Abstract 3803: The landscape of circular RNAs in metastatic colorectal cancer

Abstract

Abstract Colorectal cancer (CRC) is the most common gastrointestinal malignancy and a leading cause of cancer death in the U.S.. Approximately 50% of patients with CRC develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Circular RNAs (circRNAs), covalently closed RNA molecules produced from pre-mRNAs through backsplicing, have recently emerged as an important class of non-coding RNAs regulating CRC tumorigenesis and progression. In this study we established a comprehensive catalog of circRNAs in mCRC. To evaluate circRNAs in mCRC progression, total RNA-Seq was performed on 30 matched normal, primary, and distant metastatic samples from 14 mCRC patients. Additionally, the transcriptome of five CRC cell lines were sequenced to evaluate circRNAs expressed in cell lines. CircRNAs were identified and quantified using the number of backspliced reads, normalized against the total number of mapped reads. Differential expression (DE) analysis was performed to identify circRNAs deregulated between normal, primary, and metastatic tissues. Our analysis identified approximately 62,000 expressed circRNAs in mCRC including approximately 32,000 expressed in patients and 48,000 expressed in cell lines, originating from approximately 9200 linear genes. Approximately 42,000 circRNAs (67%) were unannotated when compared with the circRNA consortium MiOncoCirc annotation. DE analysis identified 376 circRNAs deregulated in CRC progression from normal to primary, and metastasis. A higher proportion of DE circRNAs (82%) was downregulated in primary or metastasis, consistent with earlier reports of lower circRNA concentration in tumor due to rapid cell cycles. Among DE circRNAs were the downregulation of circRNAs that have been known to suppress tumor proliferation, migration, and invasion in mCRC such as circSMARCA5, circFBXW7, and circSETD3, and the upregulation of circFIRRE, a circRNA known to promote tumor progression in osteosarcoma. A significant portion (37%) of deregulated circRNAs also had their parental linear genes found to be deregulated, suggesting parental gene regulation contributed to circRNA regulation. Interestingly, a large portion of circRNAs (63%) were found to be deregulated while their parental linear gene expression was unchanged, suggesting alternative mechanisms of circRNA deregulation. Gene set enrichment analysis showed that linear genes co-deregulated with circRNAs were enriched in signatures of tumor progression including proliferation, epithelial mesenchymal transition, and metastasis, suggesting potential involvement of deregulated circRNAs in tumor progression. Through RNA sequencing of both patients and cell lines, we established a comprehensive compendium of circRNAs and identified those deregulated in mCRC. This provides a valuable resource for further experimental characterization of circRNAs function in mCRC progression. Citation Format: Sidi Zhao, Amy Ly, Jacqueline L. Mudd, Emily B. Rozycki, Ghofran Othoum, Jingqin Luo, Ha X. Dang, Ryan C. Fields, Christopher A. Maher. The landscape of circular RNAs in metastatic colorectal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3803.