151
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Chen YT, Chang IYF, Liu H, Ma CP, Kuo YP, Shih CT, Shih YH, Kang L, Tan BCM. Tumor-associated intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation. J Biol Chem 2018; 293:10158-10171. [PMID: 29769310 DOI: 10.1074/jbc.ra117.001197] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/29/2018] [Indexed: 01/02/2023] Open
Abstract
Processing of the eukaryotic transcriptome is a dynamic regulatory mechanism that confers genetic diversity, and splicing and adenosine to inosine (A-to-I) RNA editing are well-characterized examples of such processing. Growing evidence reveals the cross-talk between the splicing and RNA editing, but there is a paucity of substantial evidence for its mechanistic details and contribution in a physiological context. Here, our findings demonstrate that tumor-associated differential RNA editing, in conjunction with splicing machinery, regulates the expression of variants of HNRPLL, a gene encoding splicing factor. We discovered an HNRPLL transcript variant containing an additional exon 12A (E12A), which is a substrate of ADAR1 and ADAR2. Adenosine deaminases acting on RNA (ADAR) direct deaminase-dependent expression of the E12A transcript, and ADAR-mediated regulation of E12A is largely splicing-based, and does not affect the stability or nucleocytoplasmic distribution of the transcript. Furthermore, ADAR-mediated modification of exon 12A generates an enhancer for the oncogenic splicing factor SRSF1 and consequently promotes the frequency of alternative splicing. Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.
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Affiliation(s)
- Yi-Tung Chen
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | | | - Hsuan Liu
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,Molecular Medicine Research Center.,Department of Biochemistry, College of Medicine, and.,the Division of Colon and Rectal Surgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Chung-Pei Ma
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Yu-Ping Kuo
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Chieh-Tien Shih
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Ying-Hsin Shih
- the Department of Biomedical Sciences, College of Medicine
| | - Lin Kang
- the Edward Via College of Osteopathic Medicine, Blacksburg, Virginia 24060, and
| | - Bertrand Chin-Ming Tan
- From the Graduate Institute of Biomedical Sciences, College of Medicine, .,the Department of Biomedical Sciences, College of Medicine.,Molecular Medicine Research Center.,the Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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152
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Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Cell 2018; 173:1191-1203.e12. [PMID: 29706542 DOI: 10.1016/j.cell.2018.03.080] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 01/02/2018] [Accepted: 03/28/2018] [Indexed: 12/26/2022]
Abstract
Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse range of double-stranded RNA (dsRNA) precursors to generate ∼22 nt microRNA (miRNA) or small interfering RNA (siRNA) products for sequence-directed gene silencing. In this work, we solved the cryoelectron microscopy (cryo-EM) structure of hDicer in complex with its cofactor protein TRBP and revealed the precise spatial arrangement of hDicer's multiple domains. We further solved structures of the hDicer-TRBP complex bound with pre-let-7 RNA in two distinct conformations. In combination with biochemical analysis, these structures reveal a property of the hDicer-TRBP complex to promote the stability of pre-miRNA's stem duplex in a pre-dicing state. These results provide insights into the mechanism of RNA processing by hDicer and illustrate the regulatory role of hDicer's N-terminal helicase domain.
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Affiliation(s)
- Zhongmin Liu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Hang Cheng
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084; Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Xin Ke
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Lei Sun
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Qiangfeng Cliff Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084.
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153
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Li J, Xie J, Liu S, Li X, Zhang D, Wang X, Jiang J, Hu W, Zhang Y, Jin B, Zhuang R, Yin W. ADAR1 attenuates allogeneic graft rejection by suppressing miR‐21 biogenesis in macrophages and promoting M2 polarization. FASEB J 2018; 32:5162-5173. [DOI: 10.1096/fj.201701449r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Junjie Li
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Jiangang Xie
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
- Department of Plastic SurgeryXijing HospitalSchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Shanshou Liu
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Xiao Li
- Department of Hepatobiliary SurgerySchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Dongliang Zhang
- Department of Plastic SurgeryXijing HospitalSchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
- Transplant Immunology Laboratory and School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Xianqi Wang
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Jinquan Jiang
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Wei Hu
- Transplant Immunology Laboratory and School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
- Department of ImmunologySchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Yuan Zhang
- Transplant Immunology Laboratory and School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Boquan Jin
- Department of ImmunologySchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Ran Zhuang
- Transplant Immunology Laboratory and School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
- Department of ImmunologySchool of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
| | - Wen Yin
- Department of Emergency School of Basic Medical SciencesFourth Military Medical UniversityXi'anChina
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154
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Roberts JT, Patterson DG, King VM, Amin SV, Polska CJ, Houserova D, Crucello A, Barnhill EC, Miller MM, Sherman TD, Borchert GM. ADAR Mediated RNA Editing Modulates MicroRNA Targeting in Human Breast Cancer. Processes (Basel) 2018; 6. [PMID: 30197877 PMCID: PMC6128407 DOI: 10.3390/pr6050042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA editing by RNA specific adenosine deaminase acting on RNA (ADAR) is increasingly being found to alter microRNA (miRNA) regulation. Editing of miRNA transcripts can affect their processing, as well as which messenger RNAs (mRNAs) they target. Further, editing of target mRNAs can also affect their complementarity to miRNAs. Notably, ADAR editing is often increased in malignancy with the effect of these RNA changes being largely unclear. In addition, numerous reports have now identified an array of miRNAs that directly contribute to various malignancies although the majority of their targets remain largely undefined. Here we propose that modulating the targets of miRNAs via mRNA editing is a frequent occurrence in cancer and an underappreciated participant in pathology. In order to more accurately characterize the relationship between these two regulatory processes, this study examined RNA editing events within mRNA sequences of two breast cancer cell lines (MCF-7 and MDA-MB-231) and determined whether or not these edits could modulate miRNA associations. Computational analyses of RNA-Seq data from these two cell lines identified over 50,000 recurrent editing sites within human mRNAs, and many of these were located in 3’ untranslated regions (UTRs). When these locations were screened against the list of currently-annotated miRNAs we discovered that editing caused a subset (~9%) to have significant alterations to mRNA complementarity. One miRNA in particular, miR-140–3p, is known to be misexpressed in many breast cancers, and we found that mRNA editing allowed this miRNA to directly target the apoptosis inducing gene DFFA in MCF-7, but not in MDA-MB-231 cells. As these two cell lines are known to have distinct characteristics in terms of morphology, invasiveness and physiological responses, we hypothesized that the differential RNA editing of DFFA in these two cell lines could contribute to their phenotypic differences. Indeed, we confirmed through western blotting that inhibiting miR-140–3p increases expression of the DFFA protein product in MCF-7, but not MDA-MB-231, and further that inhibition of miR-140–3p also increases cellular growth in MCF-7, but not MDA-MB-231. Broadly, these results suggest that the creation of miRNA targets may be an underappreciated function of ADAR and may help further elucidate the role of RNA editing in tumor pathogenicity.
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Affiliation(s)
- Justin T Roberts
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Dillon G Patterson
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Valeria M King
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Shivam V Amin
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Caroline J Polska
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Dominika Houserova
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA;
| | - Aline Crucello
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Emmaline C Barnhill
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Molly M Miller
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Timothy D Sherman
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
| | - Glen M Borchert
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA;
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155
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Dou N, Yu S, Ye X, Yang D, Li Y, Gao Y. Aberrant overexpression of ADAR1 promotes gastric cancer progression by activating mTOR/p70S6K signaling. Oncotarget 2018; 7:86161-86173. [PMID: 27863387 PMCID: PMC5349904 DOI: 10.18632/oncotarget.13354] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/08/2016] [Indexed: 12/24/2022] Open
Abstract
ADAR1, one of adenosine deaminases acting on RNA, modulates RNA transcripts through converting adenosine (A) to inosine (I) by deamination. Emerging evidence has implicated that ADAR1 plays an important role in a few of human cancers, however, its expression and physiological significance in gastric cancer remain undefined. In the present study, we demonstrated that ADAR1 was frequently overexpressed in gastric cancer samples by quantitative real-time PCR analysis. In a gastric cancer tissue microarray, ADAR1 staining was closely correlated with tumor stage (P < 0.001) and N classification (P < 0.001). Functional analysis indicated that ADAR1 overexpression promoted cell proliferation and migration in vitro, whereas ADAR1 knockdown resulted in an opposite phenotypes. Furthermore, ADAR1 knockdown also inhibited tumorigenicity and lung metastasis potential of gastric cancer cells in nude mice models. Mechanistically, ADAR1 expression had a significant effect on phosphorylation level of mTOR, p70S kinase, and S6 ribosomal protein, implying its involvement in the regulation of mTOR signaling pathway. We conclude that ADAR1 contributes to gastric cancer development and progression via activating mTOR/p70S6K/S6 ribosomal protein signaling axis. Our findings suggest that ADAR1 may be a valuable biomarker for GC diagnosis and prognosis and may represent a new novel therapeutic opportunities.
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Affiliation(s)
- Ning Dou
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Shijun Yu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaojuan Ye
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Dong Yang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
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156
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Functional Redundancy of DICER Cofactors TARBP2 and PRKRA During Murine Embryogenesis Does Not Involve miRNA Biogenesis. Genetics 2018; 208:1513-1522. [PMID: 29467169 PMCID: PMC5887145 DOI: 10.1534/genetics.118.300791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/10/2018] [Indexed: 12/21/2022] Open
Abstract
Several in vitro studies have suggested that canonical microRNA (miRNA) biogenesis requires the DICER cofactors TARBP2 and PRKRA for processing of pre-miRNAs to mature miRNAs. To investigate the roles of TARBP2 and PRKRA in miRNA biogenesis in vivo, and to determine possible functional redundancy, we first compared the phenotypes of Tarbp2 and Prkra single and double mutants. In contrast to Dicer −/− embryos, which die by embryonic day 7.5 (E7.5), single Tarbp2 −/− and Prkra −/− mice survive beyond E7.5 and either die perinatally or survive and exhibit cranial/facial abnormalities, respectively. In contrast, only a few Tarbp2 −/−; Prkra −/− double mutants survived beyond E12.5, suggesting genetic redundancy between Tarbp2 and Prkra during embryonic development. Sequencing of miRNAs from single-mutant embryos at E15.5 revealed changes in abundance and isomiR type in Tarbp2 −/−, but not Prkra −/−, embryos, demonstrating that TARBP2, but not PRKRA, functions in miRNA biogenesis of a subclass of miRNAs, and suggesting that functional redundancy between TARBP2 and PRKRA does not involve miRNA biogenesis.
