Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental Assays

Abstract

Background: Colorectal cancer (CRC) is the third most common cause of cancer deaths worldwide. Numerous studies have reported that circular RNAs (circRNAs) have important functions in CRC. It was first thought that circRNAs were non-coding RNA; however, more recently they were discovered to encode peptides and play a pivotal role in cancer development and progression. It was shown that most circRNAs possess coding potential; however, not all of them can truly encode peptides. Therefore, a practical strategy to scan for coding circRNAs is needed.Method: Sequence analyses included open reading frame (ORF) prediction, coding peptide prediction, and the identification of unique sequences. Then, experimental assays were used to verify the coded peptides, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was introduced to detect sequences of circRNAs with coding potential, and Western blot was used to identify the encoded peptides. Finally, the functions of the circRNAs were primarily explored.Result: An efficient strategy for searching circRNAs with coding potential was created. We verified this schedule using public databases and LC-MS/MS, then two of these circRNAs were selected for further verification. We used commercial antibodies that can also identify the predicted peptides to test the coded peptides. The functions of the circRNAs were explored primarily, and the results showed that they were mainly involved in the promotion of proliferation and invasion ability.Discussion: We have constructed an efficient strategy of scanning circRNAs with coding potential. Our strategy helped to provide a more convenient pathway for identifying circRNA-derived peptides, which can be a potential therapeutic target or a diagnostic biomarker.

Circular RNAs Could Encode Unique Proteins and Affect Cancer Pathways

“…Finally, we aimed to look for experimental validation of our bioinformatics investigation. We underline that it is potentially challenging to identify the peptides derived from circRNA translation, because there are not many within the proteins and they might not be readily detectable with the usual analytical techniques, for example using liquid chromatography–tandem mass spectrometry [ 42 ]. We interrogated the mass spectrometry PeptideAtlas database to identify any match with circORFs’ peptides.…”

CircRNAs in colorectal cancer: potential biomarkers and therapeutic targets

“… [ 54 ] Circ_0000725; circ_0008826 hsa_circ_0000725; hsa_circ_0008826 Up Tissues 306-a.a. and 475-a.a. peptide Promotes proliferation, and invasion. [ 156 ] Circ_0006401 hsa_circ_0006401 Up Tissues circ_0006401 peptide Promotes CRC proliferation and migration [ 157 ] CircPPP1R12a hsa_circ_0000423 Up Tissues circPPP1R12A-73aa Promotes cell proliferation, migration, and invasion. [ 100 ] AMPK AMP-activated protein kinase, BRD4 bromodomain containing 4, CBFB core-binding factor subunit beta, CRC colorectal cancer.…”

Hsa_Circ_0104206 is An Oncogenic circRNA in Colon Cancer by Targeting Mir-188–3p/CCNA2 Axis

“…Recent growing evidence supports non-coding RNAs (ncRNAs), such as circular RNA (circRNAs), long-stranded non-coding RNA (lncRNAs), and microRNAs (miRNAs), as markers of tumorigenesis [6,7]. CircRNAs are products of a back-splicing event from precursor mRNAs, and it lacks 5′ and 3′ ends in structure, conferring them high stability [8,9]. The critical role of circRNAs in cancer development has been elaborately studied, mainly based on the impacts of their aberrant expression on the biological behaviors of cancer Original Article: Endocrine Research Hsa_Circ_0104206 is An Oncogenic circRNA in Colon Cancer by Targeting Mir-188-3p/CCNA2 Axis The identification of specific biomarkers is essential to improve cancer therapy, and circular RNAs (circRNAs) have great potency to be biomarkers.…”