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Lv J, Yang F, Li Y, Gao N, Zeng Q, Ma H, He J, Zhang Y. Characterization and Function Analysis of miRNA Editing during Fat Deposition in Chinese Indigenous Ningxiang Pigs. Vet Sci 2024; 11:183. [PMID: 38668450 PMCID: PMC11054885 DOI: 10.3390/vetsci11040183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
This study aimed to identify active miRNA editing sites during adipose development in Ningxiang pigs and analyze their characteristics and functions. Based on small RNA-seq data from the subcutaneous adipose tissues of Ningxiang pigs at four stages-30 days (piglet), 90 days (nursery), 150 days (early fattening), and 210 days (late fattening)-we constructed a developmental map of miRNA editing in the adipose tissues of Ningxiang pigs. A total of 505 miRNA editing sites were identified using the revised pipeline, with C-to-U editing types being the most prevalent, followed by U-to-C, A-to-G, and G-to-U. Importantly, these four types of miRNA editing exhibited base preferences. The number of editing sites showed obvious differences among age groups, with the highest occurrence of miRNA editing events observed at 90 days of age and the lowest at 150 days of age. A total of nine miRNA editing sites were identified in the miRNA seed region, with significant differences in editing levels (p < 0.05) located in ssc-miR-23a, ssc-miR-27a, ssc-miR-30b-5p, ssc-miR-15a, ssc-miR-497, ssc-miR-15b, and ssc-miR-425-5p, respectively. Target gene prediction and KEGG enrichment analyses indicated that the editing of miR-497 might potentially regulate fat deposition by inhibiting adipose synthesis via influencing target binding. These results provide new insights into the regulatory mechanism of pig fat deposition.
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Affiliation(s)
- Jiayu Lv
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Yiyang Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
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Guo S, Mao C, Peng J, Xie S, Yang J, Xie W, Li W, Yang H, Guo H, Zhu Z, Zheng Y. Improved lung cancer classification by employing diverse molecular features of microRNAs. Heliyon 2024; 10:e26081. [PMID: 38384512 PMCID: PMC10878959 DOI: 10.1016/j.heliyon.2024.e26081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
MiRNAs are edited or modified in multiple ways during their biogenesis pathways. It was reported that miRNA editing was deregulated in tumors, suggesting the potential value of miRNA editing in cancer classification. Here we extracted three types of miRNA features from 395 LUAD and control samples, including the abundances of original miRNAs, the abundances of edited miRNAs, and the editing levels of miRNA editing sites. Our results show that eight classification algorithms selected generally had better performances on combined features than on the abundances of miRNAs or editing features of miRNAs alone. One feature selection algorithm, i.e., the DFL algorithm, selected only three features, i.e., the frequencies of hsa-miR-135b-5p, hsa-miR-210-3p and hsa-mir-182_48u (an edited miRNA), from 316 training samples. Seven classification algorithms achieved 100% accuracies on these three features for 79 independent testing samples. These results indicate that the additional information of miRNA editing is useful in improving the classification of LUAD samples.
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Affiliation(s)
- Shiyong Guo
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Chunyi Mao
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Jun Peng
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, i.e., The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, China
| | - Shaohui Xie
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, Kunming, Yunnan 650223, China
| | - Wenping Xie
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Wanran Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Huaide Yang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Hao Guo
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Zexuan Zhu
- National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yun Zheng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
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Li J, Li C, Xu W. Liver cancer-specific mutations in functional domains of ADAR2 lead to the elevation of coding and non-coding RNA editing in multiple tumor-related genes. Mol Genet Genomics 2024; 299:1. [PMID: 38170228 DOI: 10.1007/s00438-023-02091-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/17/2023] [Indexed: 01/05/2024]
Abstract
Mutation is the major cause of phenotypic innovations. Apart from DNA mutations, the alteration on RNA such as the ADAR-mediated A-to-I RNA editing could also shape the phenotype. These two layers of variations have not been systematically combined to study their collective roles in cancers. We collected the high-quality transcriptomes of ten hepatocellular carcinoma (HCC) and the matched control samples. We systematically identified HCC-specific mutations in the exonic regions and profiled the A-to-I RNA editome in each sample. All ten HCC samples had mutations in the CDS of ADAR2 gene (dsRNA-binding domain or catalytic domain). The consequence of these mutations converged to the elevation of ADAR2 efficiency as reflected by the global increase of RNA editing levels in HCC. The up-regulated editing sites (UES) were enriched in the CDS and UTR of oncogenes and tumor suppressor genes (TSG), indicating the possible roles of these target genes in HCC oncogenesis. We present the mutation-ADAR2-UES-oncogene/TSG-HCC axis that explains how mutations at different layers would finally lead to abnormal phenotype. In the light of central dogma, our work provides novel insights into how to fully take advantage of the transcriptome data to decipher the consequence of mutations.
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Affiliation(s)
- Jian Li
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Chaowei Li
- Department of PET/CT, The Second Clinical Medical College of Qingdao University (Qingdao Center Hospital), Qingdao, 266042, China
| | - Wengui Xu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
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Cui Y, Qi Y, Ding L, Ding S, Han Z, Wang Y, Du P. miRNA dosage control in development and human disease. Trends Cell Biol 2024; 34:31-47. [PMID: 37419737 DOI: 10.1016/j.tcb.2023.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 07/09/2023]
Abstract
In mammals, miRNAs recognize target mRNAs via base pairing, which leads to a complex 'multiple-to-multiple' regulatory network. Previous studies have focused on the regulatory mechanisms and functions of individual miRNAs, but alterations of many individual miRNAs do not strongly disturb the miRNA regulatory network. Recent studies revealed the important roles of global miRNA dosage control events in physiological processes and pathogenesis, suggesting that miRNAs can be considered as a 'cellular buffer' that controls cell fate. Here, we review the current state of research on how global miRNA dosage is tightly controlled to regulate development, tumorigenesis, neurophysiology, and immunity. We propose that methods of controlling global miRNA dosage may serve as effective therapeutic tools to cure human diseases.
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Affiliation(s)
- Yingzi Cui
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ye Qi
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Li Ding
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shuangjin Ding
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Zonglin Han
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China.
| | - Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
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Merdler-Rabinowicz R, Gorelik D, Park J, Meydan C, Foox J, Karmon M, Roth H, Cohen-Fultheim R, Shohat-ophir G, Eisenberg E, Ruppin E, Mason C, Levanon E. Elevated A-to-I RNA editing in COVID-19 infected individuals. NAR Genom Bioinform 2023; 5:lqad092. [PMID: 37859800 PMCID: PMC10583280 DOI: 10.1093/nargab/lqad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Given the current status of coronavirus disease 2019 (COVID-19) as a global pandemic, it is of high priority to gain a deeper understanding of the disease's development and how the virus impacts its host. Adenosine (A)-to-Inosine (I) RNA editing is a post-transcriptional modification, catalyzed by the ADAR family of enzymes, that can be considered part of the inherent cellular defense mechanism as it affects the innate immune response in a complex manner. It was previously reported that various viruses could interact with the host's ADAR enzymes, resulting in epigenetic changes both to the virus and the host. Here, we analyze RNA-seq of nasopharyngeal swab specimens as well as whole-blood samples of COVID-19 infected individuals and show a significant elevation in the global RNA editing activity in COVID-19 compared to healthy controls. We also detect specific coding sites that exhibit higher editing activity. We further show that the increment in editing activity during the disease is temporary and returns to baseline shortly after the symptomatic period. These significant epigenetic changes may contribute to the immune system response and affect adverse outcomes seen in post-viral cases.
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Affiliation(s)
- Rona Merdler-Rabinowicz
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- The Institute of Nanotechnology and Advanced Materials, Bar‐Ilan University, Ramat Gan, Israel
| | - David Gorelik
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar‐Ilan University, Ramat Gan, Israel
| | - Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Cem Meydan
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Miriam Karmon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar‐Ilan University, Ramat Gan, Israel
| | - Hillel S Roth
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar‐Ilan University, Ramat Gan, Israel
| | - Roni Cohen-Fultheim
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar‐Ilan University, Ramat Gan, Israel
| | - Galit Shohat-ophir
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Leslie and Susan Gonda Multidisciplinary Brain Research Center and The Nanotechnology Institute, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel Aviv, Israel
| | - Eytan Ruppin
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher E Mason
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar‐Ilan University, Ramat Gan, Israel
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Nguyen TA, Heng JWJ, Ng YT, Sun R, Fisher S, Oguz G, Kaewsapsak P, Xue S, Reversade B, Ramasamy A, Eisenberg E, Tan MH. Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus. BMC Biol 2023; 21:251. [PMID: 37946231 PMCID: PMC10636886 DOI: 10.1186/s12915-023-01756-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Xenopus has served as a valuable model system for biomedical research over the past decades. Notably, ADAR was first detected in frog oocytes and embryos as an activity that unwinds RNA duplexes. However, the scope of A-to-I RNA editing by the ADAR enzymes in Xenopus remains underexplored. RESULTS Here, we identify millions of editing events in Xenopus with high accuracy and systematically map the editome across developmental stages, adult organs, and species. We report diverse spatiotemporal patterns of editing with deamination activity highest in early embryogenesis before zygotic genome activation and in the ovary. Strikingly, editing events are poorly conserved across different Xenopus species. Even sites that are detected in both X. laevis and X. tropicalis show largely divergent editing levels or developmental profiles. In protein-coding regions, only a small subset of sites that are found mostly in the brain are well conserved between frogs and mammals. CONCLUSIONS Collectively, our work provides fresh insights into ADAR activity in vertebrates and suggest that species-specific editing may play a role in each animal's unique physiology or environmental adaptation.