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157
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Mingardi J, Musazzi L, De Petro G, Barbon A. miRNA Editing: New Insights into the Fast Control of Gene Expression in Health and Disease. Mol Neurobiol 2018; 55:7717-7727. [PMID: 29460265 DOI: 10.1007/s12035-018-0951-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/05/2018] [Indexed: 11/29/2022]
Abstract
Post-transcriptional modifications are essential mechanisms for mRNA biogenesis and function in eukaryotic cells. Beyond well-characterized events such as splicing, capping, and polyadenylation, there are several others, as RNA editing mechanisms and regulation of transcription mediated by miRNAs that are taking increasing attention in the last years. RNA editing through A-to-I deamination increases transcriptomic complexity, generating different proteins with amino acid substitution from the same transcript. On the other hand, miRNAs can regulate gene expression modulating target mRNA decay and translation. Interestingly, recent studies highlight the possibility that miRNAs might undergo editing themselves. This mainly translates in the degradation or uncorrected maturation of miRNAs but also in the recognition of different targets. The presence of edited and unedited forms of the same miRNA may have important biological implications in both health and disease. Here we review ongoing investigations on miRNA RNA editing with the aim to shed light on the growing importance of this mechanism in adding complexity to post-transcriptional regulation of gene expression.
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Affiliation(s)
- Jessica Mingardi
- Laboratory of Neuropsychopharmacology and Functional Neurogenomics - Dipartimento di Scienze Farmacologiche e Biomolecolari and CEND, Università degli Studi di Milano, 20133, Milan, Italy
| | - Laura Musazzi
- Laboratory of Neuropsychopharmacology and Functional Neurogenomics - Dipartimento di Scienze Farmacologiche e Biomolecolari and CEND, Università degli Studi di Milano, 20133, Milan, Italy
| | - Giuseppina De Petro
- Biology and Genetic Division, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Alessandro Barbon
- Biology and Genetic Division, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.
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158
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Marcu-Malina V, Goldberg S, Vax E, Amariglio N, Goldstein I, Rechavi G. ADAR1 is vital for B cell lineage development in the mouse bone marrow. Oncotarget 2018; 7:54370-54379. [PMID: 27494846 PMCID: PMC5342348 DOI: 10.18632/oncotarget.11029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 07/23/2016] [Indexed: 12/13/2022] Open
Abstract
Adenosine deaminase acting on RNA (ADAR) 1 is the master editor of the transcriptome, catalyzing the conversion of adenosine to inosine (A-to-I). RNA transcripts fold into a variety of secondary structures including long intramolecular RNA duplexes that are the major substrate of ADAR1. Most A-to-I editing sites occur within RNA duplexes formed by complementary pairing of inverted retrotransposable elements interspersed within noncoding regions of transcripts. This catalytic activity of ADAR1 most likely prevents the abnormal activation of cytosolic nucleic acid sensors by self-dsRNAs. Homozygous disruption of mouse Adar is embryonic lethal due to a toxic type-I interferons response and correspondingly biallelic missense mutations in human ADAR1 cause a severe congenital interferonopathy. Here, we report that Cd19-Cre-mediated Adar gene ablation in the mouse causes a significant defect in the final stages of B cell development with an almost complete absence of newly formed immature and CD23+ mature recirculating B cells in the BM. Adar ablation in pre-B cells induced upregulation of typical interferon-stimulated genes (ISGs) and apoptosis upon further maturation. ADAR1 deficiency also inhibited the in vitro, IL-7-mediated, differentiation of BM-derived B cell precursors. In summary, ADAR1 is required, non-redundantly, for normal B lymphopoiesis in the BM and peripheral maintenance.
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Affiliation(s)
- Victoria Marcu-Malina
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Israel
| | - Sanja Goldberg
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Israel
| | - Einav Vax
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Israel
| | - Ninette Amariglio
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Itamar Goldstein
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Israel.,Rheumatic Diseases Unit, Chaim Sheba Academic Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gideon Rechavi
- Sheba Cancer Research Center, Chaim Sheba Academic Medical Center, Tel Hashomer, Israel.,Department of Pediatric Hemato-Oncology, Chaim Sheba Academic Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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159
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van der Kwast RV, van Ingen E, Parma L, Peters HA, Quax PH, Nossent AY. Adenosine-to-Inosine Editing of MicroRNA-487b Alters Target Gene Selection After Ischemia and Promotes Neovascularization. Circ Res 2018; 122:444-456. [DOI: 10.1161/circresaha.117.312345] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/19/2017] [Accepted: 12/27/2017] [Indexed: 12/20/2022]
Abstract
Rationale:
Adenosine-to-inosine editing of microRNAs has the potential to cause a shift in target site selection. 2′-O-ribose-methylation of adenosine residues, however, has been shown to inhibit adenosine-to-inosine editing.
Objective:
To investigate whether angiomiR miR487b is subject to adenosine-to-inosine editing or 2′-O-ribose-methylation during neovascularization.
Methods and Results:
Complementary DNA was prepared from C57BL/6-mice subjected to hindlimb ischemia. Using Sanger sequencing and endonuclease digestion, we identified and validated adenosine-to-inosine editing of the miR487b seed sequence. In the gastrocnemius muscle, pri-miR487b editing increased from 6.7±0.4% before to 11.7±1.6% (
P
=0.02) 1 day after ischemia. Edited pri-miR487b is processed into a novel microRNA, edited miR487b, which is also upregulated after ischemia. We confirmed editing of miR487b in multiple human primary vascular cell types. Short interfering RNA–mediated knockdown demonstrated that editing is adenosine deaminase acting on RNA 1 and 2 dependent. Using reverse-transcription at low dNTP concentrations followed by quantitative-PCR, we found that the same adenosine residue is methylated in mice and human primary cells. In the murine gastrocnemius, the estimated methylation fraction increased from 32.8±14% before to 53.6±12% 1 day after ischemia. Short interfering RNA knockdown confirmed that methylation is fibrillarin dependent. Although we could not confirm that methylation directly inhibits editing, we do show that adenosine deaminase acting on RNA 1 and 2 and fibrillarin negatively influence each other’s expression. Using multiple luciferase reporter gene assays, we could demonstrate that editing results in a complete switch of target site selection. In human primary cells, we confirmed the shift in miR487b targeting after editing, resulting in a edited miR487b targetome that is enriched for multiple proangiogenic pathways. Furthermore, overexpression of edited miR487b, but not wild-type miR487b, stimulates angiogenesis in both in vitro and ex vivo assays.
Conclusions:
MiR487b is edited in the seed sequence in mice and humans, resulting in a novel, proangiogenic microRNA with a unique targetome. The rate of miR487b editing, as well as 2′-O-ribose-methylation, is increased in murine muscle tissue during postischemic neovascularization. Our findings suggest miR487b editing plays an intricate role in postischemic neovascularization.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - Eva van Ingen
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - Laura Parma
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - Hendrika A.B. Peters
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - Paul H.A. Quax
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - A. Yaël Nossent
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
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160
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Wang Y, Liang H. When MicroRNAs Meet RNA Editing in Cancer: A Nucleotide Change Can Make a Difference. Bioessays 2018; 40:10.1002/bies.201700188. [PMID: 29280160 PMCID: PMC5828010 DOI: 10.1002/bies.201700188] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/22/2017] [Indexed: 12/20/2022]
Abstract
RNA editing is a major post-transcriptional mechanism that changes specific nucleotides at the RNA level. The most common RNA editing type in humans is adenosine (A) to inosine (I) editing, which is mediated by ADAR enzymes. RNA editing events can not only change amino acids in proteins, but also affect the functions of non-coding RNAs such as miRNAs. Recent studies have characterized thousands of miRNA RNA editing events across different cancer types. Importantly, individual cases of miRNA editing have been reported to play a role in cancer development. In this review, we summarize the current knowledge of miRNA editing in cancer, and discuss the mechanisms on how miRNA-related editing events modulate the initiation and progression of human cancer. Finally, we discuss the challenges and future directions of studying miRNA editing in cancer.
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Affiliation(s)
- Yumeng Wang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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161
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Chung H, Calis JJA, Wu X, Sun T, Yu Y, Sarbanes SL, Dao Thi VL, Shilvock AR, Hoffmann HH, Rosenberg BR, Rice CM. Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown. Cell 2018; 172:811-824.e14. [PMID: 29395325 DOI: 10.1016/j.cell.2017.12.038] [Citation(s) in RCA: 344] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/30/2017] [Accepted: 12/27/2017] [Indexed: 01/12/2023]
Abstract
Type I interferon (IFN) is produced when host sensors detect foreign nucleic acids, but how sensors differentiate self from nonself nucleic acids, such as double-stranded RNA (dsRNA), is incompletely understood. Mutations in ADAR1, an adenosine-to-inosine editing enzyme of dsRNA, cause Aicardi-Goutières syndrome, an autoinflammatory disorder associated with spontaneous interferon production and neurologic sequelae. We generated ADAR1 knockout human cells to explore ADAR1 substrates and function. ADAR1 primarily edited Alu elements in RNA polymerase II (pol II)-transcribed mRNAs, but not putative pol III-transcribed Alus. During the IFN response, ADAR1 blocked translational shutdown by inhibiting hyperactivation of PKR, a dsRNA sensor. ADAR1 dsRNA binding and catalytic activities were required to fully prevent endogenous RNA from activating PKR. Remarkably, ADAR1 knockout neuronal progenitor cells exhibited MDA5 (dsRNA sensor)-dependent spontaneous interferon production, PKR activation, and cell death. Thus, human ADAR1 regulates sensing of self versus nonself RNA, allowing pathogen detection while avoiding autoinflammation.
