Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma
Cholangiocarcinomas (CCAs) are tumors that arise from the cholangiocytes. Although some genes have been shown with important roles in pathological process, interactions or cross-talks among different RNAs are important to understand the detailed molecular mechanisms in cancer development, especially...
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Elsevier
2021-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037021004360 |
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| author | Li Guo Yuyang Dou Yifei Yang Shiqi Zhang Yihao Kang Lulu Shen Lihua Tang Yaodong Zhang Changxian Li Jun Wang Tingming Liang Xiangcheng Li |
| author_facet | Li Guo Yuyang Dou Yifei Yang Shiqi Zhang Yihao Kang Lulu Shen Lihua Tang Yaodong Zhang Changxian Li Jun Wang Tingming Liang Xiangcheng Li |
| author_sort | Li Guo |
| collection | DOAJ |
| description | Cholangiocarcinomas (CCAs) are tumors that arise from the cholangiocytes. Although some genes have been shown with important roles in pathological process, interactions or cross-talks among different RNAs are important to understand the detailed molecular mechanisms in cancer development, especially discussing cross-talks among isomiRs and other RNAs. Herein, to characterize crucial genes in CCA, the protein expression profile was performed to survey potential crucial mRNAs and related non-coding RNAs (ncRNAs) in mRNA-ncRNA network, mainly including miRNAs/isomiRs and lncRNAs. Deregulated mRNAs were firstly obtained if consistent expression patterns were found at protein and mRNA levels, and related miRNAs/isomiRs were screened according to regulatory relationships. Diverse isomiRs from a given miRNA locus also contributed to interactions between the small RNAs and target mRNAs, and miRNAs were further used to survey related lncRNAs to expand the interactions. Thus, several groups of RNAs were constructed as candidate competitive endogenous RNA (ceRNA) networks. Finally, we found that RAB11FIP1:miR-101-3p:MIR3142HG may be a potential ceRNA network, and the interactions among them may be more complex due to variety of isomiRs. Simultaneously, RAB11FIP1 and miR-194-5p were also detected other related lncRNAs (FBXL19-AS1, SNHG1 and PVT1) that may be crucial in coding-non-coding RNA regulatory network. Our results show that diverse isomiRs with sequence and expression heterogeneities contribute to ceRNA regulatory network that may have crucial roles in CCA, which will expand our understanding of interactions among diverse RNAs and their contributions in cancer development. |
| first_indexed | 2024-12-24T11:18:59Z |
| format | Article |
| id | doaj.art-701f5e61128e4f0a9291ed27fc206457 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-24T11:18:59Z |
| publishDate | 2021-01-01 |
| publisher | Elsevier |
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| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-701f5e61128e4f0a9291ed27fc2064572022-12-21T16:58:19ZengElsevierComputational and Structural Biotechnology Journal2001-03702021-01-011957225734Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinomaLi Guo0Yuyang Dou1Yifei Yang2Shiqi Zhang3Yihao Kang4Lulu Shen5Lihua Tang6Yaodong Zhang7Changxian Li8Jun Wang9Tingming Liang10Xiangcheng Li11Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, ChinaDepartment of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, ChinaDepartment of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; Department of Biology, Brandeis University, Waltham, MA, USADepartment of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; Department of Biology, Brandeis University, Waltham, MA, USADepartment of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, ChinaJiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, ChinaDepartment of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, ChinaHepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, ChinaHepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, ChinaDepartment of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, ChinaJiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; Corresponding authors.Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; Corresponding authors.Cholangiocarcinomas (CCAs) are tumors that arise from the cholangiocytes. Although some genes have been shown with important roles in pathological process, interactions or cross-talks among different RNAs are important to understand the detailed molecular mechanisms in cancer development, especially discussing cross-talks among isomiRs and other RNAs. Herein, to characterize crucial genes in CCA, the protein expression profile was performed to survey potential crucial mRNAs and related non-coding RNAs (ncRNAs) in mRNA-ncRNA network, mainly including miRNAs/isomiRs and lncRNAs. Deregulated mRNAs were firstly obtained if consistent expression patterns were found at protein and mRNA levels, and related miRNAs/isomiRs were screened according to regulatory relationships. Diverse isomiRs from a given miRNA locus also contributed to interactions between the small RNAs and target mRNAs, and miRNAs were further used to survey related lncRNAs to expand the interactions. Thus, several groups of RNAs were constructed as candidate competitive endogenous RNA (ceRNA) networks. Finally, we found that RAB11FIP1:miR-101-3p:MIR3142HG may be a potential ceRNA network, and the interactions among them may be more complex due to variety of isomiRs. Simultaneously, RAB11FIP1 and miR-194-5p were also detected other related lncRNAs (FBXL19-AS1, SNHG1 and PVT1) that may be crucial in coding-non-coding RNA regulatory network. Our results show that diverse isomiRs with sequence and expression heterogeneities contribute to ceRNA regulatory network that may have crucial roles in CCA, which will expand our understanding of interactions among diverse RNAs and their contributions in cancer development.http://www.sciencedirect.com/science/article/pii/S2001037021004360Protein profilingCross-talkmicroRNA (miRNA)isomiRLong non-coding RNA (lncRNA)Cholangiocarcinoma (CCA) |
| spellingShingle | Li Guo Yuyang Dou Yifei Yang Shiqi Zhang Yihao Kang Lulu Shen Lihua Tang Yaodong Zhang Changxian Li Jun Wang Tingming Liang Xiangcheng Li Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma Computational and Structural Biotechnology Journal Protein profiling Cross-talk microRNA (miRNA) isomiR Long non-coding RNA (lncRNA) Cholangiocarcinoma (CCA) |
| title | Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma |
| title_full | Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma |
| title_fullStr | Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma |
| title_full_unstemmed | Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma |
| title_short | Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma |
| title_sort | protein profiling reveals potential isomir associated cross talks among rnas in cholangiocarcinoma |
| topic | Protein profiling Cross-talk microRNA (miRNA) isomiR Long non-coding RNA (lncRNA) Cholangiocarcinoma (CCA) |
| url | http://www.sciencedirect.com/science/article/pii/S2001037021004360 |
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