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Affiliation(s)
- Tram Anh Nguyen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Jia Wei Joel Heng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Yan Ting Ng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rui Sun
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Shira Fisher
- Faculty of Life Sciences, The Mina and Everard Goodman, Bar-Ilan University, Ramat Gan, Israel
| | - Gokce Oguz
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Pornchai Kaewsapsak
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Bruno Reversade
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medical Genetics, School of Medicine (KUSoM), Koç University, Istanbul, Turkey
| | - Adaikalavan Ramasamy
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore.
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.
- HP-NTU Digital Manufacturing Corporate Lab, Nanyang Technological University, Singapore, Singapore.
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Voss G, Cassidy JR, Ceder Y. Functional consequences of A-to-I editing of miR-379 in prostate cancer cells. Sci Rep 2023; 13:16602. [PMID: 37789115 PMCID: PMC10547749 DOI: 10.1038/s41598-023-43775-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023] Open
Abstract
Prostate cancer is the predominant cause of cancer in men, but there is still a lack of biomarkers and treatments for metastatic spread. The initial promise of microRNAs to provide avenues to solve these problems has been dampened by the realisation that microRNAs co-exist in multiple functionally distinct isoforms, for example due to A-to-I editing. We recently found that A-to-I-editing of microRNA-379 (miR-379) was associated with prostate cancer, and that only the unedited isoform was negatively correlated with aggressive disease. Here, we set out to decipher the biological effects of unedited and edited miR-379 in prostate cancer cells. After transfection of four different prostate cancer cell lines with isoform-specific miR-379 mimics, we performed assays for cell growth, colony formation, migration, cell-cell adhesion, and analysed epithelial-mesenchymal transition (EMT) and stemness markers. We found that unedited miR-379 affected cell growth, with a promoting function in androgen receptor (AR)-negative cells and an inhibiting effect in AR-positive cells. This is supported by our in silico analysis that found unedited miR-379 targets are predicted to be predominantly involved in cellular proliferation whereas the targets of edited miR-379 are not. We further found that both miR-379 isoforms could promote colony formation, migration, and cell-cell adhesion. Overall, our data suggests that editing of miR-379 attenuates the growth-suppressive function of unedited miR-379 in androgen-sensitive prostate cancer cells, thereby promoting tumor growth.
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Affiliation(s)
- Gjendine Voss
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - James R Cassidy
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Yvonne Ceder
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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Liu Y, Guo S, Xie W, Yang H, Li W, Zhou N, Yang J, Zhou G, Mao C, Zheng Y. Identification of microRNA editing sites in clear cell renal cell carcinoma. Sci Rep 2023; 13:15117. [PMID: 37704698 PMCID: PMC10499803 DOI: 10.1038/s41598-023-42302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a malignant tumor originating from the renal tubular epithelium. Although the microRNAs (miRNAs) transcriptome of ccRCC has been extensively studied, the role of miRNAs editing in ccRCC is largely unknown. By analyzing small RNA sequencing profiles of renal tissues of 154 ccRCC patients and 22 normal controls, we identified 1025 miRNA editing sites from 246 pre-miRNAs. There were 122 editing events with significantly different editing levels in ccRCC compared to normal samples, which include two A-to-I editing events in the seed regions of hsa-mir-376a-3p and hsa-mir-376c-3p, respectively, and one C-to-U editing event in the seed region of hsa-mir-29c-3p. After comparing the targets of the original and edited miRNAs, we found that hsa-mir-376a-1_49g, hsa-mir-376c_48g and hsa-mir-29c_59u had many new targets, respectively. Many of these new targets were deregulated in ccRCC, which might be related to the different editing levels of hsa-mir-376a-3p, hsa-mir-376c-3p, hsa-mir-29c-3p in ccRCC compared to normal controls. Our study sheds new light on miRNA editing events and their potential biological functions in ccRCC.
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Affiliation(s)
- Yulong Liu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Shiyong Guo
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Wenping Xie
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Huaide Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Wanran Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Nan Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, Kunming, 650223, Yunnan, China
| | - Guangchen Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Chunyi Mao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yun Zheng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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Yuan S, Liu Z, Yu S, Wang X, Shi J. CCND2 and miR-206 as potential biomarkers in the clinical diagnosis of thyroid carcinoma by fine-needle aspiration cytology. World J Surg Oncol 2023; 21:22. [PMID: 36694220 PMCID: PMC9872353 DOI: 10.1186/s12957-023-02899-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/10/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND To investigate the relationship between cyclin D2 (CCND2) and miR-206 expression in fine-needle aspiration cytology of thyroid carcinoma. METHODS A total of 65 patients with thyroid carcinoma were selected as the subjects and 65 patients with benign thyroid nodules were in control group. The fine-needle aspiration cytology of thyroid nodules was performed. CCND2 and miR-206 levels were detected by PCR. RESULTS Compared with the patients with benign thyroid nodules, the expression level of miR-206 in fine-needle aspiration cytology of thyroid cancer patients decreased significantly and the expression level of CCND2 increased significantly. CCND2 and miR-206 expression was negatively correlated in thyroid cancer tissues. Area under curve (AUC) of miR-206 level in the diagnosis of thyroid cancer was 0.889, and the sensitivity and specificity were 92.3% and 81.5%, respectively. AUC of CCND2 level in the diagnosis of thyroid cancer was 0.837, and the sensitivity and specificity were 67.7% and 89.2%, respectively. The AUC of combined detection of CCND2 and miR-206 in the diagnosis of thyroid cancer was 0.959, and the sensitivity and specificity were 93.8% and 87.7%, respectively. The levels of miR-206 and CCND2 were significantly correlated with TNM staging and lymph node metastasis. CONCLUSIONS miR-206 and CCND2 may become new biomarkers for clinical diagnosis of thyroid cancer based on the fine-needle aspiration cytology of thyroid nodules.
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Affiliation(s)
- Shifa Yuan
- Department of General Surgery, Hospital of Hebei Province Crop of Chinese Armed Police Force, Shijiazhuang, Hebei, China
| | - Zhijun Liu
- Department of General Surgery, Hospital of Hebei Province Crop of Chinese Armed Police Force, Shijiazhuang, Hebei, China
| | - Shanshan Yu
- Department of General Surgery, Hospital of Hebei Province Crop of Chinese Armed Police Force, Shijiazhuang, Hebei, China
| | - Xiaolei Wang
- Department of General Surgery, Hospital of Hebei Province Crop of Chinese Armed Police Force, Shijiazhuang, Hebei, China
| | - Jian Shi
- Department of Otolaryngology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China.
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10
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Characterizing Relevant MicroRNA Editing Sites in Parkinson's Disease. Cells 2022; 12:cells12010075. [PMID: 36611869 PMCID: PMC9818192 DOI: 10.3390/cells12010075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are extensively edited in human brains. However, the functional relevance of the miRNA editome is largely unknown in Parkinson's disease (PD). By analyzing small RNA sequencing profiles of brain tissues of 43 PD patients and 88 normal controls, we found that the editing levels of five A-to-I and two C-to-U editing sites are significantly correlated with the ages of normal controls, which is disrupted in PD patients. We totally identified 362 miRNA editing sites with significantly different editing levels in prefrontal cortices of PD patients (PD-PC) compared to results of normal controls. We experimentally validated that A-to-I edited miR-497-5p, with significantly higher expression levels in PD-PC compared to normal controls, directly represses OPA1 and VAPB. Furthermore, overexpression of A-to-I edited miR-497-5p downregulates OPA1 and VAPB in two cell lines, and inhibits proliferation of glioma cells. These results suggest that the hyperediting of miR-497-5p in PD contributes to enhanced progressive neurodegeneration of PD patients. Our results provide new insights into the mechanistic understanding, novel diagnostics, and therapeutic clues of PD.
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11
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Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance. Commun Biol 2022; 5:1400. [PMID: 36543858 PMCID: PMC9772385 DOI: 10.1038/s42003-022-04338-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Posttranscriptional modification plays an important role in key embryonic processes. Adenosine-to-inosine RNA editing, a common example of such modifications, is widespread in human adult tissues and has various functional impacts and clinical consequences. However, whether it persists in a consistent pattern in most human embryos, and whether it supports embryonic development, are poorly understood. To address this problem, we compiled the largest human embryonic editome from 2,071 transcriptomes and identified thousands of recurrent embryonic edits (>=50% chances of occurring in a given stage) for each early developmental stage. We found that these recurrent edits prefer exons consistently across stages, tend to target genes related to DNA replication, and undergo organized loss in abnormal embryos and embryos from elder mothers. In particular, these recurrent edits are likely to enhance maternal mRNA clearance, a possible mechanism of which could be introducing more microRNA binding sites to the 3'-untranslated regions of clearance targets. This study suggests a potentially important, if not indispensable, role of RNA editing in key human embryonic processes such as maternal mRNA clearance; the identified editome can aid further investigations.
