Integrative Transcriptomic Profiling Reveals Molecular Signatures of Disease Progression from Gastroesophageal Reflux Disease to Barrett's Esophagus: A Foundation for Single-Cell Resolution Studies
Abstract
BACKGROUND
Barrett's esophagus (BE) represents a critical precancerous lesion arising from chronic gastroesophageal reflux disease (GERD), with significant risk of progression to esophageal adenocarcinoma. Despite advances in transcriptomic technologies, including single-cell RNA sequencing (scRNA-seq), the molecular mechanisms underlying the GERD-to-BE transition remain incompletely understood. Comprehensive transcriptomic profiling at both bulk and, prospectively, single-cell resolution is essential for identifying disease-driving molecular signatures and cellular heterogeneity. This study aimed to systematically characterize the transcriptomic landscape of GERD and Barrett's esophagus through integrative bulk RNA-sequencing analysis, with the goal of establishing a foundational framework for future single-cell transcriptomic investigations.
METHODS
A balanced cohort of N=40 patients (n=20 GERD, n=20 Barrett's esophagus) was enrolled. Esophageal tissue samples were collected via endoscopic biopsy and subjected to high-throughput RNA sequencing. Rigorous quality control, read alignment (HISAT2), and gene expression quantification (StringTie) were performed. DESeq2 was employed for differential expression analysis with stringent criteria (|log2FC| ≥ 1.0, FDR < 0.05). Functional enrichment analysis was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Integration of gene expression data with clinical parameters enabled…
How strong is the evidence?
Evidence Hub reads this as a cohort study, done in people. Its evidence level is 3 of 5 (Moderate · trial / cohort / secondary analysis). Trials without a large randomized design, cohorts and secondary analyses give moderate evidence. Reported size: 40 participants or records.
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