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Affiliation(s)
- Hachung Chung
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jorg J A Calis
- Program in Immunogenomics, The Rockefeller University, New York, NY 10065, USA
| | - Xianfang Wu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Tony Sun
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Yingpu Yu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Stephanie L Sarbanes
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Viet Loan Dao Thi
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Abigail R Shilvock
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - H-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Brad R Rosenberg
- Program in Immunogenomics, The Rockefeller University, New York, NY 10065, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
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162
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Fareh M, Joo C. Probing RNA-Protein Interactions with Single-Molecule Pull-Down Assays. Methods Mol Biol 2018; 1814:267-285. [PMID: 29956238 DOI: 10.1007/978-1-4939-8591-3_16] [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] [Indexed: 06/08/2023]
Abstract
Recent advances in single-molecule techniques allow for dynamic observations of the interactions between various protein assemblies and RNA molecules with high spatiotemporal resolution. However, it remains challenging to obtain functional eukaryotic protein complexes and cost-effective fluorescently labeled RNAs to study their interactions at the single-molecule level. Here, we describe protocols combining single-molecule fluorescence with various protein complex pull-down techniques to determine the function of RNA-interacting protein complexes of interest. We provide step-by-step guidance for using novel single-molecule techniques including RNA labeling, protein complexes purification, and single-molecule imaging. As a proof-of-concept of the utility of our single-molecule approaches, we show how human Dicer and its cofactor TRBP orchestrate the biogenesis of microRNA in real time. These single-molecule pull-down and fluorescence assays provide sub-second time resolution and can be applied to various ribonucleoprotein complexes that are essential for cellular processes.
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Affiliation(s)
- Mohamed Fareh
- Department of BioNanoScience, Kavli Institute of NanoScience, Delft University of Technology, Building 58, vander Maasweg 9, Delft, 2629 HZ, The Netherlands.
- Cancer Immunology Program, Peter MacCallum Cancer Center, East Melbourne, Victoria,Australia. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of NanoScience, Delft University of Technology, Building 58, vander Maasweg 9, Delft, 2629 HZ, The Netherlands
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163
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Nakano M, Nakajima M. Significance of A-to-I RNA editing of transcripts modulating pharmacokinetics and pharmacodynamics. Pharmacol Ther 2018; 181:13-21. [DOI: 10.1016/j.pharmthera.2017.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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164
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Abstract
Complex immunoprecipitation (Co-IP) is a powerful technique for precipitating an intact protein complex out of solution and cell lysates using an antibody that specifically binds to a particular protein in a large complex of proteins. Mass spectrometry (MS) is used to identify, sequence, and quantify proteins. RNA-induced silencing complexes (RISCs), Ago2 centered protein assemblies, are essential for miRNA mediated RNA decay and gene expression regulation; however, the complete list of RISCs is unknown. Here we describe methods used to combine IP and MS to identify new components of RISCs.
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165
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Olejniczak M, Kotowska-Zimmer A, Krzyzosiak W. Stress-induced changes in miRNA biogenesis and functioning. Cell Mol Life Sci 2018; 75:177-191. [PMID: 28717872 PMCID: PMC5756259 DOI: 10.1007/s00018-017-2591-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/30/2017] [Accepted: 07/11/2017] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that play key roles in the regulation of cellular homeostasis in eukaryotic organisms. There is emerging evidence that some of these processes are influenced by various forms of cellular stresses, including DNA damage, pathogen invasion or chronic stress associated with diseases. Many reports over the last decade demonstrate examples of stress-induced miRNA deregulation at the level of transcription, processing, subcellular localization and functioning. Moreover, core miRNA biogenesis proteins and their interactions with partners can be selectively regulated in response to stress signaling. However, little is known about the role of isomiRs and the interactions of miRNA with non-canonical targets in the context of the stress response. In this review, we summarize the current knowledge on miRNA functions under various stresses, including chronic stress and miRNA deregulation in the pathogenesis of age-associated neurodegenerative disorders.
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Affiliation(s)
- Marta Olejniczak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Anna Kotowska-Zimmer
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Wlodzimierz Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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166
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Abstract
Thousands of unique non-coding RNA (ncRNA) sequences exist within cells. Work from the past decade has altered our perception of ncRNAs from 'junk' transcriptional products to functional regulatory molecules that mediate cellular processes including chromatin remodelling, transcription, post-transcriptional modifications and signal transduction. The networks in which ncRNAs engage can influence numerous molecular targets to drive specific cell biological responses and fates. Consequently, ncRNAs act as key regulators of physiological programmes in developmental and disease contexts. Particularly relevant in cancer, ncRNAs have been identified as oncogenic drivers and tumour suppressors in every major cancer type. Thus, a deeper understanding of the complex networks of interactions that ncRNAs coordinate would provide a unique opportunity to design better therapeutic interventions.
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Affiliation(s)
- Eleni Anastasiadou
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Leni S Jacob
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
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167
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Rayon-Estrada V, Harjanto D, Hamilton CE, Berchiche YA, Gantman EC, Sakmar TP, Bulloch K, Gagnidze K, Harroch S, McEwen BS, Papavasiliou FN. Epitranscriptomic profiling across cell types reveals associations between APOBEC1-mediated RNA editing, gene expression outcomes, and cellular function. Proc Natl Acad Sci U S A 2017; 114:13296-13301. [PMID: 29167373 PMCID: PMC5740640 DOI: 10.1073/pnas.1714227114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epitranscriptomics refers to posttranscriptional alterations on an mRNA sequence that are dynamic and reproducible, and affect gene expression in a similar way to epigenetic modifications. However, the functional relevance of those modifications for the transcript, the cell, and the organism remain poorly understood. Here, we focus on RNA editing and show that Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-1 (APOBEC1), together with its cofactor RBM47, mediates robust editing in different tissues. The majority of editing events alter the sequence of the 3'UTR of targeted transcripts, and we focus on one cell type (monocytes) and on a small set of highly edited transcripts within it to show that editing alters gene expression by modulating translation (but not RNA stability or localization). We further show that specific cellular processes (phagocytosis and transendothelial migration) are enriched for transcripts that are targets of editing and that editing alters their function. Finally, we survey bone marrow progenitors and demonstrate that common monocyte progenitor cells express high levels of APOBEC1 and are susceptible to loss of the editing enzyme. Overall, APOBEC1-mediated transcriptome diversification is required for the fine-tuning of protein expression in monocytes, suggesting an epitranscriptomic mechanism for the proper maintenance of homeostasis in innate immune cells.
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Affiliation(s)
- Violeta Rayon-Estrada
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
- The Rockefeller Graduate Program, The Rockefeller University, New York, NY 10065
| | - Dewi Harjanto
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
| | - Claire E Hamilton
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
- The Rockefeller Graduate Program, The Rockefeller University, New York, NY 10065
- The Tri-Institutional MD-PhD Program, The Rockefeller University, New York, NY 10065
| | - Yamina A Berchiche
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY 10065
| | - Emily Conn Gantman
- The Rockefeller Graduate Program, The Rockefeller University, New York, NY 10065
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, NY 10065
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY 10065
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Karen Bulloch
- The Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY 10065
| | - Khatuna Gagnidze
- The Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY 10065
| | - Sheila Harroch
- Division of Immune Diversity, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Bruce S McEwen
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY 10065
| | - F Nina Papavasiliou
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065;
- Division of Immune Diversity, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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168
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Li L, Song Y, Shi X, Liu J, Xiong S, Chen W, Fu Q, Huang Z, Gu N, Zhang R. The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting. Genome Res 2017; 28:132-143. [PMID: 29233923 PMCID: PMC5749178 DOI: 10.1101/gr.224386.117] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 10/25/2017] [Indexed: 01/23/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing regulates miRNA biogenesis and function. To date, fewer than 160 miRNA editing sites have been identified. Here, we present a quantitative atlas of miRNA A-to-I editing through the profiling of 201 pri-miRNA samples and 4694 mature miRNA samples in human, mouse, and Drosophila. We identified 4162 sites present in ∼80% of the pri-miRNAs and 574 sites in mature miRNAs. miRNA editing is prevalent in many tissue types in human. However, high-level editing is mostly found in neuronal tissues in mouse and Drosophila. Interestingly, the edited miRNAs in neuronal and non-neuronal tissues in human gain two distinct sets of new targets, which are significantly associated with cognitive and organ developmental functions, respectively. Furthermore, we reveal that miRNA editing profoundly affects asymmetric strand selection. Altogether, these data provide insight into the impact of RNA editing on miRNA biology and suggest that miRNA editing has recently gained non-neuronal functions in human.
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Affiliation(s)
- Lishi Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yulong Song
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xinrui Shi
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jianheng Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Shaolei Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wanying Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qiang Fu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zichao Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Nannan Gu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Rui Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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169
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Azad MTA, Bhakta S, Tsukahara T. Site-directed RNA editing by adenosine deaminase acting on RNA for correction of the genetic code in gene therapy. Gene Ther 2017; 24:779-786. [PMID: 28984845 DOI: 10.1038/gt.2017.90] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022]
Abstract
Site-directed RNA editing is an important technique for correcting gene sequences and ultimately tuning protein function. In this study, we engineered the deaminase domain of adenosine deaminase acting on RNA (ADAR1) and the MS2 system to target-specific adenosines, with the goal of correcting G-to-A mutations at the RNA level. For this purpose, the ADAR1 deaminase domain was fused downstream of the RNA-binding protein MS2, which has affinity for the MS2 RNA. To direct editing to specific targets, we designed guide RNAs complementary to target RNAs. The guide RNAs directed the ADAR1 deaminase to the desired editing site, where it converted adenosine to inosine. To provide proof of principle, we used an allele of enhanced green fluorescent protein (EGFP) bearing a mutation at the 58th amino acid (TGG), encoding Trp, into an amber (TAG) or ochre (TAA) stop codon. In HEK-293 cells, our system could convert stop codons to read-through codons, thereby turning on fluorescence. We confirmed the specificity of editing at the DNA level by restriction fragment length polymorphism analysis and sequencing, and at the protein level by western blotting. The editing efficiency of this enzyme system was ~5%. We believe that this system could be used to treat genetic diseases resulting from G-to-A point mutations.
