Integrative circRNA profiling from RNA-sequencing of colorectal cancer and adenoma tissues shows a downregulation in early stages of the disease

INTRODUCTION: Detection of Colorectal Cancer (CRC) at an early stage significantly improves its management, response to therapy, and overall patient survival. Circular RNAs (circRNAs) are peculiar covalently closed transcripts involved in the modulation of gene expression whose dysregulation has been extensively reported in cancer cells. However, little is known on the circRNA alterations occurring in the early stages of colorectal carcinogenesis. A concomitant deep circRNA characterization in tumor tissue samples and precancerous lesions may provide novel evidence on the alterations of these molecules in the CRC onset. MATERIAL AND METHOD: Total RNA-Seq data of lesions and matched adjacent mucosa of 96 patients with CRC and 29 with colorectal adenomas were analyzed to explore the circRNA expression profiles. CIRI2 and DESeq2 tools were applied respectively for circRNA detection and paired differential expression analysis. Integration with the expression of host genes and interacting RNA binding proteins (RBPs) was performed to further characterize the identified circRNAs. Altered circRNA levels were explored with respect to patients’ clinical data and other omics information, including miRNome from small RNA-Seq and mutational profiles from target DNA sequencing. RESULTS: A widespread circRNA downregulation was observed in advanced adenomas and early CRC stages. Specifically, out of 34 identified dysregulated circRNAs, 33 were downregulated in tumor tissue. Profiling of advanced adenoma tissue reflected this trend. Observed downregulation was coherent with the circRNA host-gene repression and the downregulation of RBPs involved in the circRNA biogenesis, such as NOVA1, RBMS3, and CIRBP. Functional analysis predicted several interactions between circRNAs, miRNAs, and RBPs supported by significant correlations between their expression levels. Moreover, analysis of cancer hallmark-related pathways showed significant associations with circRNA levels. According with a circRNA downregulation at early CRC stage, the predicted activity of cell proliferation-related pathways, DNA repair and c-Myc signaling was higher in samples with low DE circRNA expression. CONCLUSIONS: These data support that multiple molecular alterations occur in concomitance with a widespread circRNA downregulation, which can represent an early molecular perturbation in colorectal carcinogenesis. Investigating specific circRNA levels could provide a candidate signature for an early CRC diagnosis.