Integrative transcriptomic profiling reveals molecular signatures of disease progression from gastroesophageal reflux disease to Barrett's esophagus: A foundation for single-cell resolution studies

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 comprehensive clinical-molecular association analyses. Multi-dimensional visualization approaches, including volcano plots, heatmaps, principal component analysis (PCA), and network diagrams, were utilized to present the transcriptomic landscape. Results: Transcriptomic profiling identified 1,247 significantly differentially expressed genes (673 upregulated, 574 downregulated) between GERD and Barrett's esophagus, with balanced distribution of upregulated and downregulated genes. Functional enrichment analysis revealed significant involvement of DEGs in critical biological processes including extracellular matrix remodeling, epithelial cell proliferation, inflammatory response, and immune regulation. KEGG pathway analysis highlighted activation of cancer-related signaling cascades, including PI3K-Akt, cell cycle regulation, and ECM-receptor interaction pathways, suggesting that Barrett's esophagus exhibits partial molecular characteristics of malignant transformation. Correlation analysis demonstrated that specific genes (MMP7 (matrix metalloproteinase 7) and CDH17 (cadherin 17)) showed dose-response relationships with disease severity, while CXCL8 (interleukin-8) expression was significantly associated with treatment resistance. Longitudinal monitoring revealed heterogeneous disease progression trajectories among patients, with inflammation scores ranging from 3.0-6.5 points and exhibiting variable temporal dynamics. Three-dimensional clinical feature space analysis confirmed distinguishable distribution patterns between GERD and Barrett's esophagus patients, though with partial overlap indicating disease continuum characteristics. Conclusion: This comprehensive transcriptomic study unveils the molecular complexity underlying GERD-to-Barrett's esophagus progression, identifying key genes and pathways that drive pathological transformation.