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12
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de Rooij LA, Mastebroek DJ, ten Voorde N, van der Wall E, van Diest PJ, Moelans CB. The microRNA Lifecycle in Health and Cancer. Cancers (Basel) 2022; 14:cancers14235748. [PMID: 36497229 PMCID: PMC9736740 DOI: 10.3390/cancers14235748] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of ~22 nucleotides that regulate gene expression at the post-transcriptional level. They can bind to around 60% of all protein-coding genes with an average of 200 targets per miRNA, indicating their important function within physiological and pathological cellular processes. miRNAs can be quickly produced in high amounts through canonical and non-canonical pathways that involve a multitude of steps and proteins. In cancer, miRNA biogenesis, availability and regulation of target expression can be altered to promote tumour progression. This can be due to genetic causes, such as single nucleotide polymorphisms, epigenetic changes, differences in host gene expression, or chromosomal remodelling. Alternatively, post-transcriptional changes in miRNA stability, and defective or absent components and mediators of the miRNA-induced silencing complex can lead to altered miRNA function. This review provides an overview of the current knowledge on the lifecycle of miRNAs in health and cancer. Understanding miRNA function and regulation is fundamental prior to potential future application of miRNAs as cancer biomarkers.
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Affiliation(s)
- Laura Adriana de Rooij
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-887-556-557
| | - Dirk Jan Mastebroek
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Nicky ten Voorde
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Elsken van der Wall
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Paul Joannes van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Cathy Beatrice Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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13
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Li M, Yan C, Jiao Y, Xu Y, Bai C, Miao R, Jiang J, Liu J. Site-directed RNA editing by harnessing ADARs: advances and challenges. Funct Integr Genomics 2022; 22:1089-1103. [DOI: 10.1007/s10142-022-00910-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]
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14
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Distefano R, Tomasello L, Rampioni Vinciguerra GL, Gasparini P, Xiang Y, Bagnoli M, Marceca GP, Fadda P, Laganà A, Acunzo M, Ma Q, Nigita G, Croce CM. Pan-Cancer Analysis of Canonical and Modified miRNAs Enhances the Resolution of the Functional miRNAome in Cancer. Cancer Res 2022; 82:3687-3700. [PMID: 36040379 PMCID: PMC9574374 DOI: 10.1158/0008-5472.can-22-0240] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/24/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
Epitranscriptomic studies of miRNAs have added a new layer of complexity to the cancer field. Although there is fast-growing interest in adenosine-to-inosine (A-to-I) miRNA editing and alternative cleavage that shifts miRNA isoforms, simultaneous evaluation of both modifications in cancer is still missing. Here, we concurrently profiled multiple miRNA modification types, including A-to-I miRNA editing and shifted miRNA isoforms, in >13,000 adult and pediatric tumor samples across 38 distinct cancer cohorts from The Cancer Genome Atlas and The Therapeutically Applicable Research to Generate Effective Treatments data sets. The differences between canonical miRNAs and the wider miRNAome in terms of expression, clustering, dysregulation, and prognostic standpoint were investigated. The combination of canonical miRNAs and modified miRNAs boosted the quality of clustering results, outlining unique clinicopathologic features among cohorts. Certain modified miRNAs showed opposite expression from their canonical counterparts in cancer, potentially impacting their targets and function. Finally, a shifted and edited miRNA isoform was experimentally validated to directly bind and suppress a unique target. These findings outline the importance of going beyond the well-established paradigm of one mature miRNA per miRNA arm to elucidate novel mechanisms related to cancer progression. SIGNIFICANCE Modified miRNAs may act as cancer biomarkers and function as allies or antagonists of their canonical counterparts in gene regulation, suggesting the concurrent consideration of canonical and modified miRNAs can boost patient stratification.
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Affiliation(s)
- Rosario Distefano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Faculty of Medicine and Psychology, Department of Clinical and Molecular Medicine, University of Rome “Sapienza,” Santo Andrea Hospital, Rome, Italy
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Yujia Xiang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Marina Bagnoli
- Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Gioacchino P. Marceca
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Paolo Fadda
- Genomics Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
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15
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Qin JX, Liu X, Wang XL, Wang GY, Liang Q, Dong Y, Pang K, Hao L, Xue L, Zhao Y, Hu ZX, Li R, Lv Q, Chao L, Meng FL, Shi ZD, Han CH. Identification and analysis of microRNA editing events in recurrent bladder cancer based on RNA sequencing: MicroRNA editing level is a potential novel biomarker. Front Genet 2022; 13:984279. [PMID: 36199571 PMCID: PMC9527279 DOI: 10.3389/fgene.2022.984279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background: With the continued advancement of RNA-seq (RNA-sequencing), microRNA (miRNA) editing events have been demonstrated to play an important role in different malignancies. However, there is yet no description of the miRNA editing events in recurrent bladder cancer.Objective: To identify and compare miRNA editing events in primary and recurrent bladder cancer, as well as to investigate the potential molecular mechanism and its impact on patient prognosis.Methods: We examined the mRNA and miRNA transcriptomes of 12 recurrent bladder cancer cases and 13 primary bladder cancer cases. The differentially expressed mRNA sequences were analyzed. Furthermore, we identified the differentially expressed genes (DEGs) in recurrent bladder cancer. The Gene Ontology (GO) functional enrichment analyses on DEGs and gene set enrichment analysis were performed. The consensus molecular subtype (CMS) classification of bladder cancer was identified using the Consensus MIBC package in R (4.1.0); miRNA sequences were then further subjected to differentially expressed analysis and pathway enrichment analysis. MiRNA editing events were identified using miRge3.0. miRDB and TargetScanHuman were used to predict the downstream targets of specific differentially edited or expressed miRNAs. The expression levels of miR-154-5p and ADAR were validated by RT-qPCR. Finally, survival and co-expression studies were performed on the TCGA-BLCA cohort.Results: First, the mRNA expression levels in recurrent bladder cancer changed significantly, supporting progression via related molecular signal pathways. Second, significantly altered miRNAs in recurrent bladder cancer were identified, with miR-154-5p showing the highest level of editing in recurrent bladder cancer and may up-regulate the expression levels of downstream targets HS3ST3A1, AQP9, MYLK, and RAB23. The survival analysis results of TCGA data revealed that highly expressed HS3ST3A1 and RAB23 exhibited poor prognosis. In addition, miR-154 editing events were found to be significant to CMS classification.Conclusion: MiRNA editing in recurrent bladder cancer was detected and linked with poor patient prognosis, providing a reference for further uncovering the intricate molecular mechanism in recurrent bladder cancer. Therefore, inhibiting A-to-I editing of miRNA may be a viable target for bladder cancer treatment, allowing current treatment choices to be expanded and individualized.
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Affiliation(s)
- Jia-Xin Qin
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Xing Liu
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Xin-Lei Wang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Guang-Yue Wang
- Graduate School of Bengbu Medical College, Bengbu, China
| | - Qing Liang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yang Dong
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Kun Pang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Lin Hao
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Liang Xue
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yan Zhao
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Zheng-Xiang Hu
- Graduate School of Jinzhou Medical College, Jinzhou, China
| | - Rui Li
- Central Laboratory, Xuzhou Central Hospital, Xuzhou, China
| | - Qian Lv
- Central Laboratory, Xuzhou Central Hospital, Xuzhou, China
| | - Liu Chao
- Department of Urology, The Suqian Affiliated Hospital of Xuzhou Medical University School, Suqian, China
| | - Fan-Lai Meng
- Department of Pathology, The Suqian Affiliated Hospital of Xuzhou Medical University School, Suqian, China
| | - Zhen-Duo Shi
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Zhen-Duo Shi, ; Cong-Hui Han,
| | - Cong-Hui Han
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Urology, Heilongjiang Provincial Hospital, Harbin, China
- *Correspondence: Zhen-Duo Shi, ; Cong-Hui Han,
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16
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del Valle-Morales D, Le P, Saviana M, Romano G, Nigita G, Nana-Sinkam P, Acunzo M. The Epitranscriptome in miRNAs: Crosstalk, Detection, and Function in Cancer. Genes (Basel) 2022; 13:1289. [PMID: 35886072 PMCID: PMC9316458 DOI: 10.3390/genes13071289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
The epitranscriptome encompasses all post-transcriptional modifications that occur on RNAs. These modifications can alter the function and regulation of their RNA targets, which, if dysregulated, result in various diseases and cancers. As with other RNAs, miRNAs are highly modified by epitranscriptomic modifications such as m6A methylation, 2'-O-methylation, m5C methylation, m7G methylation, polyuridine, and A-to-I editing. miRNAs are a class of small non-coding RNAs that regulates gene expression at the post-transcriptional level. miRNAs have gathered high clinical interest due to their role in disease, development, and cancer progression. Epitranscriptomic modifications alter the targeting, regulation, and biogenesis of miRNAs, increasing the complexity of miRNA regulation. In addition, emerging studies have revealed crosstalk between these modifications. In this review, we will summarize the epitranscriptomic modifications-focusing on those relevant to miRNAs-examine the recent crosstalk between these modifications, and give a perspective on how this crosstalk expands the complexity of miRNA biology.
