Early detection of esophageal squamous cell carcinoma via a CACNA1E-SNTG1 cfDNA methylation signature.
12 affiliations
- 1State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China. [email protected].
- 2School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China. [email protected].
- 3State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China.
- 4Department of Gastroenterology, Zhongda Hospital Southeast University, Nanjing, 210009, China.
- 5Department of Thoracic Surgery, Nanjing Drum Tower Hospital, The First Affiliated Hospital of Nanjing University Medical College, Nanjing, 210008, Jiangsu, China.
- 6Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
- 7Department of Gastroenterology, Baoying Hospital of Traditional Chinese Medicine, Yangzhou, 225800, Jiangsu, China.
- 8Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
- 9Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China. [email protected].
- 10Department of Gastroenterology, Zhongda Hospital Southeast University, Nanjing, 210009, China. [email protected].
- 11State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210096, China. [email protected].
- 12School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China. [email protected].
Abstract
Background
Esophageal squamous cell carcinoma (ESCC) is characterized by high mortality primarily due to late-stage diagnosis. While circulating cell-free DNA (cfDNA) methylation offers a promising avenue for non-invasive screening, achieving high diagnostic sensitivity for early-stage disease using scalable clinical assays remains a technical challenge. This study aimed to identify robust methylation biomarkers and validate their diagnostic performance and biological relevance using a liquid biopsy approach and patient-derived models.Methods
Differentially methylated regions were identified through whole-genome enzymatic methyl sequencing (WEM-seq) of clinical ESCC tissues and matched normal adjacent tissues, integrated with public microarray repositories. Following a rigorous dual-filter strategy to eliminate normal blood background noise, two hypermethylated loci, CACNA1E and SNTG1, were prioritized. A targeted quantitative methylation-specific PCR (qMSP) assay was developed and evaluated in a plasma cohort of 355 individuals (215 ESCC patients across stages 0-IV and 140 healthy controls). Five independent ESCC patient-derived organoid (PDO) models were established to investigate the mechanistic coupling between promoter hypermethylation and transcriptional silencing through paired qMSP and RNA sequencing.Results
The CACNA1E/SNTG1 dual-marker cfDNA panel demonstrated high diagnostic accuracy. In the independent validation cohort, the combined classifier discriminated ESCC from healthy controls with an area under the curve (AUC) of 0.918, yielding an optimal sensitivity of 90.5% and a specificity of 85.7%. For early-stage (Stage 0-I) ESCC, the panel maintained a highly robust AUC of 0.950 with 90.0% sensitivity and 87.5% specificity. In the PDO models, Actin-normalized qMSP analysis revealed intense promoter hypermethylation at CACNA1E and SNTG1, which strictly correlated with profound transcript depletion, providing direct in situ evidence of methylation-mediated gene silencing.Conclusion
The CACNA1E/SNTG1 methylation panel, combined with a qMSP workflow, provides a highly sensitive and specific strategy for the non-invasive early detection of ESCC. The integration of PDO-based multi-omics validation confirms the biological relevance of these epigenetic alterations, supporting the panel's broad utility for scalable clinical screening programs.
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BibTeX
@article{song2026early,
title = {{Early detection of esophageal squamous cell carcinoma via a CACNA1E-SNTG1 cfDNA methylation signature.}},
author = {Chao Song and Jiyu Tang and Hailu Wu and Xiaoming Shi and Di Wu and Jiahuan Liu and Chenye Shao and Binxiang Xu and Linchao Dai and Sijia Li and Chenrong Huang and Ruihua Shi and Zhongze Gu},
journal = {Clinical epigenetics},
year = {2026},
month = jul,
doi = {10.1186/s13148-026-02198-7},
url = {https://europepmc.org/article/MED/42934728},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Early detection of esophageal squamous cell carcinoma via a CACNA1E-SNTG1 cfDNA methylation signature.
AU - Chao Song
AU - Jiyu Tang
AU - Hailu Wu
AU - Xiaoming Shi
AU - Di Wu
AU - Jiahuan Liu
AU - Chenye Shao
AU - Binxiang Xu
AU - Linchao Dai
AU - Sijia Li
AU - Chenrong Huang
AU - Ruihua Shi
AU - Zhongze Gu
PY - 2026
DA - 2026/07/29
JO - Clinical epigenetics
DO - 10.1186/s13148-026-02198-7
UR - https://europepmc.org/article/MED/42934728
AB - Background Esophageal squamous cell carcinoma (ESCC) is characterized by high mortality primarily due to late-stage diagnosis. While circulating cell-free DNA (cfDNA) methylation offers a promising avenue for non-invasive screening, achieving high diagnostic sensitivity for early-stage disease using scalable clinical assays remains a technical challenge. This study aimed to identify robust methylation biomarkers and validate their diagnostic performance and biological relevance using a liquid biopsy approach and patient-derived models.Methods Differentially methylated regions were identified through whole-genome enzymatic methyl sequencing (WEM-seq) of clinical ESCC tissues and matched normal adjacent tissues, integrated with public microarray repositories. Following a rigorous dual-filter strategy to eliminate normal blood background noise, two hypermethylated loci, CACNA1E and SNTG1, were prioritized. A targeted quantitative methylation-specific PCR (qMSP) assay was developed and evaluated in a plasma cohort of 355 individuals (215 ESCC patients across stages 0-IV and 140 healthy controls). Five independent ESCC patient-derived organoid (PDO) models were established to investigate the mechanistic coupling between promoter hypermethylation and transcriptional silencing through paired qMSP and RNA sequencing.Results The CACNA1E/SNTG1 dual-marker cfDNA panel demonstrated high diagnostic accuracy. In the independent validation cohort, the combined classifier discriminated ESCC from healthy controls with an area under the curve (AUC) of 0.918, yielding an optimal sensitivity of 90.5% and a specificity of 85.7%. For early-stage (Stage 0-I) ESCC, the panel maintained a highly robust AUC of 0.950 with 90.0% sensitivity and 87.5% specificity. In the PDO models, Actin-normalized qMSP analysis revealed intense promoter hypermethylation at CACNA1E and SNTG1, which strictly correlated with profound transcript depletion, providing direct in situ evidence of methylation-mediated gene silencing.Conclusion The CACNA1E/SNTG1 methylation panel, combined with a qMSP workflow, provides a highly sensitive and specific strategy for the non-invasive early detection of ESCC. The integration of PDO-based multi-omics validation confirms the biological relevance of these epigenetic alterations, supporting the panel's broad utility for scalable clinical screening programs.
SN - 1868-7083
ER -