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Affiliation(s)
- Md T A Azad
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan
- Department of Veterinary and Animal Sciences, Faculty of Agriculture, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - S Bhakta
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan
| | - T Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan
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170
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Qi L, Song Y, Chan THM, Yang H, Lin CH, Tay DJT, Hong H, Tang SJ, Tan KT, Huang XX, Lin JS, Ng VHE, Maury JJP, Tenen DG, Chen L. An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer. Nucleic Acids Res 2017; 45:10436-10451. [PMID: 28985428 PMCID: PMC5737565 DOI: 10.1093/nar/gkx667] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 07/19/2017] [Indexed: 12/16/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by Adenosine DeAminases acting on double-stranded RNA(dsRNA) (ADAR), occurs predominantly in the 3′ untranslated regions (3′UTRs) of spliced mRNA. Here we uncover an unanticipated link between ADARs (ADAR1 and ADAR2) and the expression of target genes undergoing extensive 3′UTR editing. Using METTL7A (Methyltransferase Like 7A), a novel tumor suppressor gene with multiple editing sites at its 3′UTR, we demonstrate that its expression could be repressed by ADARs beyond their RNA editing and double-stranded RNA (dsRNA) binding functions. ADARs interact with Dicer to augment the processing of pre-miR-27a to mature miR-27a. Consequently, mature miR-27a targets the METTL7A 3′UTR to repress its expression level. In sum, our study unveils that the extensive 3′UTR editing of METTL7A is merely a footprint of ADAR binding, and there are a subset of target genes that are equivalently regulated by ADAR1 and ADAR2 through their non-canonical RNA editing and dsRNA binding-independent functions, albeit maybe less common. The functional significance of ADARs is much more diverse than previously appreciated and this gene regulatory function of ADARs is most likely to be of high biological importance beyond the best-studied editing function. This non-editing side of ADARs opens another door to target cancer.
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Affiliation(s)
- Lihua Qi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Chi Ho Lin
- Centre for Genomic Sciences, the University of Hong Kong, Hong Kong
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - HuiQi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Kar Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xi Xiao Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jaymie Siqi Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Anatomy, National University of Singapore, Singapore
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171
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Abstract
One of the most prevalent forms of post-transcritpional RNA modification is the conversion of adenosine nucleosides to inosine (A-to-I), mediated by the ADAR family of enzymes. The functional requirement and regulatory landscape for the majority of A-to-I editing events are, at present, uncertain. Recent studies have identified key in vivo functions of ADAR enzymes, informing our understanding of the biological importance of A-to-I editing. Large-scale studies have revealed how editing is regulated both in cis and in trans. This review will explore these recent studies and how they broaden our understanding of the functions and regulation of ADAR-mediated RNA editing.
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Affiliation(s)
- Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia. .,Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, 3065, Australia.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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172
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Abstract
Adenosine-to-inosine RNA editing is a conserved process, which is performed by ADAR enzymes. By changing nucleotides in coding regions of genes and altering codons, ADARs expand the cell's protein repertoire. This function of the ADAR enzymes is essential for human brain development. However, most of the known editing sites are in non-coding repetitive regions in the transcriptome and the purpose of editing in these regions is unclear. Recent studies, which have shown that editing levels of transcripts vary between tissues and developmental stages in many organisms, suggest that the targeted RNA and ADAR editing are both regulated. We discuss the implications of these findings, and the possible role of RNA editing in innate immunity.
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Affiliation(s)
- Nabeel S Ganem
- a Faculty of Biology , Technion- Israel Institute of Technology , Technion City , Haifa , Israel
| | - Ayelet T Lamm
- a Faculty of Biology , Technion- Israel Institute of Technology , Technion City , Haifa , Israel
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173
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Medrano LM, Berenguer J, Jiménez-Sousa MA, Aldámiz-Echevarria T, Tejerina F, Diez C, Vigón L, Fernández-Rodríguez A, Resino S. ADAR1 polymorphisms are related to severity of liver fibrosis in HIV/HCV-coinfected patients. Sci Rep 2017; 7:12918. [PMID: 29018269 PMCID: PMC5635123 DOI: 10.1038/s41598-017-12885-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/15/2017] [Indexed: 01/07/2023] Open
Abstract
The adenosine deaminase acting on RNA (ADAR1) gene is an interferon-stimulated gene involved in liver injury protection. Our aim was to analyze the association of polymorphisms within this gene with the severity of liver disease in European HIV/HCV-coinfected patients. We performed a cross-sectional study in 220 patients that underwent a liver biopsy. Five SNPs in the ADAR1 gene (rs1127326, rs1127317, rs1127314, rs1127313, rs2229857) were genotyped by GoldenGate assay. The outcome variables were fibrosis stage and necroinflammatory activity grade by METAVIR-score, aspartate aminotransferase to platelet ratio index (APRI), FIB-4 index, and fibrosis progression rate (FPR). In multivariate analysis, fibrosis progression rate (FPR) (aAMRs = 0.97) decreased in a dose-dependent manner with the presence of rs2229857_T, rs1127313_G, rs1127314_G and rs1127317_G; while rs1127326_T allele had only significant associations with FIB-4 (aAMRs ≤ 0.63) and FPR (aAMRs ≤ 0.97). Moreover, carriers of rs2229857_T, rs1127314_G, rs1127317_G, and rs1127326_T alleles were protected against advanced fibrosis (F ≥ 3) (adjusted ORs (aORs) ≤ 0.44), APRI ≥ 1.5 (aORs ≤ 0.33), and FPR ≥ 0.075 (aORs ≤ 0.45). rs1127313_G carriers showed lower odds of having F ≥ 3 (aORs = 0.39), FIB4 ≥ 3.25 (aOR = 0.22) and FPR ≥ 0.075 (aORs = 0.44). In conclusion, ADAR1 polymorphisms protected against severe liver disease in HIV/HCV-coinfected patients. These results could be used to improve therapeutic decision-making in clinical practice.
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Affiliation(s)
- Luz M Medrano
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Juan Berenguer
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario "Gregorio Marañón", Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - María A Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Teresa Aldámiz-Echevarria
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario "Gregorio Marañón", Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Francisco Tejerina
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario "Gregorio Marañón", Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Cristina Diez
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario "Gregorio Marañón", Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Lorena Vigón
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Amanda Fernández-Rodríguez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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174
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Licht K, Jantsch MF. The Other Face of an Editor: ADAR1 Functions in Editing-Independent Ways. Bioessays 2017; 39. [DOI: 10.1002/bies.201700129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/29/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Konstantin Licht
- Department of Cell and Developmental Biology Center for Anatomy and Cell Biology; Medical University of Vienna; Schwarzspanierstrasse 17 A-1090 Vienna Austria
| | - Michael F. Jantsch
- Department of Cell and Developmental Biology Center for Anatomy and Cell Biology; Medical University of Vienna; Schwarzspanierstrasse 17 A-1090 Vienna Austria
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175
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Amin EM, Liu Y, Deng S, Tan KS, Chudgar N, Mayo MW, Sanchez-Vega F, Adusumilli PS, Schultz N, Jones DR. The RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizing FAK. Sci Signal 2017; 10:eaah3941. [PMID: 28928239 PMCID: PMC5771642 DOI: 10.1126/scisignal.aah3941] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Large-scale, genome-wide studies report that RNA binding proteins are altered in cancers, but it is unclear how these proteins control tumor progression. We found that the RNA-editing protein ADAR (adenosine deaminase acting on double-stranded RNA) acted as a facilitator of lung adenocarcinoma (LUAD) progression through its ability to stabilize transcripts encoding focal adhesion kinase (FAK). In samples from 802 stage I LUAD patients, increased abundance of ADAR at both the mRNA and protein level correlated with tumor recurrence. Knocking down ADAR in LUAD cells suppressed their mesenchymal properties, migration, and invasion in culture. Analysis of gene expression patterns in LUAD cells identified ADAR-associated enrichment of a subset of genes involved in cell migration pathways; among these, FAK is the most notable gene whose expression was increased in the presence of ADAR. Molecular analyses revealed that ADAR posttranscriptionally increased FAK protein abundance by binding to the FAK transcript and editing a specific intronic site that resulted in the increased stabilization of FAK mRNA. Pharmacological inhibition of FAK blocked ADAR-induced invasiveness of LUAD cells, suggesting a potential therapeutic application for LUAD that has a high abundance of ADAR.
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Affiliation(s)
- Elianna M Amin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuan Liu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Su Deng
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neel Chudgar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marty W Mayo
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Francisco Sanchez-Vega
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Prasad S Adusumilli
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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176
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Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis. Genome Biol 2017; 18:166. [PMID: 28874170 PMCID: PMC5585977 DOI: 10.1186/s13059-017-1301-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023] Open
Abstract
Background Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most is unknown. Editing causing protein recoding is the essential function of ADAR2, but an essential role for recoding by ADAR1 has not been demonstrated. ADAR1 has been proposed to have editing-dependent and editing-independent functions. The relative contribution of these in vivo has not been clearly defined. A critical function of ADAR1 is editing of endogenous RNA to prevent activation of the dsRNA sensor MDA5 (Ifih1). Outside of this, how ADAR1 editing contributes to normal development and homeostasis is uncertain. Results We describe the consequences of ADAR1 editing deficiency on murine homeostasis. Adar1E861A/E861AIfih1-/- mice are strikingly normal, including their lifespan. There is a mild, non-pathogenic innate immune activation signature in the Adar1E861A/E861AIfih1-/- mice. Assessing A-to-I editing across adult tissues demonstrates that outside of the brain, ADAR1 performs the majority of editing and that ADAR2 cannot compensate in its absence. Direct comparison of the Adar1-/- and Adar1E861A/E861A alleles demonstrates a high degree of concordance on both Ifih1+/+ and Ifih1-/- backgrounds, suggesting no substantial contribution from ADAR1 editing-independent functions. Conclusions These analyses demonstrate that the lifetime absence of ADAR1-editing is well tolerated in the absence of MDA5. We conclude that protein recoding arising from ADAR1-mediated editing is not essential for organismal homeostasis. Additionally, the phenotypes associated with loss of ADAR1 are the result of RNA editing and MDA5-dependent functions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1301-4) contains supplementary material, which is available to authorized users.
