Pinto Elisa, Lazzarini Elisabetta, Pelizzaro Filippo, Gambato Martina, Santarelli Laura, Potente Sara, Zanaga Paola, Zappitelli Teresa, Cardin Romilda, Burra Patrizia, Farinati Fabio, Romualdi Chiara, Boscarino Diego, Tosello Valeria, Indraccolo Stefano, Russo Francesco Paolo
Department of Surgery, Oncology and Gastroenterology, University of Padova, 35121 Padua, Italy.
Gastroenterology Unit, Azienda Ospedale-Università di Padova, 35121 Padua, Italy.
Cancers (Basel). 2025 Mar 26;17(7):1115. doi: 10.3390/cancers17071115.
BACKGROUND/OBJECTIVES: Despite advances in hepatocellular carcinoma (HCC) management, prognosis remains poor. Advanced-stage diagnosis often excludes curative treatments, and current biomarkers (e.g., alpha-fetoprotein [AFP]) have limited utility in early detection. Liquid biopsy has emerged as a promising cancer detection tool, with circulating cell-free DNA (ccfDNA) showing significant diagnostic potential. This proof-of-concept study aimed to investigate the potential role of tumor fraction (TF) within ccfDNA as a biomarker in HCC patients.
A total of sixty patients were recruited, including thirteen with chronic liver disease (CLD), twenty-four with cirrhosis, and twenty-three with HCC. Plasma samples were collected, and ccfDNA was extracted for shallow whole genome sequencing (sWGS) analysis. The TF was calculated by focusing on somatic copy number alterations (SCNAs) within the ccfDNA.
Among patients with CLD and cirrhosis (n = 37), ctDNA was undetectable in all but one cirrhotic patient who exhibited a significant tumor fraction (TF) of 17% and subsequently developed HCC. Conversely, five out of twenty-three HCC patients (21.7%) displayed detectable ctDNA with TF levels ranging from 3.0% to 32.6%. Patients with detectable ctDNA were characterized by more aggressive oncological features, including a higher number of nodules ( = 0.005), advanced-stage disease (60% BCLC C, = 0.010), and poorer response to therapy (80% PD, = 0.001). Moreover, the overall survival (OS) was significantly reduced in patients with detectable ctDNA (median OS: 17 months; CI 95% 4.5-26.5) compared to those without (median OS: 24.0 months; CI 95% 7.0-66.0; log-rank = 0.002).
Our results suggest that the analysis of TF by sWGS is a promising non-invasive tool for the identification of HCC with aggressive clinical behavior, whereas it is not sensitive enough for early HCC detection. This molecular assay can improve prognostic stratification in HCC patients.
背景/目的：尽管肝细胞癌（HCC）的治疗取得了进展，但其预后仍然很差。晚期诊断往往排除了根治性治疗方法，而且目前的生物标志物（如甲胎蛋白[AFP]）在早期检测中的作用有限。液体活检已成为一种有前景的癌症检测工具，循环游离DNA（ccfDNA）显示出显著的诊断潜力。这项概念验证研究旨在探讨ccfDNA中的肿瘤分数（TF）作为HCC患者生物标志物的潜在作用。
共招募了60名患者，包括13名慢性肝病（CLD）患者、24名肝硬化患者和23名HCC患者。采集血浆样本，提取ccfDNA进行浅层全基因组测序（sWGS）分析。通过关注ccfDNA中的体细胞拷贝数改变（SCNAs）来计算TF。
在CLD和肝硬化患者（n = 37）中，除一名肝硬化患者外，所有患者的ctDNA均未检测到，该患者的肿瘤分数（TF）为17%，随后发展为HCC。相反，23名HCC患者中有5名（21.7%）显示可检测到ctDNA，TF水平在3.0%至32.6%之间。ctDNA可检测到的患者具有更具侵袭性的肿瘤学特征，包括更多的结节数量（P = 0.005）、晚期疾病（60%为BCLC C期，P = 0.010）以及对治疗的反应较差（80%为疾病进展，P = 0.001）。此外，与ctDNA不可检测的患者相比，ctDNA可检测到的患者的总生存期（OS）显著缩短（中位OS：17个月；95%CI 4.5 - 26.5），而ctDNA不可检测的患者中位OS为24.0个月（95%CI 7.0 - 66.0；对数秩检验P = 0.002）。
我们的结果表明，通过sWGS分析TF是一种有前景的非侵入性工具，可用于识别具有侵袭性临床行为的HCC，然而其对早期HCC检测的敏感性不足。这种分子检测方法可以改善HCC患者的预后分层。
