1
|
Crane AB, Jetti SK, Littleton JT. A stochastic RNA editing process targets a limited number of sites in individual Drosophila glutamatergic motoneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594696. [PMID: 38798345 PMCID: PMC11118563 DOI: 10.1101/2024.05.17.594696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
RNA editing is a post-transcriptional source of protein diversity and occurs across the animal kingdom. Given the complete profile of mRNA targets and their editing rate in individual cells is unclear, we analyzed single cell RNA transcriptomes from Drosophila larval tonic and phasic glutamatergic motoneuron subtypes to determine the most highly edited targets and identify cell-type specific editing. From ∼15,000 genes encoded in the genome, 316 high confidence A-to-I canonical RNA edit sites were identified, with 102 causing missense amino acid changes in proteins regulating membrane excitability, synaptic transmission, and cellular function. Some sites showed 100% editing in single neurons as observed with mRNAs encoding mammalian AMPA receptors. However, most sites were edited at lower levels and generated variable expression of edited and unedited mRNAs within individual neurons. Together, these data provide insights into how the RNA editing landscape alters protein function to modulate the properties of two well-characterized neuronal populations in Drosophila .
Collapse
|
2
|
Dhakal A, Salim C, Skelly M, Amichan Y, Lamm AT, Hundley HA. ADARs regulate cuticle collagen expression and promote survival to pathogen infection. BMC Biol 2024; 22:37. [PMID: 38360623 PMCID: PMC10870475 DOI: 10.1186/s12915-024-01840-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND In all organisms, the innate immune system defends against pathogens through basal expression of molecules that provide critical barriers to invasion and inducible expression of effectors that combat infection. The adenosine deaminase that act on RNA (ADAR) family of RNA-binding proteins has been reported to influence innate immunity in metazoans. However, studies on the susceptibility of ADAR mutant animals to infection are largely lacking. RESULTS Here, by analyzing adr-1 and adr-2 null mutants in well-established slow-killing assays, we find that both Caenorhabditis elegans ADARs are important for organismal survival to gram-negative and gram-positive bacteria, all of which are pathogenic to humans. Furthermore, our high-throughput sequencing and genetic analysis reveal that ADR-1 and ADR-2 function in the same pathway to regulate collagen expression. Consistent with this finding, our scanning electron microscopy studies indicate adr-1;adr-2 mutant animals also have altered cuticle morphology prior to pathogen exposure. CONCLUSIONS Our data uncover a critical role of the C. elegans ADAR family of RNA-binding proteins in promoting cuticular collagen expression, which represents a new post-transcriptional regulatory node that influences the extracellular matrix. In addition, we provide the first evidence that ADAR mutant animals have altered susceptibility to infection with several opportunistic human pathogens, suggesting a broader role of ADARs in altering physical barriers to infection to influence innate immunity.
Collapse
Affiliation(s)
- Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, 47405, USA
| | - Chinnu Salim
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Mary Skelly
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Yarden Amichan
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Ayelet T Lamm
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
| |
Collapse
|
3
|
Montagud‐Martínez R, Márquez‐Costa R, Heras‐Hernández M, Dolcemascolo R, Rodrigo G. On the ever-growing functional versatility of the CRISPR-Cas13 system. Microb Biotechnol 2024; 17:e14418. [PMID: 38381083 PMCID: PMC10880580 DOI: 10.1111/1751-7915.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
CRISPR-Cas systems evolved in prokaryotes to implement a powerful antiviral immune response as a result of sequence-specific targeting by ribonucleoproteins. One of such systems consists of an RNA-guided RNA endonuclease, known as CRISPR-Cas13. In very recent years, this system is being repurposed in different ways in order to decipher and engineer gene expression programmes. Here, we discuss the functional versatility of the CRISPR-Cas13 system, which includes the ability for RNA silencing, RNA editing, RNA tracking, nucleic acid detection and translation regulation. This functional palette makes the CRISPR-Cas13 system a relevant tool in the broad field of systems and synthetic biology.