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177
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Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. Proc Natl Acad Sci U S A 2017; 114:E7939-E7948. [PMID: 28874570 DOI: 10.1073/pnas.1707063114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Loquacious-PD (Loqs-PD) is required for biogenesis of many endogenous siRNAs in Drosophila In vitro, Loqs-PD enhances the rate of dsRNA cleavage by Dicer-2 and also enables processing of substrates normally refractory to cleavage. Using purified components, and Loqs-PD truncations, we provide a mechanistic basis for Loqs-PD functions. Our studies indicate that the 22 amino acids at the C terminus of Loqs-PD, including an FDF-like motif, directly interact with the Hel2 subdomain of Dicer-2's helicase domain. This interaction is RNA-independent, but we find that modulation of Dicer-2 cleavage also requires dsRNA binding by Loqs-PD. Furthermore, while the first dsRNA-binding motif of Loqs-PD is dispensable for enhancing cleavage of optimal substrates, it is essential for enhancing cleavage of suboptimal substrates. Finally, our studies define a previously unrecognized Dicer interaction interface and suggest that Loqs-PD is well positioned to recruit substrates into the helicase domain of Dicer-2.
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178
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Novel insights of microRNAs in the development of systemic lupus erythematosus. Curr Opin Rheumatol 2017; 29:450-457. [DOI: 10.1097/bor.0000000000000420] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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179
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Keegan L, Khan A, Vukic D, O'Connell M. ADAR RNA editing below the backbone. RNA (NEW YORK, N.Y.) 2017; 23:1317-1328. [PMID: 28559490 PMCID: PMC5558901 DOI: 10.1261/rna.060921.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
ADAR RNA editing enzymes (adenosine deaminases acting on RNA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster, which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems.
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Affiliation(s)
- Liam Keegan
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Anzer Khan
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Dragana Vukic
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Mary O'Connell
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
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180
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Jiang Q, Crews LA, Holm F, Jamieson CHM. RNA editing-dependent epitranscriptome diversity in cancer stem cells. Nat Rev Cancer 2017; 17:381-392. [PMID: 28416802 PMCID: PMC5665169 DOI: 10.1038/nrc.2017.23] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer stem cells (CSCs) can regenerate all facets of a tumour as a result of their stem cell-like capacity to self-renew, survive and become dormant in protective microenvironments. CSCs evolve during tumour progression in a manner that conforms to Charles Darwin's principle of natural selection. Although somatic DNA mutations and epigenetic alterations promote evolution, post-transcriptional RNA modifications together with RNA binding protein activity (the 'epitranscriptome') might also contribute to clonal evolution through dynamic determination of RNA function and gene expression diversity in response to environmental stimuli. Deregulation of these epitranscriptomic events contributes to CSC generation and maintenance, which governs cancer progression and drug resistance. In this Review, we discuss the role of malignant RNA processing in CSC generation and maintenance, including mechanisms of RNA methylation, RNA editing and RNA splicing, and the functional consequences of their aberrant regulation in human malignancies. Finally, we highlight the potential of these events as novel CSC biomarkers as well as therapeutic targets.
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Affiliation(s)
- Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Leslie A Crews
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Frida Holm
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
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181
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Abstract
Constitutive and regulated turnover of RNAs is necessary to eliminate aberrant RNA molecules and control the level of specific mRNAs to maintain homeostasis or to respond to signals in living cells. Modifications of nucleosides in specific RNAs are important in modulating the functions of these transcripts, but they can also dramatically impact their fate and turnover. This chapter will review how RNA modifications impact the activities of ribonucleases that target these RNAs for degradation or cleavage, focusing more particularly on tRNAs and mRNAs in eukaryotic cells. Many nucleoside modifications are important to promote proper folding of tRNAs, and the absence of specific modifications makes them susceptible to degradation by quality control pathways that eliminate improperly folded species. Modifications in tRNAs can also modulate their cleavage during stress or by fungal toxins that target modified nucleosides. Modifications of the cap structure found at the 5'-end of eukaryotic mRNAs are essential to control the degradation of these mRNAs. In addition, internal modifications of eukaryotic mRNAs can change their secondary structures or provide binding sites for reader proteins, which can dramatically impact their stability. Recent examples show that mRNA modifications play important roles in regulating mRNA stability during development, cellular differentiation and physiological responses. Finally, many modifications can impact microRNA- and siRNA-mediated gene regulation by direct or indirect effects. With the growing number of genomic techniques able to identify modifications genome wide, it is anticipated that novel chemical modifications or new modification sites will be identified, which will play additional regulatory functions for RNA turnover.
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182
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ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay. Nat Struct Mol Biol 2017; 24:534-543. [PMID: 28436945 PMCID: PMC5461201 DOI: 10.1038/nsmb.3403] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/27/2017] [Indexed: 01/10/2023]
Abstract
Both p150 and p110 isoforms of ADAR1 convert adenosine to inosine in double-stranded RNA (dsRNA). ADAR1p150 suppresses the dsRNA sensing mechanism that activates MDA5-MAVS-IFN signaling in the cytoplasm. In contrast, the biological function of the ADAR1p110 isoform, usually located in the nucleus, remains largely unknown. Here we show that stress-activated phosphorylation of ADAR1p110 by MKK6-p38-MSK MAP kinases promotes its binding to Exportin-5 and export from the nucleus. Once translocated to the cytoplasm, ADAR1p110 suppresses apoptosis of stressed cells by protecting many anti-apoptotic gene transcripts that contain 3′UTR dsRNA structures primarily made from inverted Alu repeats. ADAR1p110 competitively inhibits binding of Staufen1 to the 3′UTR dsRNAs and antagonizes the Staufen1-mediated mRNA decay. Our studies revealed a new stress response mechanism, in which human ADAR1p110 and Staufen1 regulate surveillance of a set of mRNAs required for survival of stressed cells.
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183
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Fruci D, Rota R, Gallo A. The Role of HCMV and HIV-1 MicroRNAs: Processing, and Mechanisms of Action during Viral Infection. Front Microbiol 2017; 8:689. [PMID: 28484438 PMCID: PMC5399795 DOI: 10.3389/fmicb.2017.00689] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 04/04/2017] [Indexed: 11/23/2022] Open
Abstract
Viruses infect host cells releasing their genome (DNA or RNA) containing all information needed to replicate themselves. The viral genome takes control of the cells and helps the virus to evade the host immune system. Some viruses alter the functions of infected cells without killing them. In some cases infected cells lose control over normal cell proliferation and becomes cancerous. Viruses, such as HCMV and HIV-1, may leave their viral genome in the host cells for a certain period (latency) and begin to replicate when the cells are stressed causing diseases. HCMV and HIV-1 have developed multiple strategies to avoid recognition and elimination by the host’s immune system. These strategies rely on viral products that mimic specific components of the host cells to prevent immune recognition of virally infected cells. In addition to viral proteins, viruses encode short non-coding RNAs (vmiRNAs) that regulate both viral and host cellular transcripts to favor viral infection and actively curtail the host’s antiviral immune response. In this review, we will give an overview of the general functions of microRNAs generated by HCMV and HIV-1, their processing and interaction with the host’s immune system.
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Affiliation(s)
- Doriana Fruci
- Immuno-Oncology Laboratory, Oncohaematology Department, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere ScientificoRome, Italy
| | - Rossella Rota
- Angiogenesis Laboratory, Oncohaematology Department, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere ScientificoRome, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere ScientificoRome, Italy
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184
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ADAR1 and MicroRNA; A Hidden Crosstalk in Cancer. Int J Mol Sci 2017; 18:ijms18040799. [PMID: 28398248 PMCID: PMC5412383 DOI: 10.3390/ijms18040799] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 11/17/2022] Open
Abstract
The evolution of cancer cells is believed to be dependent on genetic or epigenetic alterations. However, this concept has recently been challenged by another mode of nucleotide alteration, RNA editing, which is frequently up-regulated in cancer. RNA editing is a biochemical process in which either Adenosine or Cytosine is deaminated by a group of RNA editing enzymes including ADAR (Adenosine deaminase; RNA specific) or APOBEC3B (Apolipoprotein B mRNA Editing Enzyme Catalytic Subunit 3B). The result of RNA editing is usually adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) transition, which can affect protein coding, RNA stability, splicing and microRNA-target interactions. The functional impact of these alterations is largely unclear and is a subject of extensive research. In the present review, we will specifically focus on the influence of ADARs on carcinogenesis via the regulation of microRNA processing and functioning. This follows a brief review of the current knowledge of properties of ADAR enzyme, RNA editing, and microRNA processing.