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Affiliation(s)
- Daniel del Valle-Morales
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Patricia Le
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Michela Saviana
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giovanni Nigita
- Comprehensive Cancer Center, Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA;
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
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17
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Liu J, Wang F, Zhang Y, Liu J, Zhao B. ADAR1-Mediated RNA Editing and Its Role in Cancer. Front Cell Dev Biol 2022; 10:956649. [PMID: 35898396 PMCID: PMC9309331 DOI: 10.3389/fcell.2022.956649] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
It is well known that the stability of RNA, the interaction between RNA and protein, and the correct translation of protein are significant forces that drive the transition from normal cell to malignant tumor. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that catalyzes the deamination of adenosine to inosine (A-to-I), which is one dynamic modification that in a combinatorial manner can give rise to a very diverse transcriptome. ADAR1-mediated RNA editing is essential for survival in mammals and its dysregulation results in aberrant editing of its substrates that may affect the phenotypic changes in cancer. This overediting phenomenon occurs in many cancers, such as liver, lung, breast, and esophageal cancers, and promotes tumor progression in most cases. In addition to its editing role, ADAR1 can also play an editing-independent role, although current research on this mechanism is relatively shallowly explored in tumors. In this review, we summarize the nature of ADAR1, mechanisms of ADAR1 editing-dependent and editing-independent and implications for tumorigenesis and prognosis, and pay special attention to effects of ADAR1 on cancers by regulating non-coding RNA formation and function.
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Affiliation(s)
- Jizhe Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Yindan Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Jingfeng Liu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
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18
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Kokot KE, Kneuer JM, John D, Rebs S, Möbius-Winkler MN, Erbe S, Müller M, Andritschke M, Gaul S, Sheikh BN, Haas J, Thiele H, Müller OJ, Hille S, Leuschner F, Dimmeler S, Streckfuss-Bömeke K, Meder B, Laufs U, Boeckel JN. Reduction of A-to-I RNA editing in the failing human heart regulates formation of circular RNAs. Basic Res Cardiol 2022; 117:32. [PMID: 35737129 PMCID: PMC9226085 DOI: 10.1007/s00395-022-00940-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 01/31/2023]
Abstract
Alterations of RNA editing that affect the secondary structure of RNAs can cause human diseases. We therefore studied RNA editing in failing human hearts. Transcriptome sequencing showed that adenosine-to-inosine (A-to-I) RNA editing was responsible for 80% of the editing events in the myocardium. Failing human hearts were characterized by reduced RNA editing. This was primarily attributable to Alu elements in introns of protein-coding genes. In the failing left ventricle, 166 circRNAs were upregulated and 7 circRNAs were downregulated compared to non-failing controls. Most of the upregulated circRNAs were associated with reduced RNA editing in the host gene. ADAR2, which binds to RNA regions that are edited from A-to-I, was decreased in failing human hearts. In vitro, reduction of ADAR2 increased circRNA levels suggesting a causal effect of reduced ADAR2 levels on increased circRNAs in the failing human heart. To gain mechanistic insight, one of the identified upregulated circRNAs with a high reduction of editing in heart failure, AKAP13, was further characterized. ADAR2 reduced the formation of double-stranded structures in AKAP13 pre-mRNA, thereby reducing the stability of Alu elements and the circularization of the resulting circRNA. Overexpression of circAKAP13 impaired the sarcomere regularity of human induced pluripotent stem cell-derived cardiomyocytes. These data show that ADAR2 mediates A-to-I RNA editing in the human heart. A-to-I RNA editing represses the formation of dsRNA structures of Alu elements favoring canonical linear mRNA splicing and inhibiting the formation of circRNAs. The findings are relevant to diseases with reduced RNA editing and increased circRNA levels and provide insights into the human-specific regulation of circRNA formation.
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Affiliation(s)
- Karoline E Kokot
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Jasmin M Kneuer
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - David John
- Institute for Cardiovascular Regeneration, Goethe-University Hospital, Theodor Stern Kai 7, Frankfurt, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Sabine Rebs
- Institute of Pharmacology and Toxicology, Versbacher-Str. 9, Würzburg, Germany
- Heartcenter - Clinic for Cardiology and Pneumology, University Medicine Goettingen, Robert-Koch-Str. 40, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | | | - Stephan Erbe
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Marion Müller
- Department of General and Interventional Cardiology/Angiology, Ruhr University of Bochum, Heart-and Diabetes Center North Rhine-Westphalia, Bad Oeynhausen, Germany
| | - Michael Andritschke
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Susanne Gaul
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Bilal N Sheikh
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Jan Haas
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Holger Thiele
- Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute, Leipzig, Germany
| | - Oliver J Müller
- Department of Internal Medicine III, University of Kiel, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Susanne Hille
- Department of Internal Medicine III, University of Kiel, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Florian Leuschner
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe-University Hospital, Theodor Stern Kai 7, Frankfurt, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Katrin Streckfuss-Bömeke
- Institute of Pharmacology and Toxicology, Versbacher-Str. 9, Würzburg, Germany
- Heartcenter - Clinic for Cardiology and Pneumology, University Medicine Goettingen, Robert-Koch-Str. 40, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Ulrich Laufs
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Jes-Niels Boeckel
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany.
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19
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Zhang S, Kuang G, Huang Y, Huang X, Wang W, Wang G. Cross talk between RNA modification writers and tumor development as a basis for guiding personalized therapy of gastric cancer. Hum Genomics 2022; 16:14. [PMID: 35449086 PMCID: PMC9027049 DOI: 10.1186/s40246-022-00386-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/28/2022] [Indexed: 12/29/2022] Open
Abstract
Background Gastric cancer (GC) shows high metastasis and low survival. RNA modification writers play critical roles in tumor development. This study examined the clinical significance of RNA modification writers in GC prognosis based on four types of adenosine modifications (m1A, m6A, APA and A-to-I). Results Writers demonstrated high mutation and expression in GC patients. Different expressions of 26 RNA modification writers were differentially associated with GC prognosis. High-WM score group appeared worse overall survival, higher immune infiltration and activation of EMT pathways than low-WM score group. WM score was correlated with both miRNAs-targeted signaling pathways and patients’ sensitivity to chemotherapeutic drugs and efficacy of immunotherapy. Conclusions This study further revealed the close association between adenosine-related RNA modifications and progression of GC. A cross talk between EMT and RNA modification was identified to be one of the mechanisms underlying GC development. Our WM scoring system could serve as a clinical indicator for predicting GC prognosis. Importantly, the WM score could guide personalized treatments such as chemotherapy and immunotherapy for GC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00386-z.
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Affiliation(s)
- Shi Zhang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China
| | - Guanghao Kuang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China
| | - Yao Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China
| | - Xinxin Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China
| | - Weiyu Wang
- Department of Oncology, HaploX Biotechnology, Co., Ltd., Shenzhen, 518057, China
| | - Guoqiang Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China.
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20
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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21
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Distefano R, Nigita G, Le P, Romano G, Acunzo M, Nana-Sinkam P. Disparities in Lung Cancer: miRNA Isoform Characterization in Lung Adenocarcinoma. Cancers (Basel) 2022; 14:773. [PMID: 35159038 PMCID: PMC8833952 DOI: 10.3390/cancers14030773] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 02/04/2023] Open
Abstract
Despite the development of targeted therapeutics, immunotherapy, and strategies for early detection, lung cancer carries a high mortality. Further, significant racial disparities in outcomes exist for which the molecular drivers have yet to be fully elucidated. The growing field of Epitranscriptomics has introduced a new layer of complexity to the molecular pathogenesis of cancer. RNA modifications can occur in coding and non-coding RNAs, such as miRNAs, possibly altering their gene regulatory function. The potential role for such modifications as clinically informative biomarkers remains largely unknown. Here, we concurrently profiled canonical miRNAs, shifted isomiRs (templated and non-templated), and miRNAs with single-point modification events (RNA and DNA) in White American (W) and Black or African American (B/AA) lung adenocarcinoma (LUAD) patients. We found that while most deregulated miRNA isoforms were similar in W and B/AA LUAD tissues compared to normal adjacent tissues, there was a subgroup of isoforms with deregulation according to race. We specifically investigated an edited miRNA, miR-151a-3p with an A-to-I editing event at position 3, to determine how its altered expression may be associated with activation of divergent biological pathways between W and B/AA LUAD patients. Finally, we identified distinct race-specific miRNA isoforms that correlated with prognosis for both Ws and B/AAs. Our results suggested that concurrently profiling canonical and non-canonical miRNAs may have potential as a strategy for identifying additional distinct biological pathways and biomarkers in lung cancer.
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Affiliation(s)
- Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (R.D.); (G.N.)
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (R.D.); (G.N.)
| | - Patricia Le
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (G.R.)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (G.R.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (G.R.)
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (G.R.)