Collapse
Affiliation(s)
- Roser Montagud‐Martínez
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Rosa Márquez‐Costa
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - María Heras‐Hernández
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| |
Collapse
|
4
|
Collins JM, Wang D. A Comprehensive Evaluation of the Effects of RNA-Editing Proteins ADAR and ADARB1 on the Expression of the Drug-Metabolizing Enzymes in HepaRG Cells. Drug Metab Dispos 2023; 51:1508-1514. [PMID: 37532539 PMCID: PMC10586505 DOI: 10.1124/dmd.123.001396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023] Open
Abstract
Two RNA-editing proteins, the adenosine deaminase acting on RNA, ADAR, and ADARB1, broadly regulate gene expression in editing-dependent and editing-independent manners. Previous studies showed that the expression of the drug-metabolizing cytochrome P450s (P450s) and UDP glucuronosyltransferases (UGTs) changes upon knockdown (KD) of ADAR or ADARB1 in different hepatic cell lines. To systematically survey the effects of these two ADARs on the expression of P450s and UGTs, we used small interfering RNA in HepaRG cells and tested the association between the expression of the P450s and ADARs in a liver sample cohort (n = 246). KD of ADAR increased the expression of the CYP3As and CYP2C9 and reduced the expression of the others, whereas KD of ADARB1 reduced the expression of nearly all genes tested. ADAR KD also suppressed the induction of most P450s, whereas ADARB1 KD had mixed effects depending on the inducer/gene combination. P450 expression was positively associated with both ADARs in liver samples, consistent with the KD results. However, after adjusting for the expression of transcription factors (TFs) known to regulate P450 expression, the associations disappeared, indicating that the effects of ADAR or ADARB1 primarily occur through TFs. Moreover, we found that the expression of normally spliced CYP3A5 transcripts is increased in both KDs, indicating a direct effect of the ADARs on promoting the usage of the cryptic splice site generated by CYP3A5*3. Taken together, our results revealed the nonoverlapping regulatory effects of ADAR and ADARB1 and supported their broad roles in controlling the expression of drug-metabolizing enzymes in the liver. SIGNIFICANCE STATEMENT: Here, this study systematically surveyed the roles of ADAR and ADARB1 in both basal and induced expression of drug-metabolizing enzymes and assessed their coexpression in liver samples. This study's results support that ADAR and ADARB1 regulate the expression of the drug-metabolizing enzymes in the liver, suggesting that factors affecting ADAR expression also have the potential to impact drug metabolism.
Collapse
Affiliation(s)
- Joseph M Collins
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for Pharmacogenomics, University of Florida, Gainesville, Florida
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for Pharmacogenomics, University of Florida, Gainesville, Florida
| |
Collapse
|
5
|
Wang F, Cao H, Xia Q, Liu Z, Wang M, Gao F, Xu D, Deng B, Diao Y, Kapranov P. Lessons from discovery of true ADAR RNA editing sites in a human cell line. BMC Biol 2023; 21:160. [PMID: 37468903 PMCID: PMC10357658 DOI: 10.1186/s12915-023-01651-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Conversion or editing of adenosine (A) into inosine (I) catalyzed by specialized cellular enzymes represents one of the most common post-transcriptional RNA modifications with emerging connection to disease. A-to-I conversions can happen at specific sites and lead to increase in proteome diversity and changes in RNA stability, splicing, and regulation. Such sites can be detected as adenine-to-guanine sequence changes by next-generation RNA sequencing which resulted in millions reported sites from multiple genome-wide surveys. Nonetheless, the lack of extensive independent validation in such endeavors, which is critical considering the relatively high error rate of next-generation sequencing, leads to lingering questions about the validity of the current compendiums of the editing sites and conclusions based on them. RESULTS Strikingly, we found that the current analytical methods suffer from very high false positive rates and that a significant fraction of sites in the public databases cannot be validated. In this work, we present potential solutions to these problems and provide a comprehensive and extensively validated list of A-to-I editing sites in a human cancer cell line. Our findings demonstrate that most of true A-to-I editing sites in a human cancer cell line are located in the non-coding transcripts, the so-called RNA 'dark matter'. On the other hand, many ADAR editing events occurring in exons of human protein-coding mRNAs, including those that can recode the transcriptome, represent false positives and need to be interpreted with caution. Nonetheless, yet undiscovered authentic ADAR sites that increase the diversity of human proteome exist and warrant further identification. CONCLUSIONS Accurate identification of human ADAR sites remains a challenging problem, particularly for the sites in exons of protein-coding mRNAs. As a result, genome-wide surveys of ADAR editome must still be accompanied by extensive Sanger validation efforts. However, given the vast number of unknown human ADAR sites, there is a need for further developments of the analytical techniques, potentially those that are based on deep learning solutions, in order to provide a quick and reliable identification of the editome in any sample.