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185
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Oakes E, Anderson A, Cohen-Gadol A, Hundley HA. Adenosine Deaminase That Acts on RNA 3 (ADAR3) Binding to Glutamate Receptor Subunit B Pre-mRNA Inhibits RNA Editing in Glioblastoma. J Biol Chem 2017; 292:4326-4335. [PMID: 28167531 DOI: 10.1074/jbc.m117.779868] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/05/2017] [Indexed: 01/08/2023] Open
Abstract
RNA editing is a cellular process that precisely alters nucleotide sequences, thus regulating gene expression and generating protein diversity. Over 60% of human transcripts undergo adenosine to inosine RNA editing, and editing is required for normal development and proper neuronal function of animals. Editing of one adenosine in the transcript encoding the glutamate receptor subunit B, glutamate receptor ionotropic AMPA 2 (GRIA2), modifies a codon, replacing the genomically encoded glutamine (Q) with arginine (R); thus this editing site is referred to as the Q/R site. Editing at the Q/R site of GRIA2 is essential, and reduced editing of GRIA2 transcripts has been observed in patients suffering from glioblastoma. In glioblastoma, incorporation of unedited GRIA2 subunits leads to a calcium-permeable glutamate receptor, which can promote cell migration and tumor invasion. In this study, we identify adenosine deaminase that acts on RNA 3 (ADAR3) as an important regulator of Q/R site editing, investigate its mode of action, and detect elevated ADAR3 expression in glioblastoma tumors compared with adjacent brain tissue. Overexpression of ADAR3 in astrocyte and astrocytoma cell lines inhibits RNA editing at the Q/R site of GRIA2 Furthermore, the double-stranded RNA binding domains of ADAR3 are required for repression of RNA editing. As the Q/R site of GRIA2 is specifically edited by ADAR2, we suggest that ADAR3 directly competes with ADAR2 for binding to GRIA2 transcript, inhibiting RNA editing, as evidenced by the direct binding of ADAR3 to the GRIA2 pre-mRNA. Finally, we provide evidence that both ADAR2 and ADAR3 expression contributes to the relative level of GRIA2 editing in tumors from patients suffering from glioblastoma.
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Affiliation(s)
| | - Ashley Anderson
- Medical Sciences Program, Indiana University, Bloomington, Indiana 47405 and
| | - Aaron Cohen-Gadol
- Department of Neurological Surgery, Goodman Campbell Brain and Spine, Indianapolis, Indiana 46202
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, Indiana 47405 and
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186
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Fang Y, Zhang L, Li Z, Li Y, Huang C, Lu X. MicroRNAs in DNA Damage Response, Carcinogenesis, and Chemoresistance. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 333:1-49. [DOI: 10.1016/bs.ircmb.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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187
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Abstract
Organisms throughout biology need to maintain the integrity of their genome. From bacteria to vertebrates, life has established sophisticated mechanisms to detect and eliminate foreign genetic material or to restrict its function and replication. Tremendous progress has been made in the understanding of these mechanisms which keep foreign or unwanted nucleic acids from viruses or phages in check. Mechanisms reach from restriction-modification systems and CRISPR/Cas in bacteria and archaea to RNA interference and immune sensing of nucleic acids, altogether integral parts of a system which is now appreciated as nucleic acid immunity. With inherited receptors and acquired sequence information, nucleic acid immunity comprises innate and adaptive components. Effector functions include diverse nuclease systems, intrinsic activities to directly restrict the function of foreign nucleic acids (e.g., PKR, ADAR1, IFIT1), and extrinsic pathways to alert the immune system and to elicit cytotoxic immune responses. These effects act in concert to restrict viral replication and to eliminate virus-infected cells. The principles of nucleic acid immunity are highly relevant for human disease. Besides its essential contribution to antiviral defense and restriction of endogenous retroelements, dysregulation of nucleic acid immunity can also lead to erroneous detection and response to self nucleic acids then causing sterile inflammation and autoimmunity. Even mechanisms of nucleic acid immunity which are not established in vertebrates are relevant for human disease when they are present in pathogens such as bacteria, parasites, or helminths or in pathogen-transmitting organisms such as insects. This review aims to provide an overview of the diverse mechanisms of nucleic acid immunity which mostly have been looked at separately in the past and to integrate them under the framework nucleic acid immunity as a basic principle of life, the understanding of which has great potential to advance medicine.
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Affiliation(s)
- G Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Bonn, Germany.
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188
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Functions of the RNA Editing Enzyme ADAR1 and Their Relevance to Human Diseases. Genes (Basel) 2016; 7:genes7120129. [PMID: 27999332 PMCID: PMC5192505 DOI: 10.3390/genes7120129] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 12/17/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA (dsRNA). Among the three types of mammalian ADARs, ADAR1 has long been recognized as an essential enzyme for normal development. The interferon-inducible ADAR1p150 is involved in immune responses to both exogenous and endogenous triggers, whereas the functions of the constitutively expressed ADAR1p110 are variable. Recent findings that ADAR1 is involved in the recognition of self versus non-self dsRNA provide potential explanations for its links to hematopoiesis, type I interferonopathies, and viral infections. Editing in both coding and noncoding sequences results in diseases ranging from cancers to neurological abnormalities. Furthermore, editing of noncoding sequences, like microRNAs, can regulate protein expression, while editing of Alu sequences can affect translational efficiency and editing of proximal sequences. Novel identifications of long noncoding RNA and retrotransposons as editing targets further expand the effects of A-to-I editing. Besides editing, ADAR1 also interacts with other dsRNA-binding proteins in editing-independent manners. Elucidating the disease-specific patterns of editing and/or ADAR1 expression may be useful in making diagnoses and prognoses. In this review, we relate the mechanisms of ADAR1′s actions to its pathological implications, and suggest possible mechanisms for the unexplained associations between ADAR1 and human diseases.
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189
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TRBP ensures efficient Dicer processing of precursor microRNA in RNA-crowded environments. Nat Commun 2016; 7:13694. [PMID: 27934859 PMCID: PMC5155159 DOI: 10.1038/ncomms13694] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 01/03/2023] Open
Abstract
The RNA-binding protein TRBP is a central component of the Dicer complex. Despite a decade of biochemical and structural studies, the essential functionality of TRBP in microRNA (miRNA) biogenesis remains unknown. Here we show that TRBP is an integral cofactor for time-efficient Dicer processing in RNA-crowded environments. We competed for Dicer processing of pre-miRNA with a large amount of cellular RNA species and found that Dicer-TRBP, but not Dicer alone, remains resilient. To apprehend the mechanism of this substrate selectivity, we use single-molecule fluorescence. The real-time observation reveals that TRBP acts as a gatekeeper, precluding Dicer from engaging with pre-miRNA-like substrates. TRBP acquires the selectivity using the PAZ domain of Dicer, whereas Dicer moderates the RNA-binding affinity of TRBP for fast turnover. This coordinated action between TRBP and Dicer accomplishes an efficient way of discarding pre-miRNA-like substrates. The RNA binding protein TRBP is a component of the Dicer complex but its role in microRNA biogenesis remains poorly understood. Here the authors use a crowded RNA environment and single-molecule imaging to show that TRBP acts as a gatekeeper to prevent Dicer engagement with pre miRNA-like substrates.
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190
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Germanguz I, Lowry WE. RNA editing as an activator of self-renewal in cancer. Stem Cell Investig 2016; 3:68. [PMID: 27868050 DOI: 10.21037/sci.2016.10.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 10/05/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Igal Germanguz
- Jonsson Comprehensive Cancer Center, Molecular Biology Institute, UCLA, MCDB, UCLA, Los Angeles, CA, USA;; Eli and Edythe Broad Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA
| | - William E Lowry
- Jonsson Comprehensive Cancer Center, Molecular Biology Institute, UCLA, MCDB, UCLA, Los Angeles, CA, USA;; Eli and Edythe Broad Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA
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191
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Chan THM, Qamra A, Tan KT, Guo J, Yang H, Qi L, Lin JS, Ng VHE, Song Y, Hong H, Tay ST, Liu Y, Lee J, Rha SY, Zhu F, So JBY, Teh BT, Yeoh KG, Rozen S, Tenen DG, Tan P, Chen L. ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer. Gastroenterology 2016; 151:637-650.e10. [PMID: 27373511 PMCID: PMC8286172 DOI: 10.1053/j.gastro.2016.06.043] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUD & AIMS Gastric cancer (GC) is the third leading cause of global cancer mortality. Adenosine-to-inosine RNA editing is a recently described novel epigenetic mechanism involving sequence alterations at the RNA but not DNA level, primarily mediated by ADAR (adenosine deaminase that act on RNA) enzymes. Emerging evidence suggests a role for RNA editing and ADARs in cancer, however, the relationship between RNA editing and GC development and progression remains unknown. METHODS In this study, we leveraged on the next-generation sequencing transcriptomics to demarcate the GC RNA editing landscape and the role of ADARs in this deadly malignancy. RESULTS Relative to normal gastric tissues, almost all GCs displayed a clear RNA misediting phenotype with ADAR1/2 dysregulation arising from the genomic gain and loss of the ADAR1 and ADAR2 gene in primary GCs, respectively. Clinically, patients with GCs exhibiting ADAR1/2 imbalance demonstrated extremely poor prognoses in multiple independent cohorts. Functionally, we demonstrate in vitro and in vivo that ADAR-mediated RNA misediting is closely associated with GC pathogenesis, with ADAR1 and ADAR2 playing reciprocal oncogenic and tumor suppressive roles through their catalytic deaminase domains, respectively. Using an exemplary target gene PODXL (podocalyxin-like), we demonstrate that the ADAR2-regulated recoding editing at codon 241 (His to Arg) confers a loss-of-function phenotype that neutralizes the tumorigenic ability of the unedited PODXL. CONCLUSIONS Our study highlights a major role for RNA editing in GC disease and progression, an observation potentially missed by previous next-generation sequencing analyses of GC focused on DNA alterations alone. Our findings also suggest new GC therapeutic opportunities through ADAR1 enzymatic inhibition or the potential restoration of ADAR2 activity.
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Affiliation(s)
- Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Aditi Qamra
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kar Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jing Guo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lihua Qi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jaymie Siqi Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Huiqi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore
| | - Yujing Liu
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Singapore–Massachusetts Institute of Technology Alliance, Singapore
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sun Yong Rha
- Yonsei Cancer Center, Seodaemun-gu, Seoul, South Korea
| | - Feng Zhu
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jimmy Bok Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bin Tean Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore,Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Department of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Steve Rozen
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Centre for Computational Biology, Duke–National University of Singapore Graduate Medical School, Singapore
| | - Daniel G. Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore,Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore; Genome Institute of Singapore, Singapore.
