Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental Assays
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 p...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Cell and Developmental Biology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcell.2021.815895/full |
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| author | Zhanghan Chen Zhanghan Chen Zhipeng Qi Zhipeng Qi Dongli He Jingyi Liu Jingyi Liu Enpan Xu Enpan Xu Bing Li Bing Li Shilun Cai Shilun Cai Di Sun Di Sun Yirong Cheng Yirong Cheng Qiang Shi Qiang Shi Yunshi Zhong Yunshi Zhong |
| author_facet | Zhanghan Chen Zhanghan Chen Zhipeng Qi Zhipeng Qi Dongli He Jingyi Liu Jingyi Liu Enpan Xu Enpan Xu Bing Li Bing Li Shilun Cai Shilun Cai Di Sun Di Sun Yirong Cheng Yirong Cheng Qiang Shi Qiang Shi Yunshi Zhong Yunshi Zhong |
| author_sort | Zhanghan Chen |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-20T19:00:45Z |
| format | Article |
| id | doaj.art-e56383926124473faa0f0337ac1c0489 |
| institution | Directory Open Access Journal |
| issn | 2296-634X |
| language | English |
| last_indexed | 2024-12-20T19:00:45Z |
| publishDate | 2022-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cell and Developmental Biology |
| spelling | doaj.art-e56383926124473faa0f0337ac1c04892022-12-21T19:29:25ZengFrontiers Media S.A.Frontiers in Cell and Developmental Biology2296-634X2022-02-01910.3389/fcell.2021.815895815895Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental AssaysZhanghan Chen0Zhanghan Chen1Zhipeng Qi2Zhipeng Qi3Dongli He4Jingyi Liu5Jingyi Liu6Enpan Xu7Enpan Xu8Bing Li9Bing Li10Shilun Cai11Shilun Cai12Di Sun13Di Sun14Yirong Cheng15Yirong Cheng16Qiang Shi17Qiang Shi18Yunshi Zhong19Yunshi Zhong20Endoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaDepartment of Internal Medicine of Xuhui Hospital, Affiliated Zhongshan Hospital, Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaEndoscopy Center, Zhongshan Hospital of Fudan University, Shanghai, ChinaEndoscopy Research Institute of Fudan University, Shanghai, ChinaBackground: 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.https://www.frontiersin.org/articles/10.3389/fcell.2021.815895/fullcolorectal cancercircRNAsshort peptidesLC-MS/MSbioinformatic analysis |
| spellingShingle | Zhanghan Chen Zhanghan Chen Zhipeng Qi Zhipeng Qi Dongli He Jingyi Liu Jingyi Liu Enpan Xu Enpan Xu Bing Li Bing Li Shilun Cai Shilun Cai Di Sun Di Sun Yirong Cheng Yirong Cheng Qiang Shi Qiang Shi Yunshi Zhong Yunshi Zhong Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental Assays Frontiers in Cell and Developmental Biology colorectal cancer circRNAs short peptides LC-MS/MS bioinformatic analysis |
| title | Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental Assays |
| title_full | Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental Assays |
| title_fullStr | Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental Assays |
| title_full_unstemmed | Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental Assays |
| title_short | Strategy for Scanning Peptide-Coding Circular RNAs in Colorectal Cancer Based on Bioinformatics Analysis and Experimental Assays |
| title_sort | strategy for scanning peptide coding circular rnas in colorectal cancer based on bioinformatics analysis and experimental assays |
| topic | colorectal cancer circRNAs short peptides LC-MS/MS bioinformatic analysis |
| url | https://www.frontiersin.org/articles/10.3389/fcell.2021.815895/full |
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