Collapse
Affiliation(s)
- Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
| | - Qiu Xia
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ziheng Liu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ming Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Bolin Deng
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
| |
Collapse
|
6
|
de Morree A, Rando TA. Regulation of adult stem cell quiescence and its functions in the maintenance of tissue integrity. Nat Rev Mol Cell Biol 2023; 24:334-354. [PMID: 36922629 PMCID: PMC10725182 DOI: 10.1038/s41580-022-00568-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 03/18/2023]
Abstract
Adult stem cells are important for mammalian tissues, where they act as a cell reserve that supports normal tissue turnover and can mount a regenerative response following acute injuries. Quiescent stem cells are well established in certain tissues, such as skeletal muscle, brain, and bone marrow. The quiescent state is actively controlled and is essential for long-term maintenance of stem cell pools. In this Review, we discuss the importance of maintaining a functional pool of quiescent adult stem cells, including haematopoietic stem cells, skeletal muscle stem cells, neural stem cells, hair follicle stem cells, and mesenchymal stem cells such as fibro-adipogenic progenitors, to ensure tissue maintenance and repair. We discuss the molecular mechanisms that regulate the entry into, maintenance of, and exit from the quiescent state in mice. Recent studies revealed that quiescent stem cells have a discordance between RNA and protein levels, indicating the importance of post-transcriptional mechanisms, such as alternative polyadenylation, alternative splicing, and translation repression, in the control of stem cell quiescence. Understanding how these mechanisms guide stem cell function during homeostasis and regeneration has important implications for regenerative medicine.
Collapse
Affiliation(s)
- Antoine de Morree
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Thomas A Rando
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
7
|
Broni E, Striegel A, Ashley C, Sakyi PO, Peracha S, Velazquez M, Bebla K, Sodhi M, Kwofie SK, Ademokunwa A, Khan S, Miller WA. Molecular Docking and Dynamics Simulation Studies Predict Potential Anti-ADAR2 Inhibitors: Implications for the Treatment of Cancer, Neurological, Immunological and Infectious Diseases. Int J Mol Sci 2023; 24:ijms24076795. [PMID: 37047766 PMCID: PMC10095294 DOI: 10.3390/ijms24076795] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
Altered RNA editing has been linked to several neurodevelopmental disorders, including autism spectrum disorder (ASD) and intellectual disability, in addition to depression, schizophrenia, some cancers, viral infections and autoimmune disorders. The human ADAR2 is a potential therapeutic target for managing these various disorders due to its crucial role in adenosine to inosine editing. This study applied consensus scoring to rank potential ADAR2 inhibitors after performing molecular docking with AutoDock Vina and Glide (Maestro), using a library of 35,161 compounds obtained from traditional Chinese medicine. A total of 47 compounds were predicted to be good binders of the human ADAR2 and had insignificant toxicity concerns. Molecular dynamics (MD) simulations, including the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) procedure, also emphasized the binding of the shortlisted compounds. The potential compounds had plausible binding free energies ranging from −81.304 to −1068.26 kJ/mol from the MM/PBSA calculations. ZINC000085511995, a naphthoquinone had more negative binding free energy (−1068.26 kJ/mol) than inositol hexakisphosphate (IHP) [−873.873 kJ/mol], an agonist and a strong binder of ADAR2. The potential displacement of IHP by ZINC000085511995 in the IHP binding site of ADAR2 could be explored for possible deactivation of ADAR2. Bayesian-based biological activity prediction corroborates the neuropharmacological, antineoplastic and antiviral activity of the potential lead compounds. All the potential lead compounds, except ZINC000014612330 and ZINC000013462928, were predicted to be inhibitors of various deaminases. The potential lead compounds also had probability of activity (Pa) > 0.442 and probability of inactivity (Pi) < 0.116 values for treating acute neurologic disorders, except for ZINC000085996580 and ZINC000013462928. Pursuing these compounds for their anti-ADAR2 activities holds a promising future, especially against neurological disorders, some