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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192
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Liu X, Huang K, Hou Q, Sun Z, Wang B, Lin G, Li D, Liu Y, Xu X, Hu C. Identification and characterization of a constitutively expressed Ctenopharyngodon idella ADAR1 splicing isoform (CiADAR1a). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 63:10-17. [PMID: 27185203 DOI: 10.1016/j.dci.2016.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 06/05/2023]
Abstract
As one member of ADAR family, ADAR1 (adenosine deaminase acting on RNA 1) can convert adenosine to inosine within dsRNA. There are many ADAR1 splicing isoforms in mammals, including an interferon (IFN) inducible ∼150 kD protein (ADAR1-p150) and a constitutively expressed ∼110 kD protein (ADAR1-p110). The structural diversity of ADAR1 splicing isoforms may reflect their multiple functions. ADAR1 splicing isoforms were also found in fish. In our previous study, we have cloned and identified two different grass carp ADAR1 splicing isoforms, i.e. CiADAR1 and CiADAR1-like, both of them are IFN-inducible proteins. In this paper, we identified a novel CiADAR1 splicing isoform gene (named CiADAR1a). CiADAR1a gene contains 15 exons and 14 introns. Its full-length cDNA is comprised of a 5' UTR (359 bp), a 3' UTR (229 bp) and a 2952 bp ORF encoding a polypeptide of 983 amino acids with one Z-DNA binding domain, three dsRNA binding motifs and a highly conserved hydrolytic deamination domain. CiADAR1a was constitutively expressed in Ctenopharyngodon idella kidney (CIK) cells regardless of Poly I:C stimulation by Western blot assay. In normal condition, CiADAR1a was found to be present mainly in the nucleus. After treatment with Poly I:C, it gradually shifted to cytoplasm. To further investigate the mechanism of transcriptional regulation of CiADAR1a, we cloned and identified its promoter sequence. The transcriptional start site of CiADAR1a is mapped within the truncated exon 2. CiADAR1a promoter is 1303 bp in length containing 4 IRF-Es. In the present study, we constructed pcDNA3.1 eukaryotic expression vectors with IRF1 and IRF3 and co-transfected them with pGL3-CiADAR1a promoter into CIK cells. The results showed that neither the over-expression of IRF1 or IRF3 nor Poly I:C stimulation significantly impacted CiADAR1a promoter activity in CIK cells. Together, according to the molecular and expression characteristics, subcellular localization and transcriptional regulatory mechanism, we deduced that CiADAR1a shared a high degree of homology with mammalian ADAR1-p110.
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Affiliation(s)
- Xiancheng Liu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Keyi Huang
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Qunhao Hou
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Zhicheng Sun
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Binhua Wang
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Gang Lin
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Dongming Li
- Fuzhou Medical College, Nanchang University, Fuzhou 344000, China
| | - Yong Liu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Xiaowen Xu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Chengyu Hu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
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193
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Orecchini E, Doria M, Antonioni A, Galardi S, Ciafrè SA, Frassinelli L, Mancone C, Montaldo C, Tripodi M, Michienzi A. ADAR1 restricts LINE-1 retrotransposition. Nucleic Acids Res 2016; 45:155-168. [PMID: 27658966 PMCID: PMC5224506 DOI: 10.1093/nar/gkw834] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 12/16/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) are involved in RNA editing that converts adenosines to inosines in double-stranded RNAs. ADAR1 was demonstrated to be functional on different viruses exerting either antiviral or proviral effects. Concerning HIV-1, several studies showed that ADAR1 favors viral replication. The aim of this study was to investigate the composition of the ADAR1 ribonucleoprotein complex during HIV-1 expression. By using a dual-tag affinity purification procedure in cells expressing HIV-1 followed by mass spectrometry analysis, we identified 14 non-ribosomal ADAR1-interacting proteins, most of which are novel. A significant fraction of these proteins were previously demonstrated to be associated to the Long INterspersed Element 1 (LINE1 or L1) ribonucleoparticles and to regulate the life cycle of L1 retrotransposons that continuously re-enter host-genome. Hence, we investigated the function of ADAR1 in the regulation of L1 activity. By using different cell-culture based retrotransposition assays in HeLa cells, we demonstrated a novel function of ADAR1 as suppressor of L1 retrotransposition. Apparently, this inhibitory mechanism does not occur through ADAR1 editing activity. Furthermore, we showed that ADAR1 binds the basal L1 RNP complex. Overall, these data support the role of ADAR1 as regulator of L1 life cycle.
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Affiliation(s)
- Elisa Orecchini
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Margherita Doria
- Laboratory of Immunoinfectivology, Bambino Gesù Children's Hospital, IRCCS, Piazza S. Onofrio 4, Rome 00165, Italy
| | - Ambra Antonioni
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Silvia Galardi
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Loredana Frassinelli
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
| | - Carmine Mancone
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Italy.,L. Spallanzani National Institute for Infectious Diseases, IRCCS, via Portuense 292, Rome 00149, Italy
| | - Claudia Montaldo
- L. Spallanzani National Institute for Infectious Diseases, IRCCS, via Portuense 292, Rome 00149, Italy
| | - Marco Tripodi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Italy.,L. Spallanzani National Institute for Infectious Diseases, IRCCS, via Portuense 292, Rome 00149, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Via Montpellier 1, Rome 00133, Italy
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194
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Stellos K, Gatsiou A, Stamatelopoulos K, Perisic Matic L, John D, Lunella FF, Jaé N, Rossbach O, Amrhein C, Sigala F, Boon RA, Fürtig B, Manavski Y, You X, Uchida S, Keller T, Boeckel JN, Franco-Cereceda A, Maegdefessel L, Chen W, Schwalbe H, Bindereif A, Eriksson P, Hedin U, Zeiher AM, Dimmeler S. Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation. Nat Med 2016; 22:1140-1150. [PMID: 27595325 DOI: 10.1038/nm.4172] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/20/2016] [Indexed: 12/14/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase acting on RNA (ADAR) enzymes, is important in the epitranscriptomic regulation of RNA metabolism. However, the role of A-to-I RNA editing in vascular disease is unknown. Here we show that cathepsin S mRNA (CTSS), which encodes a cysteine protease associated with angiogenesis and atherosclerosis, is highly edited in human endothelial cells. The 3' untranslated region (3' UTR) of the CTSS transcript contains two inverted repeats, the AluJo and AluSx+ regions, which form a long stem-loop structure that is recognized by ADAR1 as a substrate for editing. RNA editing enables the recruitment of the stabilizing RNA-binding protein human antigen R (HuR; encoded by ELAVL1) to the 3' UTR of the CTSS transcript, thereby controlling CTSS mRNA stability and expression. In endothelial cells, ADAR1 overexpression or treatment of cells with hypoxia or with the inflammatory cytokines interferon-γ and tumor-necrosis-factor-α induces CTSS RNA editing and consequently increases cathepsin S expression. ADAR1 levels and the extent of CTSS RNA editing are associated with changes in cathepsin S levels in patients with atherosclerotic vascular diseases, including subclinical atherosclerosis, coronary artery disease, aortic aneurysms and advanced carotid atherosclerotic disease. These results reveal a previously unrecognized role of RNA editing in gene expression in human atherosclerotic vascular diseases.
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Affiliation(s)
- Konstantinos Stellos
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Department of Cardiology, Center of Internal Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Aikaterini Gatsiou
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Kimon Stamatelopoulos
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Ljubica Perisic Matic
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - David John
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Federica Francesca Lunella
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Nicolas Jaé
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Carolin Amrhein
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Frangiska Sigala
- Department of Vascular Surgery, 1st Propaedeutic Department of Surgery, Hippocratio General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Reinier A Boon
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt, Germany
| | - Yosif Manavski
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Xintian You
- Laboratory of Functional Genomics and Systems Biology, Max Delbrück Center for Molecular Medicine Berlin-Buch, Berlin, Germany
| | - Shizuka Uchida
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Till Keller
- Department of Cardiology, Center of Internal Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Jes-Niels Boeckel
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Anders Franco-Cereceda
- Cardiothoracic Surgery Unit, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Lars Maegdefessel
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Vascular and Endovascular Surgery, Technical University Munich, Munich, Germany
| | - Wei Chen
- Laboratory of Functional Genomics and Systems Biology, Max Delbrück Center for Molecular Medicine Berlin-Buch, Berlin, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Per Eriksson
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Andreas M Zeiher
- Department of Cardiology, Center of Internal Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,German Center of Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung; DZHK), Rhein-Main Partner Site, Frankfurt, Germany
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195
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Zipeto MA, Court AC, Sadarangani A, Delos Santos NP, Balaian L, Chun HJ, Pineda G, Morris SR, Mason CN, Geron I, Barrett C, Goff DJ, Wall R, Pellecchia M, Minden M, Frazer KA, Marra MA, Crews LA, Jiang Q, Jamieson CHM. ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis. Cell Stem Cell 2016; 19:177-191. [PMID: 27292188 PMCID: PMC4975616 DOI: 10.1016/j.stem.2016.05.004] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 04/12/2016] [Accepted: 05/06/2016] [Indexed: 12/17/2022]
Abstract
Post-transcriptional adenosine-to-inosine RNA editing mediated by adenosine deaminase acting on RNA1 (ADAR1) promotes cancer progression and therapeutic resistance. However, ADAR1 editase-dependent mechanisms governing leukemia stem cell (LSC) generation have not been elucidated. In blast crisis chronic myeloid leukemia (BC CML), we show that increased JAK2 signaling and BCR-ABL1 amplification activate ADAR1. In a humanized BC CML mouse model, combined JAK2 and BCR-ABL1 inhibition prevents LSC self-renewal commensurate with ADAR1 downregulation. Lentiviral ADAR1 wild-type, but not an editing-defective ADAR1(E912A) mutant, induces self-renewal gene expression and impairs biogenesis of stem cell regulatory let-7 microRNAs. Combined RNA sequencing, qRT-PCR, CLIP-ADAR1, and pri-let-7 mutagenesis data suggest that ADAR1 promotes LSC generation via let-7 pri-microRNA editing and LIN28B upregulation. A small-molecule tool compound antagonizes ADAR1's effect on LSC self-renewal in stromal co-cultures and restores let-7 biogenesis. Thus, ADAR1 activation represents a unique therapeutic vulnerability in LSCs with active JAK2 signaling.
