Identification and Functional Validation of Radioresistance-Related Genes AHNAK2 and EVPL in Esophageal Squamous Cell Carcinoma by Exome and Transcriptome Sequencing Analyses

INTRODUCTION: Esophageal squamous cell carcinoma (ESCC) is often resistant to radiotherapy, likely due to sub-clones that survive and repopulate in the tumor. The analysis of genomic sequencing data related to radiotherapy will provide a better understanding of the intratumoral heterogeneity and genetic evolution of ESCC during radiotherapy. METHODS: We analyzed whole-exome sequencing data from pre- and post-irradiation ESCC patients at single-cell and bulk levels in public datasets. We investigated the gene functions involving radioresistance in ESCC cell lines. Furthermore, we established gene knockdown cell lines and explored the transcriptional alterations induced by RNA interference (RNAi) of these genes in KYSE-150 ESCC cell line. RESULTS: We identified three candidate genes related to radioresistance: AHNAK2, EVPL and LAMA5. Knockdown of AHNAK2 and EVPL genes led to increased radioresistance in ESCC cell lines, but not LAMA5. The transcriptome analysis indicated that these genes may regulate the expression of interleukins, interleukin receptors and chemokines by inhibiting the NF-κB and TNF signaling pathways in radioresistant ESCC cells, thereby suppressing their immune response. CONCLUSION: These data may provide new therapeutic strategies by targeting general ESCC radioresistance-related genes, which may eventually help the development of targeted therapies.