cancers and viral infections caused by RNA viruses. Molecular interaction, hydrogen bond and per-residue decomposition analyses predicted Arg400, Arg401, Lys519, Trp687, Glu689, and Lys690 as hot-spot residues in the ADAR2 IHP binding site. Most of the top compounds were observed to have naphthoquinone, indole, furanocoumarin or benzofuran moieties. Serotonin and tryptophan, which are beneficial in digestive regulation, improving sleep cycle and mood, are indole derivatives. These chemical series may have the potential to treat neurological disorders, prion diseases, some cancers, specific viral infections, metabolic disorders and eating disorders through the disruption of ADAR2 pathways. A total of nine potential lead compounds were shortlisted as plausible modulators of ADAR2.
Collapse
Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Andrew Striegel
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Chemical and Biochemistry, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Patrick O. Sakyi
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Department of Chemical Sciences, School of Sciences, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Saqib Peracha
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Miriam Velazquez
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Kristeen Bebla
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Monsheel Sodhi
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Adesanya Ademokunwa
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Cognitive and Behavioral Neuroscience, Loyola University Chicago, Chicago, IL 60660, USA
| | - Sufia Khan
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| |
Collapse
|
8
|
Qin JX, Liu X, Wang XL, Wang GY, Liang Q, Dong Y, Pang K, Hao L, Xue L, Zhao Y, Hu ZX, Li R, Lv Q, Chao L, Meng FL, Shi ZD, Han CH. Identification and analysis of microRNA editing events in recurrent bladder cancer based on RNA sequencing: MicroRNA editing level is a potential novel biomarker. Front Genet 2022; 13:984279. [PMID: 36199571 PMCID: PMC9527279 DOI: 10.3389/fgene.2022.984279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background: With the continued advancement of RNA-seq (RNA-sequencing), microRNA (miRNA) editing events have been demonstrated to play an important role in different malignancies. However, there is yet no description of the miRNA editing events in recurrent bladder cancer.Objective: To identify and compare miRNA editing events in primary and recurrent bladder cancer, as well as to investigate the potential molecular mechanism and its impact on patient prognosis.Methods: We examined the mRNA and miRNA transcriptomes of 12 recurrent bladder cancer cases and 13 primary bladder cancer cases. The differentially expressed mRNA sequences were analyzed. Furthermore, we identified the differentially expressed genes (DEGs) in recurrent bladder cancer. The Gene Ontology (GO) functional enrichment analyses on DEGs and gene set enrichment analysis were performed. The consensus molecular subtype (CMS) classification of bladder cancer was identified using the Consensus MIBC package in R (4.1.0); miRNA sequences were then further subjected to differentially expressed analysis and pathway enrichment analysis. MiRNA editing events were identified using miRge3.0. miRDB and TargetScanHuman were used to predict the downstream targets of specific differentially edited or expressed miRNAs. The expression levels of miR-154-5p and ADAR were validated by RT-qPCR. Finally, survival and co-expression studies were performed on the TCGA-BLCA cohort.Results: First, the mRNA expression levels in recurrent bladder cancer changed significantly, supporting progression via related molecular signal pathways. Second, significantly altered miRNAs in recurrent bladder cancer were identified, with miR-154-5p showing the highest level of editing in recurrent bladder cancer and may up-regulate the expression levels of downstream targets HS3ST3A1, AQP9, MYLK, and RAB23. The survival analysis results of TCGA data revealed that highly expressed HS3ST3A1 and RAB23 exhibited poor prognosis. In addition, miR-154 editing events were found to be significant to CMS classification.Conclusion: MiRNA editing in recurrent bladder cancer was detected and linked with poor patient prognosis, providing a reference for further uncovering the intricate molecular mechanism in recurrent bladder cancer. Therefore, inhibiting A-to-I editing of miRNA may be a viable target for bladder cancer treatment, allowing current treatment choices to be expanded and individualized.
