Scholarlink

Background <p>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.</p> Methods <p>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.</p> Results <p>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.</p> Conclusion <p>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.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Early detection of esophageal squamous cell carcinoma via a CACNA1E–SNTG1 cfDNA methylation signature

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月29日

查看全文
  • Chao Song,
  • Jiyu Tang,
  • Hailu Wu,
  • Xiaoming Shi,
  • Di Wu,
  • Jiahuan Liu,
  • Chenye Shao,
  • Binxiang Xu,
  • Linchao Dai,
  • Sijia Li,
  • Chenrong Huang,
  • Ruihua Shi,
  • Zhongze Gu

摘要

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.