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22
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Voss G, Edsjö A, Bjartell A, Ceder Y. Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery. RNA (NEW YORK, N.Y.) 2021; 27:1412-1424. [PMID: 34433636 PMCID: PMC8522694 DOI: 10.1261/rna.078867.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Even though microRNAs have been viewed as promising biomarkers for years, their clinical implementation is still lagging far behind. This is in part due to the lack of RT-qPCR technologies that can differentiate between microRNA isoforms. For example, A-to-I editing of microRNAs through adenosine deaminase acting on RNA (ADAR) enzymes can affect their expression levels and functional roles, but editing isoform-specific assays are not commercially available. Here, we describe RT-qPCR assays that are specific for editing isoforms, using microRNA-379 (miR-379) as a model. The assays are based on two-tailed RT-qPCR, and we show them to be compatible both with SYBR Green and hydrolysis-based chemistries, as well as with both qPCR and digital PCR. The assays could readily detect different miR-379 editing isoforms in various human tissues as well as changes of editing levels in ADAR-overexpressing cell lines. We found that the miR-379 editing frequency was higher in prostate cancer samples compared to benign prostatic hyperplasia samples. Furthermore, decreased expression of unedited miR-379, but not edited miR-379, was associated with treatment resistance, metastasis, and shorter overall survival. Taken together, this study presents the first RT-qPCR assays that were demonstrated to distinguish A-to-I-edited microRNAs, and shows that they can be useful in the identification of biomarkers that previously have been masked by other isoforms.
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Affiliation(s)
- Gjendine Voss
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, 22381 Lund, Sweden
| | - Anders Edsjö
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Region Skåne, 22185 Lund, Sweden
| | - Anders Bjartell
- Department of Urology, Skåne University Hospital, 20502 Malmö, Sweden
| | - Yvonne Ceder
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, 22381 Lund, Sweden
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23
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Li J, Yu CP, Li Q, Chang S, Xie LL, Wang S. Large-scale omics data reveal the cooperation of mutation-circRNA-miRNA-target gene network in liver cancer oncogenesis. Future Oncol 2021; 18:163-178. [PMID: 34677082 DOI: 10.2217/fon-2021-0940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aims: Clarifying the initial trigger of the differentially expressed genes in cancers helps researchers understand the cellular system as a whole network. Materials & methods: We retrieve the transcriptome and translatome of tumor and normal tissues from ten liver cancer patients and define differentially expressed genes and tumor-specific mutations. We associate the oncogenesis with the mutations by target prediction and experimental verification. Results: Upregulated genes have tumor-specific mutations in 3'UTRs that abolish the binding of miRNAs. For downregulated genes, their corresponding miRNAs are mutually targeted by two circRNAs, with mutations in base-pairing regions. Transfection experiments support the oncogenic role of these mutations. Conclusions: The tumor-specific mutations serve as the initial trigger of liver cancer. The mutation-circRNA-miRNA-target gene chain is completed.
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Affiliation(s)
- Jian Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Chun-Peng Yu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Qun Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Shuai Chang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Ling-Ling Xie
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Song Wang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
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24
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De Paolis V, Lorefice E, Orecchini E, Carissimi C, Laudadio I, Fulci V. Epitranscriptomics: A New Layer of microRNA Regulation in Cancer. Cancers (Basel) 2021; 13:3372. [PMID: 34282776 PMCID: PMC8268402 DOI: 10.3390/cancers13133372] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are pervasive regulators of gene expression at the post-transcriptional level in metazoan, playing key roles in several physiological and pathological processes. Accordingly, these small non-coding RNAs are also involved in cancer development and progression. Furthermore, miRNAs represent valuable diagnostic and prognostic biomarkers in malignancies. In the last twenty years, the role of RNA modifications in fine-tuning gene expressions at several levels has been unraveled. All RNA species may undergo post-transcriptional modifications, collectively referred to as epitranscriptomic modifications, which, in many instances, affect RNA molecule properties. miRNAs are not an exception, in this respect, and they have been shown to undergo several post-transcriptional modifications. In this review, we will summarize the recent findings concerning miRNA epitranscriptomic modifications, focusing on their potential role in cancer development and progression.
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Affiliation(s)
| | | | | | - Claudia Carissimi
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
| | - Ilaria Laudadio
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
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25
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Tomasello L, Distefano R, Nigita G, Croce CM. The MicroRNA Family Gets Wider: The IsomiRs Classification and Role. Front Cell Dev Biol 2021; 9:668648. [PMID: 34178993 PMCID: PMC8220208 DOI: 10.3389/fcell.2021.668648] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are the most characterized class of non-coding RNAs and are engaged in many cellular processes, including cell differentiation, development, and homeostasis. MicroRNA dysregulation was observed in several diseases, cancer included. Epitranscriptomics is a branch of epigenomics that embraces all RNA modifications occurring after DNA transcription and RNA synthesis and involving coding and non-coding RNAs. The development of new high-throughput technologies, especially deep RNA sequencing, has facilitated the discovery of miRNA isoforms (named isomiRs) resulting from RNA modifications mediated by enzymes, such as deaminases and exonucleases, and differing from the canonical ones in length, sequence, or both. In this review, we summarize the distinct classes of isomiRs, their regulation and biogenesis, and the active role of these newly discovered molecules in cancer and other diseases.
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Affiliation(s)
- Luisa Tomasello
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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26
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Duan Y, Tang X, Lu J. Evolutionary driving forces of A-to-I editing in metazoans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1666. [PMID: 33998151 DOI: 10.1002/wrna.1666] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/24/2021] [Indexed: 11/05/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is an evolutionarily conserved mechanism that converts adenosines to inosines in metazoans' transcriptomes. However, the landscapes of editomes have considerably changed during evolution. Here, we review some of our current knowledge of A-to-I editing in the metazoan transcriptomes, focusing on the possible evolutionary driving forces underlying the editing events. First, we review the evolution of ADAR gene family in animals. Then, we summarize the recent advances in characterizing the editomes of various metazoan species. Next, we highlight several factors contributing to the interspecies differences in editomes, including variations in copy number and expression patterns of ADAR genes, the differences in genomic architectures and contents, and the differences in the efficacy of natural selection. After that, we review the possible diversifying and restorative effects of the editing (recoding) events that change the protein sequences. Finally, we discuss the possible convergent evolution of RNA editing in distantly related clades. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
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27
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Abstract
C6 deamination of adenosine (A) to inosine (I) in double-stranded RNA (dsRNA) is catalyzed by a family of enzymes known as ADARs (adenosine deaminases acting on RNA) encoded by three genes in mammals. Alternative promoters and splicing produce two ADAR1 proteins, an interferon-inducible cytoplasmic p150 and a constitutively expressed p110 that like ADAR2 is a nuclear enzyme. ADAR3 lacks deaminase activity. A-to-I editing occurs with both viral and cellular RNAs. Deamination activity is dependent on dsRNA substrate structure and regulatory RNA-binding proteins and ranges from highly site selective with hepatitis D RNA and glutamate receptor precursor messenger RNA (pre-mRNA) to hyperediting of measles virus and polyomavirus transcripts and cellular inverted Alu elements. Because I base-pairs as guanosine instead of A, editing can alter mRNA decoding, pre-mRNA splicing, and microRNA silencing. Editing also alters dsRNA structure, thereby suppressing innate immune responses including interferon production and action. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen 63225, Germany
| | - Cyril X George
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Charles E Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
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28
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Marceca GP, Tomasello L, Distefano R, Acunzo M, Croce CM, Nigita G. Detecting and Characterizing A-To-I microRNA Editing in Cancer. Cancers (Basel) 2021; 13:1699. [PMID: 33916692 PMCID: PMC8038323 DOI: 10.3390/cancers13071699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. The employment of powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.
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Affiliation(s)
- Gioacchino P. Marceca
- Department of Clinical and Experimental Medicine, University of Catania, 95125 Catania, Italy
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
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29
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Le P, Romano G, Nana-Sinkam P, Acunzo M. Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer. Cancers (Basel) 2021; 13:cancers13061372. [PMID: 33803619 PMCID: PMC8003033 DOI: 10.3390/cancers13061372] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
Over the last several decades, clinical evaluation and treatment of lung cancers have largely improved with the classification of genetic drivers of the disease, such as EGFR, ALK, and ROS1. There are numerous regulatory factors that exert cellular control over key oncogenic pathways involved in lung cancers. In particular, non-coding RNAs (ncRNAs) have a diversity of regulatory roles in lung cancers such that they have been shown to be involved in inducing proliferation, suppressing apoptotic pathways, increasing metastatic potential of cancer cells, and acquiring drug resistance. The dysregulation of various ncRNAs in human cancers has prompted preclinical studies examining the therapeutic potential of restoring and/or inhibiting these ncRNAs. Furthermore, ncRNAs demonstrate tissue-specific expression in addition to high stability within biological fluids. This makes them excellent candidates as cancer biomarkers. This review aims to discuss the relevance of ncRNAs in cancer pathology, diagnosis, and therapy, with a focus on lung cancer.
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30
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Abstract
RNA editing is an RNA modification that alters the RNA sequence relative to its genomic blueprint. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Editing of a protein-coding region within the RNA molecule may result in non-synonymous substitutions, leading to a modified protein product. These editing sites, also known as "recoding" sites, contribute to the complexity and diversification of the proteome. Recent computational transcriptomic studies have identified thousands of recoding sites in multiple species, many of which are conserved within (but not usually across) lineages and have functional and evolutionary importance. In this chapter we describe the recoding phenomenon across species, consider its potential utility for diversity and adaptation, and discuss its evolution.
