部分:白色组织、红色材料和活细胞计数缓冲液。按照制造商的方案进行scrna测序。使用癌症基因组图谱(TCGA)中的胰腺腺癌数据集作为外部验证。结果共纳入患者20例,标本40份。抽吸组的成功率为80%(16/20),明显高于非抽吸组10%(2/20)的成功率(P <;0.001)。生成了4例患者的scRNA-seq数据,包括2例早期和2例晚期。总的来说,在早期和晚期发现了15种主要的细胞亚型,包括4种癌症亚克隆。差异表达基因分析鉴定出一个侵袭性亚克隆,其中泛素结合酶E2C (UBE2C)高表达,通常在晚期表达。TCGA数据还显示,UBE2C高表达胰腺癌预后较差。结论5ml负压的seus - fnb在临床应用中是可行的。UBE2C高表达亚克隆与不良预后相关,可能成为未来研究的新治疗靶点。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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