Gene-specific ctDNA dynamics predict tumour burden and survival outcomes in ESCC: A prospective cohort study

Abstract

Background: Oesophageal squamous cell carcinoma (ESCC) remains a highly aggressive malignancy with limited biomarkers for monitoring tumour burden and prognosis. Circulating tumour DNA (ctDNA) has emerged as a promising tool for real-time disease assessment, but its clinical utility in ESCC remains underexplored.

Methods: In this prospective cohort study, we analysed preoperative and postoperative ctDNA from 54 treatment-naïve ESCC patients undergoing radical surgery using a 61-gene panel. Associations between ctDNA mutations, clinicopathological characteristics and survival outcomes were evaluated.

Results: Preoperative ctDNA mutations were detected in 96.3% of patients (52/54), with Tumour Protein 53 (TP53) (59.3%), Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) (31.5%) and Phosphatase and Tensin Homologue (PTEN) (13.0%) being most prevalent. Surgical resection significantly reduced ctDNA positivity (p < .0001). Advanced-stage tumours exhibited higher frequencies of PIK3CA (47.8% vs. 19.4%, p = .026) and PTEN mutations (26.1% vs. 3.2%, p = .034). Survival analysis revealed that postoperative TP53 ctDNA positivity predicted worse disease-free survival (DFS; Hazard Ratio (HR) = 3.64, p = .005) and overall survival (OS; HR = 3.29, p = .009), while PIK3CA positivity was associated with improved OS (p = .032). Strikingly, preoperative PTEN ctDNA-positive patients showed dramatically worse outcomes, with median DFS of 4.01 versus 33.27 months (HR = 7.53, p < .001) and OS of 11.80 versus 45.17 months (HR = 5.35, p < .001). In multivariate analysis, preoperative PTEN positivity remained the strongest independent prognostic factor for both DFS (HR = 7.28, p = .002) and OS (HR = 3.76, p = .028), surpassing Tumour, Node, Metastasis (TNM) stage.

Conclusions: Our findings highlight the dynamic role of ctDNA in reflecting ESCC tumour burden and prognosis. While tumour-agnostic ctDNA analysis showed limited clinical utility, gene-specific mutations (TP53, PIK3CA and PTEN) demonstrated significant prognostic value. Preoperative PTEN ctDNA positivity emerged as a robust predictor of aggressive disease, suggesting its potential for risk stratification and personalised therapeutic strategies in ESCC.

Keywords

circulating tumour DNA (ctDNA) / oesophageal squamous cell carcinoma (ESCC) / PIK3CA / prognosis / PTEN / TP53

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2025 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.