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31
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Torsin LI, Petrescu GED, Sabo AA, Chen B, Brehar FM, Dragomir MP, Calin GA. Editing and Chemical Modifications on Non-Coding RNAs in Cancer: A New Tale with Clinical Significance. Int J Mol Sci 2021; 22:ijms22020581. [PMID: 33430133 PMCID: PMC7827606 DOI: 10.3390/ijms22020581] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
Currently, for seemingly every type of cancer, dysregulated levels of non-coding RNAs (ncRNAs) are reported and non-coding transcripts are expected to be the next class of diagnostic and therapeutic tools in oncology. Recently, alterations to the ncRNAs transcriptome have emerged as a novel hallmark of cancer. Historically, ncRNAs were characterized mainly as regulators and little attention was paid to the mechanisms that regulate them. The role of modifications, which can control the function of ncRNAs post-transcriptionally, only recently began to emerge. Typically, these modifications can be divided into reversible (i.e., chemical modifications: m5C, hm5C, m6A, m1A, and pseudouridine) and non-reversible (i.e., editing: ADAR dependent, APOBEC dependent and ADAR/APOBEC independent). The first research papers showed that levels of these modifications are altered in cancer and can be part of the tumorigenic process. Hence, the aim of this review paper is to describe the most common regulatory modifications (editing and chemical modifications) of the traditionally considered “non-functional” ncRNAs (i.e., microRNAs, long non-coding RNAs and circular RNAs) in the context of malignant disease. We consider that only by understanding this extra regulatory layer it is possible to translate the knowledge about ncRNAs and their modifications into clinical practice.
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Affiliation(s)
- Ligia I. Torsin
- Department of Anesthesiology and Critical Care, Elias Clinical Emergency Hospital, 011461 Bucharest, Romania;
| | - George E. D. Petrescu
- Department of Neurosurgery, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (G.E.D.P.); (F.M.B.)
- Department of Neurosurgery, Bagdasar-Arseni Clinical Emergency Hospital, 041915 Bucharest, Romania
| | - Alexandru A. Sabo
- Zentrum für Kinder, Jugend und Frauenmedizin, Pediatrics 2 (General and Special Pediatrics), Klinikum Stuttgart, Olgahospital, 70174 Stuttgart, Germany;
| | - Baoqing Chen
- State Key Laboratory of Oncology in South China, Department of Radiation Oncology, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Research Institute, Guangzhou 510060, China
| | - Felix M. Brehar
- Department of Neurosurgery, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (G.E.D.P.); (F.M.B.)
- Department of Neurosurgery, Bagdasar-Arseni Clinical Emergency Hospital, 041915 Bucharest, Romania
| | - Mihnea P. Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Correspondence: or (M.P.D.); (G.A.C.); Tel.: +40-254-219-493 (M.P.D.); +1-713-792-5461 (G.A.C.)
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Correspondence: or (M.P.D.); (G.A.C.); Tel.: +40-254-219-493 (M.P.D.); +1-713-792-5461 (G.A.C.)
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32
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Schaffer AA, Levanon EY. ALU A-to-I RNA Editing: Millions of Sites and Many Open Questions. Methods Mol Biol 2021; 2181:149-162. [PMID: 32729079 DOI: 10.1007/978-1-0716-0787-9_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alu elements are repetitive short interspersed elements prevalent in the primate genome. These repeats account for over 10% of the genome with more than a million highly similar copies. A direct outcome of this is an enrichment in long structures of stable dsRNA, which are the target of adenosine deaminases acting on RNAs (ADARs), the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, despite the radical increase in ADAR targets brought on by the introduction of Alu elements, the few evolutionary conserved editing sites manage to retain their editing levels. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which possibly contributed to accelerating primate evolution.
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Affiliation(s)
- Amos A Schaffer
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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Erdmann EA, Mahapatra A, Mukherjee P, Yang B, Hundley HA. To protect and modify double-stranded RNA - the critical roles of ADARs in development, immunity and oncogenesis. Crit Rev Biochem Mol Biol 2020; 56:54-87. [PMID: 33356612 DOI: 10.1080/10409238.2020.1856768] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) are present in all animals and function to both bind double-stranded RNA (dsRNA) and catalyze the deamination of adenosine (A) to inosine (I). As inosine is a biological mimic of guanosine, deamination by ADARs changes the genetic information in the RNA sequence and is commonly referred to as RNA editing. Millions of A-to-I editing events have been reported for metazoan transcriptomes, indicating that RNA editing is a widespread mechanism used to generate molecular and phenotypic diversity. Loss of ADARs results in lethality in mice and behavioral phenotypes in worm and fly model systems. Furthermore, alterations in RNA editing occur in over 35 human pathologies, including several neurological disorders, metabolic diseases, and cancers. In this review, a basic introduction to ADAR structure and target recognition will be provided before summarizing how ADARs affect the fate of cellular RNAs and how researchers are using this knowledge to engineer ADARs for personalized medicine. In addition, we will highlight the important roles of ADARs and RNA editing in innate immunity and cancer biology.
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Affiliation(s)
- Emily A Erdmann
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Priyanka Mukherjee
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
| | - Boyoon Yang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
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Kim WR, Park EG, Kang KW, Lee SM, Kim B, Kim HS. Expression Analyses of MicroRNAs in Hamster Lung Tissues Infected by SARS-CoV-2. Mol Cells 2020; 43:953-963. [PMID: 33199671 PMCID: PMC7700842 DOI: 10.14348/molcells.2020.0177] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an infectious disease with multiple severe symptoms, such as fever over 37.5°C, cough, dyspnea, and pneumonia. In our research, microRNAs (miRNAs) binding to the genome sequences of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory-related coronavirus (MERS-CoV), and SARS-CoV-2 were identified by bioinformatic tools. Five miRNAs (hsa-miR-15a-5p, hsa-miR-15b-5p, hsa-miR-195-5p, hsa-miR-16-5p, and hsa-miR-196a-1-3p) were found to commonly bind to SARS-CoV, MERS-CoV, and SARS-CoV-2. We also identified miRNAs that bind to receptor proteins, such as ACE2, ADAM17, and TMPRSS2, which are important for understanding the infection mechanism of SARS-CoV-2. The expression patterns of those miRNAs were examined in hamster lung samples infected by SARS-CoV-2. Five miRNAs (hsa-miR-15b-5p, hsa-miR-195-5p, hsa-miR-221-3p, hsa-miR-140-3p, and hsa-miR-422a) showed differential expression patterns in lung tissues before and after infection. Especially, hsa-miR-15b-5p and hsa-miR-195-5p showed a large difference in expression, indicating that they may potentially be diagnostic biomarkers for SARS-CoV-2 infection.
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Affiliation(s)
- Woo Ryung Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Eun Gyung Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Kyung-Won Kang
- Division of Biotechnology, College of Environmental and Bioresources, Jeonbuk National University, Iksan 54596, Korea
| | - Sang-Myeong Lee
- Division of Biotechnology, College of Environmental and Bioresources, Jeonbuk National University, Iksan 54596, Korea
- Present address: College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Bumseok Kim
- Korea Zoonosis Research Institute and College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
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35
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Moreno C, Santos RM, Burns R, Zhang WC. Succinate Dehydrogenase and Ribonucleic Acid Networks in Cancer and Other Diseases. Cancers (Basel) 2020; 12:cancers12113237. [PMID: 33153035 PMCID: PMC7693138 DOI: 10.3390/cancers12113237] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/24/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Although the dysfunction of the succinate dehydrogenase complex in mitochondria leads to cancer and other diseases due to aberrant metabolic reactions and signaling pathways, it is not well known how the succinate dehydrogenase complex is regulated. Our review highlights that non-coding ribonucleic acids (RNAs), RNA editing enzymes, and RNA modifying enzymes regulate expressions and functions of the succinate dehydrogenase complex. This research will provide new strategies for treating succinate dehydrogenase-relevant diseases in a clinic. Abstract Succinate dehydrogenase (SDH) complex connects both the tricarboxylic acid (TCA) cycle and the electron transport chain (ETC) in the mitochondria. However, SDH mutation or dysfunction-induced succinate accumulation results in multiple cancers and non-cancer diseases. The mechanistic studies show that succinate activates hypoxia response and other signal pathways via binding to 2-oxoglutarate-dependent oxygenases and succinate receptors. Recently, the increasing knowledge of ribonucleic acid (RNA) networks, including non-coding RNAs, RNA editors, and RNA modifiers has expanded our understanding of the interplay between SDH and RNA networks in cancer and other diseases. Here, we summarize recent discoveries in the RNA networks and their connections to SDH. Additionally, we discuss current therapeutics targeting SDH in both pre-clinical and clinical trials. Thus, we propose a new model of SDH–RNA network interaction and bring promising RNA therapeutics against SDH-relevant cancer and other diseases.
