Tumor-suppressive circRNAs in colorectal cancer spheroids and patients

Cancer stem cells pose significant clinical challenges in patients with colorectal cancer, as they complicate chemotherapy treatment and reduce survival rates. Investigating cancer stem cells may help elucidate the mechanisms driving therapeutic resistance and disease progression. Recent studies suggest that circular RNAs (circRNAs) play crucial roles in tumor formation and may offer potential for early diagnosis and novel treatment strategies. However, comprehensive validations of these circRNAs remain limited to date. The aim of this study was to elucidate the molecular roles of circRNAs that are downregulated in colorectal cancer stem-like cell populations.

We established 3D spheroid cultures using HCT-15 and WiDr cell lines as cancer stem cell models. Bulk RNA sequencing profiled circRNA and mRNA expression, followed by bioinformatic analyses using CircInteractome, CircBank, miRDB, and TargetScan to construct circRNA-miRNA-mRNA interaction networks.

CircRNA sequencing revealed predominant downregulation of circRNAs in spheroid cultures. Integration with clinical datasets comprising 788 colorectal cancer patients identified 15 circRNAs consistently downregulated in both spheroid models and metastatic tissues. Among these, hsa_circ_0039776 and hsa_circ_0067353 emerged as key tumor-suppressive candidates, predicted to regulate three oncogenic miRNAs-hsa-miR-614, hsa-miR-645, and hsa-miR-4689-significantly upregulated in advanced-stage patients. Cross-validation confirmed circRNA-miRNA and miRNA-mRNA interactions, and four tumor-suppressive genes ( CCL5 , INSC , SLC9A1 , SLC34A1 ) were associated with improved survival. Gene set enrichment analysis suggested these networks modulate cancer stem cell phenotypes, including inhibition of differentiation, resistance to apoptosis, and enhancement of DNA damage repair.

This study identifies hsa_circ_0039776 and hsa_circ_0067353 as novel tumor-suppressive circRNAs reduced in colorectal cancer spheroids and metastatic lesions. The circRNA-miRNA-mRNA regulatory network implicates oncogenic miRNAs and downstream tumor-suppressive targets correlating with favorable survival and cancer stemness. These findings underscore the potential of circRNAs as diagnostic biomarkers and therapeutic targets in colorectal cancer.