Computational-based integrative methylome-transcriptome analysis reveals widespread enhancer hypomethylation in...

Esophageal carcinoma (ESCA), comprising esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC), has a poor prognosis due to late diagnosis and incomplete molecular characterization. We sought to define the ESCA epigenomic landscape by integrating methylome and transcriptome data across both subtypes.

TCGA-ESCA HumanMethylation450K and RNA-seq profiles (182 tumors: 95 ESCC and 87 EAC; 64 normal tissues) were analyzed using ELMER and Bioconductor workflows. Differentially methylated probes were annotated by genomic category, probe-gene coupling was tested by Spearman correlation, and a LASSO-penalized 12-CpG classifier was trained and externally validated in an independent GEO cohort (GSE68303; n = 43).

ESCA showed pervasive enhancer hypomethylation, with 72.5% of the hypomethylated probes mapping to the distal enhancers. Methylation-expression coupling identified LINC02547 and PYGL as candidate effector genes, and enriched transcription factor motifs included AP-1 and NFIL3. The classifier achieved a cross-validated AUC of 0.996, approximately 0.99, sensitivity at 95% specificity, and reproducible performance across ESCC and EAC subtypes. Advanced disease stage was the dominant prognostic factor in multivariable survival models.

Enhancer hypomethylation is a hallmark of ESCA, nominating LINC02547 and PYGL as biomarker candidates with diagnostic/prognostic promise. Limitations include retrospective design and need for experimental validation.