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36
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Nakahama T, Kawahara Y. Adenosine-to-inosine RNA editing in the immune system: friend or foe? Cell Mol Life Sci 2020; 77:2931-2948. [PMID: 31996954 PMCID: PMC11104962 DOI: 10.1007/s00018-020-03466-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/27/2019] [Accepted: 01/14/2020] [Indexed: 12/19/2022]
Abstract
Our body expresses sensors to detect pathogens through the recognition of expressed molecules, including nucleic acids, lipids, and proteins, while immune tolerance prevents an overreaction with self and the development of autoimmune disease. Adenosine (A)-to-inosine (I) RNA editing, catalyzed by adenosine deaminases acting on RNA (ADARs), is a post-transcriptional modification that can potentially occur at over 100 million sites in the human genome, mainly in Alu repetitive elements that preferentially form a double-stranded RNA (dsRNA) structure. A-to-I conversion within dsRNA, which may induce a structural change, is required to escape from the host immune system, given that endogenous dsRNAs transcribed from Alu repetitive elements are potentially recognized by melanoma differentiation-associated protein 5 (MDA5) as non-self. Of note, loss-of-function mutations in the ADAR1 gene cause Aicardi-Goutières syndrome, a congenital autoimmune disease characterized by encephalopathy and a type I interferon (IFN) signature. However, the loss of ADAR1 in cancer cells with an IFN signature induces lethality via the activation of protein kinase R in addition to MDA5. This makes cells more sensitive to immunotherapy, highlighting the opposing immune status of autoimmune diseases (overreaction) and cancer (tolerance). In this review, we provide an overview of insights into two opposing aspects of RNA editing that functions as a modulator of the immune system in autoimmune diseases and cancer.
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Affiliation(s)
- Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
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37
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van der Kwast RVCT, Parma L, van der Bent ML, van Ingen E, Baganha F, Peters HAB, Goossens EAC, Simons KH, Palmen M, de Vries MR, Quax PHA, Nossent AY. Adenosine-to-Inosine Editing of Vasoactive MicroRNAs Alters Their Targetome and Function in Ischemia. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:932-953. [PMID: 32814251 PMCID: PMC7452086 DOI: 10.1016/j.omtn.2020.07.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 12/17/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing in the seed sequence of microRNAs can shift the microRNAs’ targetomes and thus their function. Using public RNA-sequencing data, we identified 35 vasoactive microRNAs that are A-to-I edited. We quantified A-to-I editing of the primary (pri-)microRNAs in vascular fibroblasts and endothelial cells. Nine pri-microRNAs were indeed edited, and editing consistently increased under ischemia. We determined mature microRNA editing for the highest expressed microRNAs, i.e., miR-376a-3p, miR-376c-3p, miR-381-3p, and miR-411-5p. All four mature microRNAs were edited in their seed sequence. We show that both ADAR1 and ADAR2 (adenosine deaminase acting on RNA 1 and RNA 2) can edit pri-microRNAs in a microRNA-specific manner. MicroRNA editing also increased under ischemia in vivo in a murine hindlimb ischemia model and ex vivo in human veins. For each edited microRNA, we confirmed a shift in targetome. Expression of the edited microRNA targetomes, not the wild-type targetomes, was downregulated under ischemia in vivo. Furthermore, microRNA editing enhanced angiogenesis in vitro and ex vivo. In conclusion, we show that microRNA A-to-I editing is a widespread phenomenon, induced by ischemia. Each editing event results in a novel microRNA with a unique targetome, leading to increased angiogenesis.
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Affiliation(s)
- Reginald V C T van der Kwast
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Laura Parma
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - M Leontien van der Bent
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eva van Ingen
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Fabiana Baganha
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hendrika A B Peters
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eveline A C Goossens
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Karin H Simons
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Meindert Palmen
- Department of Cardiothoracic Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Margreet R de Vries
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria.
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38
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Non-Coding RNA Editing in Cancer Pathogenesis. Cancers (Basel) 2020; 12:cancers12071845. [PMID: 32650588 PMCID: PMC7408896 DOI: 10.3390/cancers12071845] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.
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39
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Lee HE, Huh JW, Kim HS. Bioinformatics Analysis of Evolution and Human Disease Related Transposable Element-Derived microRNAs. Life (Basel) 2020; 10:life10060095. [PMID: 32630504 PMCID: PMC7345915 DOI: 10.3390/life10060095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/22/2022] Open
Abstract
Transposable element (TE) has the ability to insert into certain parts of the genome, and due to this event, it is possible for TEs to generate new factors and one of these factors are microRNAs (miRNA). miRNAs are non-coding RNAs made up of 19 to 24 nucleotides and numerous miRNAs are derived from TE. In this study, to support general knowledge on TE and miRNAs derived from TE, several bioinformatics tools and databases were used to analyze miRNAs derived from TE in two aspects: evolution and human disease. The distribution of TEs in diverse species presents that almost half of the genome is covered with TE in mammalians and less than a half in other vertebrates and invertebrates. Based on selected evolution-related miRNAs studies, a total of 51 miRNAs derived from TE were found and analyzed. For the human disease-related miRNAs, total of 34 miRNAs derived from TE were organized from the previous studies. In summary, abundant miRNAs derived from TE are found, however, the function of miRNAs derived from TE is not informed either. Therefore, this study provides theoretical understanding of miRNAs derived from TE by using various bioinformatics tools.
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Affiliation(s)
- Hee-Eun Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (H.-E.L.); (J.-W.H.)
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (H.-E.L.); (J.-W.H.)
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2259; Fax: +82-51-581-2962
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40
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Schaffer AA, Kopel E, Hendel A, Picardi E, Levanon E, Eisenberg E. The cell line A-to-I RNA editing catalogue. Nucleic Acids Res 2020; 48:5849-5858. [PMID: 32383740 PMCID: PMC7293008 DOI: 10.1093/nar/gkaa305] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/30/2020] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular diseases as well as cancer. In addition, the endogenous A-to-I editing machinery has been recently harnessed for RNA engineering. The study of RNA editing in humans relies heavily on the usage of cell lines as an important and commonly-used research tool. In particular, manipulations of the editing enzymes and their targets are often developed using cell line platforms. However, RNA editing in cell lines behaves very differently than in normal and diseased tissues, and most cell lines exhibit low editing levels, requiring over-expression of the enzymes. Here, we explore the A-to-I RNA editing landscape across over 1000 human cell lines types and show that for almost every editing target of interest a suitable cell line that mimics normal tissue condition may be found. We provide CLAIRE, a searchable catalogue of RNA editing levels across cell lines available at http://srv00.recas.ba.infn.it/atlas/claire.html, to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing.
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Affiliation(s)
- Amos A Schaffer
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Kopel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ayal Hendel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, I-70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, I-70126 Bari, Italy
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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41
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Liu S, Li B, Liang Q, Liu A, Qu L, Yang J. Classification and function of RNA-protein interactions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1601. [PMID: 32488992 DOI: 10.1002/wrna.1601] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 12/11/2022]
Abstract
Almost all RNAs need to interact with proteins to fully exert their functions, and proteins also bind to RNAs to act as regulators. It has now become clear that RNA-protein interactions play important roles in many biological processes among organisms. Despite the great progress that has been made in the field, there is still no precise classification system for RNA-protein interactions, which makes it challenging to further decipher the functions and mechanisms of these interactions. In this review, we propose four different categories of RNA-protein interactions according to their basic characteristics: RNA motif-dependent RNA-protein interactions, RNA structure-dependent RNA-protein interactions, RNA modification-dependent RNA-protein interactions, and RNA guide-based RNA-protein interactions. Moreover, the integration of different types of RNA-protein interactions and the regulatory factors implicated in these interactions are discussed. Furthermore, we emphasize the functional diversity of these four types of interactions in biological processes and disease development and assess emerging trends in this exciting research field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiaoxia Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anrui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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42
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Lo Giudice C, Tangaro MA, Pesole G, Picardi E. Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal. Nat Protoc 2020; 15:1098-1131. [PMID: 31996844 DOI: 10.1038/s41596-019-0279-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/05/2019] [Indexed: 12/14/2022]
Abstract
RNA editing is a widespread post-transcriptional mechanism able to modify transcripts through insertions/deletions or base substitutions. It is prominent in mammals, in which millions of adenosines are deaminated to inosines by members of the ADAR family of enzymes. A-to-I RNA editing has a plethora of biological functions, but its detection in large-scale transcriptome datasets is still an unsolved computational task. To this aim, we developed REDItools, the first software package devoted to the RNA editing profiling in RNA-sequencing (RNAseq) data. It has been successfully used in human transcriptomes, proving the tissue and cell type specificity of RNA editing as well as its pervasive nature. Outcomes from large-scale REDItools analyses on human RNAseq data have been collected in our specialized REDIportal database, containing more than 4.5 million events. Here we describe in detail two bioinformatic procedures based on our computational resources, REDItools and REDIportal. In the first procedure, we outline a workflow to detect RNA editing in the human cell line NA12878, for which transcriptome and whole genome data are available. In the second procedure, we show how to identify dysregulated editing at specific recoding sites in post-mortem brain samples of Huntington disease donors. On a 64-bit computer running Linux with ≥32 GB of random-access memory (RAM), both procedures should take ~76 h, using 4 to 24 cores. Our protocols have been designed to investigate RNA editing in different organisms with available transcriptomic and/or genomic reads. Scripts to complete both procedures and a docker image are available at https://github.com/BioinfoUNIBA/REDItools.