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Affiliation(s)
- Maria Anna Zipeto
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angela C Court
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anil Sadarangani
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathaniel P Delos Santos
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Larisa Balaian
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hye-Jung Chun
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Gabriel Pineda
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sheldon R Morris
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cayla N Mason
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ifat Geron
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christian Barrett
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel J Goff
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Russell Wall
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maurizio Pellecchia
- School of Medicine, University of California Riverside, Riverside, CA 92521, USA
| | - Mark Minden
- Princess Margaret Hospital, Toronto, ON M5G 2M9, Canada
| | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Leslie A Crews
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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196
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Identification of novel candidate drivers connecting different dysfunctional levels for lung adenocarcinoma using protein-protein interactions and a shortest path approach. Sci Rep 2016; 6:29849. [PMID: 27412431 PMCID: PMC4944139 DOI: 10.1038/srep29849] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/24/2016] [Indexed: 12/21/2022] Open
Abstract
Tumors are formed by the abnormal proliferation of somatic cells with disordered growth regulation under the influence of tumorigenic factors. Recently, the theory of “cancer drivers” connects tumor initiation with several specific mutations in the so-called cancer driver genes. According to the differentiation of four basic levels between tumor and adjacent normal tissues, the cancer drivers can be divided into the following: (1) Methylation level, (2) microRNA level, (3) mutation level, and (4) mRNA level. In this study, a computational method is proposed to identify novel lung adenocarcinoma drivers based on dysfunctional genes on the methylation, microRNA, mutation and mRNA levels. First, a large network was constructed using protein-protein interactions. Next, we searched all of the shortest paths connecting dysfunctional genes on different levels and extracted new candidate genes lying on these paths. Finally, the obtained candidate genes were filtered by a permutation test and an additional strict selection procedure involving a betweenness ratio and an interaction score. Several candidate genes remained, which are deemed to be related to two different levels of cancer. The analyses confirmed our assertions that some have the potential to contribute to the tumorigenesis process on multiple levels.
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197
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Liddicoat BJ, Hartner JC, Piskol R, Ramaswami G, Chalk AM, Kingsley PD, Sankaran VG, Wall M, Purton LE, Seeburg PH, Palis J, Orkin SH, Lu J, Li JB, Walkley CR. Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis. Exp Hematol 2016; 44:947-63. [PMID: 27373493 DOI: 10.1016/j.exphem.2016.06.250] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/17/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) convert adenosine residues to inosine in double-stranded RNA. In vivo, ADAR1 is essential for the maintenance of hematopoietic stem/progenitors. Whether other hematopoietic cell types also require ADAR1 has not been assessed. Using erythroid- and myeloid-restricted deletion of Adar1, we demonstrate that ADAR1 is dispensable for myelopoiesis but is essential for normal erythropoiesis. Adar1-deficient erythroid cells display a profound activation of innate immune signaling and high levels of cell death. No changes in microRNA levels were found in ADAR1-deficient erythroid cells. Using an editing-deficient allele, we demonstrate that RNA editing is the essential function of ADAR1 during erythropoiesis. Mapping of adenosine-to-inosine editing in purified erythroid cells identified clusters of hyperedited adenosines located in long 3'-untranslated regions of erythroid-specific transcripts and these are ADAR1-specific editing events. ADAR1-mediated RNA editing is essential for normal erythropoiesis.
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Affiliation(s)
- Brian J Liddicoat
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Jochen C Hartner
- Taconic Biosciences, Cologne, Germany; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Robert Piskol
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alistair M Chalk
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Paul D Kingsley
- Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Vijay G Sankaran
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, Fitzroy, Victoria, Australia
| | - Louise E Purton
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Peter H Seeburg
- Department of Molecular Neurobiology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James Palis
- Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA
| | - Jun Lu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia.
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198
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Ben-Shoshan SO, Kagan P, Sultan M, Barabash Z, Dor C, Jacob-Hirsch J, Harmelin A, Pappo O, Marcu-Malina V, Ben-Ari Z, Amariglio N, Rechavi G, Goldstein I, Safran M. ADAR1 deletion induces NFκB and interferon signaling dependent liver inflammation and fibrosis. RNA Biol 2016; 14:587-602. [PMID: 27362366 DOI: 10.1080/15476286.2016.1203501] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Adenosine deaminase acting on RNA (ADAR) 1 binds and edits double-stranded (ds) RNA secondary structures found mainly within untranslated regions of many transcripts. In the current research, our aim was to study the role of ADAR1 in liver homeostasis. As previous studies show a conserved immunoregulatory function for ADAR1 in mammalians, we focused on its role in preventing chronic hepatic inflammation and the associated activation of hepatic stellate cells to produce extracellular matrix and promote fibrosis. We show that hepatocytes specific ADAR1 knock out (KO) mice display massive liver damage with multifocal inflammation and fibrogenesis. The bioinformatics analysis of the microarray gene-expression datasets of ADAR1 KO livers reveled a type-I interferons signature and an enrichment for immune response genes compared to control littermate livers. Furthermore, we found that in vitro silencing of ADAR1 expression in HepG2 cells leads to enhanced transcription of NFκB target genes, foremost of the pro-inflammatory cytokines IL6 and IL8. We also discovered immune cell-independent paracrine signaling among ADAR1-depleted HepG2 cells and hepatic stellate cells, leading to the activation of the latter cell type to adopt a profibrogenic phenotype. This paracrine communication dependent mainly on the production and secretion of the cytokine IL6 induced by ADAR1 silencing in hepatocytes. Thus, our findings shed a new light on the vital regulatory role of ADAR1 in hepatic immune homeostasis, chiefly its inhibitory function on the crosstalk between the NFκB and type-I interferons signaling cascades, restraining the development of liver inflammation and fibrosis.
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Affiliation(s)
- Shirley Oren Ben-Shoshan
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Polina Kagan
- b Liver Research Laboratory , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Maya Sultan
- b Liver Research Laboratory , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Zohar Barabash
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Chen Dor
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Jasmine Jacob-Hirsch
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,e The Mina and Everard Goodman Faculty of Life Sciences , Bar Ilan University , Ramat Gan , Israel
| | - Alon Harmelin
- f Department of Veterinary Resources , Weizmann Institute of Science , Rehovot , Israel
| | - Orit Pappo
- c Department of Pathology , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Victoria Marcu-Malina
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Ziv Ben-Ari
- b Liver Research Laboratory , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Ninette Amariglio
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,e The Mina and Everard Goodman Faculty of Life Sciences , Bar Ilan University , Ramat Gan , Israel
| | - Gideon Rechavi
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Itamar Goldstein
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Michal Safran
- b Liver Research Laboratory , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
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199
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Abstract
All true metazoans modify their RNAs by converting specific adenosine residues to inosine. Because inosine binds to cytosine, it is a biological mimic for guanosine. This subtle change, termed RNA editing, can have diverse effects on various RNA-mediated cellular pathways, including RNA interference, innate immunity, retrotransposon defense and messenger RNA recoding. Because RNA editing can be regulated, it is an ideal tool for increasing genetic diversity, adaptation and environmental acclimation. This review will cover the following themes related to RNA editing: (1) how it is used to modify different cellular RNAs, (2) how frequently it is used by different organisms to recode mRNA, (3) how specific recoding events regulate protein function, (4) how it is used in adaptation and (5) emerging evidence that it can be used for acclimation. Organismal biologists with an interest in adaptation and acclimation, but with little knowledge of RNA editing, are the intended audience.
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Affiliation(s)
- Joshua J C Rosenthal
- Universidad de Puerto Rico, Recinto de Ciencias Medicas, Instituto de Neurobiologia, 201 Blvd. del Valle, San Juan, PR 00901, USA
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200
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Lim MYT, Ng AWT, Chou Y, Lim TP, Simcox A, Tucker-Kellogg G, Okamura K. The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site. Cell Rep 2016; 15:1795-808. [PMID: 27184838 DOI: 10.1016/j.celrep.2016.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/03/2016] [Accepted: 04/15/2016] [Indexed: 12/24/2022] Open
Abstract
In Drosophila, Dicer-1 binds Loquacious-PB (Loqs-PB) as its major co-factor. Previous analyses indicated that loqs mutants only partially impede miRNA processing, but the activity of minor isoforms or maternally deposited Loqs was not eliminated in these studies. We addressed this by generating a cell line from loqs-null embryos and found that only ∼40% of miRNAs showed clear Loqs dependence. Genome-wide comparison of the hairpin structure and Loqs dependence suggested that Loqs substrates are influenced by base-pairing status at the dicing site. Artificial alteration of base-pairing stability at this position in model miRNA hairpins resulted in predicted changes in Loqs dependence, providing evidence for this hypothesis. Finally, we found that evolutionarily young miRNA genes tended to be Loqs dependent. We propose that Loqs may have roles in assisting the de novo emergence of miRNA genes by facilitating dicing of suboptimal hairpin substrates.
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Affiliation(s)
- Mandy Yu Theng Lim
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore
| | - Alvin Wei Tian Ng
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - Yuting Chou
- Sloan-Kettering Institute, Department of Developmental Biology, New York, NY 10065, USA
| | - Teck Por Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - Amanda Simcox
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Greg Tucker-Kellogg
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore.
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