Transcript isoform diversity in esophageal squamous cell carcinoma: Insights into tumor heterogeneity and therapeutic targets in Africa

Background: Esophageal squamous cell carcinoma (ESCC) is a major cause of cancer mortality in sub-Saharan Africa, particularly African ESCC corridor. The region's complex etiology, including viral infections, may influence RNA processing such as alternative splicing (AS), a critical but understudied mechanism in ESCC biology. This study characterized the transcriptome wide AS landscape in African ESCC and assessed whether HPV and HIV infections contribute to splicing dysregulation and structural protein alterations. Methods: A cross-sectional study was conducted between February to December 2024 involving 29 patients with histologically confirmed ESCC and verified HIV status. Paired tumor/ adjacent normal endoscopic biopsies were collected and subjected to histological evaluation, HPV genotyping, and RNA sequencing. Alternative splicing profiles were investigated, with a focus on their association with viral status. Computational structural modeling and molecular docking was used to predict the functional impact of tumor-specific splice variant. Results and Discussion: Skipped exons were the predominant AS event, followed by alternative 5′ and 3′ splice sites. Substantial patient-specific heterogeneity emerged, with the protocadherin gene family most affected, implicating disrupted cellular adhesion and invasion. Dysregulated non-coding RNAs (DGCR5, LINC00641) further reflected loss of tumor-suppressive control. A tumor-enriched 3′ splice-site variant in CXADR was predicted to alter junctional signaling. Stratification by viral status (HIV+/HPV+, HIV+/HPV-, HIV-/HPV+, HIV-/HPV-) revealed no significant effect on overall splicing burden. Conclusion: African ESCC exhibits a distinct, skipped-exon-dominated AS signature that drives molecular diversity independent of HIV/HPV status, highlighting AS as a promising diagnostic and therapeutic axis for precision oncology in Africa.