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Affiliation(s)
- Claudio Lo Giudice
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy
| | - Marco Antonio Tangaro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.,National Institute of Biostructures and Biosystems (INBB), Rome, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy. .,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy. .,National Institute of Biostructures and Biosystems (INBB), Rome, Italy.
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43
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van der Kwast RV, Quax PH, Nossent AY. An Emerging Role for isomiRs and the microRNA Epitranscriptome in Neovascularization. Cells 2019; 9:cells9010061. [PMID: 31881725 PMCID: PMC7017316 DOI: 10.3390/cells9010061] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Therapeutic neovascularization can facilitate blood flow recovery in patients with ischemic cardiovascular disease, the leading cause of death worldwide. Neovascularization encompasses both angiogenesis, the sprouting of new capillaries from existing vessels, and arteriogenesis, the maturation of preexisting collateral arterioles into fully functional arteries. Both angiogenesis and arteriogenesis are highly multifactorial processes that require a multifactorial regulator to be stimulated simultaneously. MicroRNAs can regulate both angiogenesis and arteriogenesis due to their ability to modulate expression of many genes simultaneously. Recent studies have revealed that many microRNAs have variants with altered terminal sequences, known as isomiRs. Additionally, endogenous microRNAs have been identified that carry biochemically modified nucleotides, revealing a dynamic microRNA epitranscriptome. Both types of microRNA alterations were shown to be dynamically regulated in response to ischemia and are able to influence neovascularization by affecting the microRNA’s biogenesis, or even its silencing activity. Therefore, these novel regulatory layers influence microRNA functioning and could provide new opportunities to stimulate neovascularization. In this review we will highlight the formation and function of isomiRs and various forms of microRNA modifications, and discuss recent findings that demonstrate that both isomiRs and microRNA modifications directly affect neovascularization and vascular remodeling.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul H.A. Quax
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Laboratory Medicine and Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
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44
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Matsuyama H, Suzuki HI. Systems and Synthetic microRNA Biology: From Biogenesis to Disease Pathogenesis. Int J Mol Sci 2019; 21:E132. [PMID: 31878193 PMCID: PMC6981965 DOI: 10.3390/ijms21010132] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are approximately 22-nucleotide-long, small non-coding RNAs that post-transcriptionally regulate gene expression. The biogenesis of miRNAs involves multiple steps, including the transcription of primary miRNAs (pri-miRNAs), nuclear Drosha-mediated processing, cytoplasmic Dicer-mediated processing, and loading onto Argonaute (Ago) proteins. Further, miRNAs control diverse biological and pathological processes via the silencing of target mRNAs. This review summarizes recent findings regarding the quantitative aspects of miRNA homeostasis, including Drosha-mediated pri-miRNA processing, Ago-mediated asymmetric miRNA strand selection, and modifications of miRNA pathway components, as well as the roles of RNA modifications (epitranscriptomics), epigenetics, transcription factor circuits, and super-enhancers in miRNA regulation. These recent advances have facilitated a system-level understanding of miRNA networks, as well as the improvement of RNAi performance for both gene-specific targeting and genome-wide screening. The comprehensive understanding and modeling of miRNA biogenesis and function have been applied to the design of synthetic gene circuits. In addition, the relationships between miRNA genes and super-enhancers provide the molecular basis for the highly biased cell type-specific expression patterns of miRNAs and the evolution of miRNA-target connections, while highlighting the importance of alterations of super-enhancer-associated miRNAs in a variety of human diseases.
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Affiliation(s)
- Hironori Matsuyama
- Fujii Memorial Research Institute, Otsuka Pharmaceutical Co., Ltd., 1-11-1 Karasaki, Otsu-shi, Shiga 520-0106, Japan;
| | - Hiroshi I. Suzuki
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium. Cells 2019; 8:cells8121634. [PMID: 31847302 PMCID: PMC6953095 DOI: 10.3390/cells8121634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
: Post-transcriptional regulation plays a key role in modulating gene expression, and the perturbation of transcriptomic equilibrium has been shown to drive the development of multiple diseases including cancer. Recent studies have revealed the existence of multiple post-transcriptional processes that coordinatively regulate the expression and function of each RNA transcript. In this review, we summarize the latest research describing various mechanisms by which small alterations in RNA processing or function can potentially reshape the transcriptomic landscape, and the impact that this may have on cancer development.
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46
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Gjorgjieva M, Sobolewski C, Dolicka D, Correia de Sousa M, Foti M. miRNAs and NAFLD: from pathophysiology to therapy. Gut 2019; 68:2065-2079. [PMID: 31300518 DOI: 10.1136/gutjnl-2018-318146] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 12/11/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is associated with a thorough reprogramming of hepatic metabolism. Epigenetic mechanisms, in particular those associated with deregulation of the expressions and activities of microRNAs (miRNAs), play a major role in metabolic disorders associated with NAFLD and their progression towards more severe stages of the disease. In this review, we discuss the recent progress addressing the role of the many facets of complex miRNA regulatory networks in the development and progression of NAFLD. The basic concepts and mechanisms of miRNA-mediated gene regulation as well as the various setbacks encountered in basic and translational research in this field are debated. miRNAs identified so far, whose expressions/activities are deregulated in NAFLD, and which contribute to the outcomes of this pathology are further reviewed. Finally, the potential therapeutic usages in a short to medium term of miRNA-based strategies in NAFLD, in particular to identify non-invasive biomarkers, or to design pharmacological analogues/inhibitors having a broad range of actions on hepatic metabolism, are highlighted.
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Affiliation(s)
- Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Abstract
Modifications of RNA affect its function and stability. RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters their sequence relative to the genome. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Recent transcriptomic studies have identified a number of 'recoding' sites at which A-to-I editing results in non-synonymous substitutions in protein-coding sequences. Many of these recoding sites are conserved within (but not usually across) lineages, are under positive selection and have functional and evolutionary importance. However, systematic mapping of the editome across the animal kingdom has revealed that most A-to-I editing sites are located within mobile elements in non-coding parts of the genome. Editing of these non-coding sites is thought to have a critical role in protecting against activation of innate immunity by self-transcripts. Both recoding and non-coding events have implications for genome evolution and, when deregulated, may lead to disease. Finally, ADARs are now being adapted for RNA engineering purposes.
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48
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RNA editing is abundant and correlates with task performance in a social bumblebee. Nat Commun 2019; 10:1605. [PMID: 30962428 PMCID: PMC6453909 DOI: 10.1038/s41467-019-09543-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/15/2019] [Indexed: 12/17/2022] Open
Abstract
Colonies of the bumblebee Bombus terrestris are characterized by wide phenotypic variability among genetically similar full-sister workers, suggesting a major role for epigenetic processes. Here, we report a high level of ADAR-mediated RNA editing in the bumblebee, despite the lack of an ADAR1-homolog. We identify 1.15 million unique genomic sites, and 164 recoding sites residing in 100 protein coding genes, including ion channels, transporters, and receptors predicted to affect brain function and behavior. Some edited sites are similarly edited in other insects, cephalopods and even mammals. The global editing level of protein coding and non-coding transcripts weakly correlates with task performance (brood care vs. foraging), but not affected by dominance rank or juvenile hormone known to influence physiology and behavior. Taken together, our findings show that brain editing levels are high in naturally behaving bees, and may be regulated by relatively short-term effects associated with brood care or foraging activities.
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Weston WW, Ganey T, Temple HT. The Relationship between Exosomes and Cancer: Implications for Diagnostics and Therapeutics. BioDrugs 2019; 33:137-158. [DOI: 10.1007/s40259-019-00338-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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50
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Samuel CE. Adenosine deaminase acting on RNA (ADAR1), a suppressor of double-stranded RNA-triggered innate immune responses. J Biol Chem 2019; 294:1710-1720. [PMID: 30710018 PMCID: PMC6364763 DOI: 10.1074/jbc.tm118.004166] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Herbert "Herb" Tabor, who celebrated his 100th birthday this past year, served the Journal of Biological Chemistry as a member of the Editorial Board beginning in 1961, as an Associate Editor, and as Editor-in-Chief for 40 years, from 1971 until 2010. Among the many discoveries in biological chemistry during this period was the identification of RNA modification by C6 deamination of adenosine (A) to produce inosine (I) in double-stranded (ds) RNA. This posttranscriptional RNA modification by adenosine deamination, known as A-to-I RNA editing, diversifies the transcriptome and modulates the innate immune interferon response. A-to-I editing is catalyzed by a family of enzymes, adenosine deaminases acting on dsRNA (ADARs). The roles of A-to-I editing are varied and include effects on mRNA translation, pre-mRNA splicing, and micro-RNA silencing. Suppression of dsRNA-triggered induction and action of interferon, the cornerstone of innate immunity, has emerged as a key function of ADAR1 editing of self (cellular) and nonself (viral) dsRNAs. A-to-I modification of RNA is essential for the normal regulation of cellular processes. Dysregulation of A-to-I editing by ADAR1 can have profound consequences, ranging from effects on cell growth and development to autoimmune disorders.
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Affiliation(s)
- Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106.
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