Unlocking Esophageal Carcinoma’s Secrets: An integrated Omics Approach Unveils DNA Methylation as a pivotal Early Detection Biomarker with Clinical Implications

Abstract

1AbstractEsophageal carcinoma (EC) ranks among the top six most prevalent malignancies worldwide with a recent surge in incidence. An innovative integrated omics technique is presented for discerning the two primary types of esophageal carcinoma (EC) AND Squamous cell carcinoma and adenocarcinoma. Utilizing The Cancer Genome Atlas (TCGA) data via Bioconductor, the research integrated DNA methylation and RNA expression analyses for esophageal cancer (ESCA). Key findings revealed DNA methylation’s pivotal role in ESCA progression and its potential as an early detection biomarker. Significant disparities in methylation patterns offered insights into the disease’s pathogenesis. A comparison with the TCGA Pan-Cancer dataset using Bioconductor tools enriched the understanding of ESCA genomics. Specifically, 131,220 hypomethylated probes were detected in tumors compared to 6,248 in healthy tissues. Additionally, 42,060 probe-gene pairs linked methylation variations to expression alterations, with 768 hypomethylated motifs identified. Thirteen of these motifs emerged as potential diagnostic markers. Transcription factor analyses spotlighted crucial regulators, including NFL3, ATF4, JUN, and CEBPG, revealing intricate regulatory networks in ESCA. Survival statistics further correlated clinical factors with patient longevity. This research recommends an innovative approach to identifying oesophageal abnormalities through DNA methylation and gene expression mechanisms. Research suggests DNA methylation may serve as an early detection biomarker, aiding in identifying esophagus cancer prior to more advanced stages.