Collapse
Affiliation(s)
- Jia-Xin Qin
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Xing Liu
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Xin-Lei Wang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Guang-Yue Wang
- Graduate School of Bengbu Medical College, Bengbu, China
| | - Qing Liang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yang Dong
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Kun Pang
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Lin Hao
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Liang Xue
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yan Zhao
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Zheng-Xiang Hu
- Graduate School of Jinzhou Medical College, Jinzhou, China
| | - Rui Li
- Central Laboratory, Xuzhou Central Hospital, Xuzhou, China
| | - Qian Lv
- Central Laboratory, Xuzhou Central Hospital, Xuzhou, China
| | - Liu Chao
- Department of Urology, The Suqian Affiliated Hospital of Xuzhou Medical University School, Suqian, China
| | - Fan-Lai Meng
- Department of Pathology, The Suqian Affiliated Hospital of Xuzhou Medical University School, Suqian, China
| | - Zhen-Duo Shi
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Zhen-Duo Shi, ; Cong-Hui Han,
| | - Cong-Hui Han
- Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Urology, Heilongjiang Provincial Hospital, Harbin, China
- *Correspondence: Zhen-Duo Shi, ; Cong-Hui Han,
| |
Collapse
|
9
|
Garcia-Gonzalez C, Dieterich C, Maroli G, Wiesnet M, Wietelmann A, Li X, Yuan X, Graumann J, Stellos K, Kubin T, Schneider A, Braun T. ADAR1 Prevents Autoinflammatory Processes in the Heart Mediated by IRF7. Circ Res 2022; 131:580-597. [PMID: 36000401 DOI: 10.1161/circresaha.122.320839] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND ADAR1 (adenosine deaminase acting on RNA-1)-mediated adenosine to inosine (A-to-I) RNA editing plays an essential role for distinguishing endogenous from exogenous RNAs, preventing autoinflammatory ADAR1 also regulates cellular processes by recoding specific mRNAs, thereby altering protein functions, but may also act in an editing-independent manner. The specific role of ADAR1 in cardiomyocytes and its mode of action in the heart is not fully understood. To determine the role of ADAR1 in the heart, we used different mutant mouse strains, which allows to distinguish immunogenic, editing-dependent, and editing-independent functions of ADAR1. METHODS Different Adar1-mutant mouse strains were employed for gene deletion or specific inactivation of ADAR1 enzymatic activity in cardiomyocytes, either alone or in combination with Ifih1 (interferon induced with helicase C domain 1) or Irf7 (interferon regulatory factor 7) gene inactivation. Mutant mice were investigated by immunofluorescence, Western blot, RNAseq, proteomics, and functional MRI analysis. RESULTS Inactivation of Adar1 in cardiomyocytes resulted in late-onset autoinflammatory myocarditis progressing into dilated cardiomyopathy and heart failure at 6 months of age. Adar1 depletion activated interferon signaling genes but not NFκB (nuclear factor kappa B) signaling or apoptosis and reduced cardiac hypertrophy during pressure overload via induction of Irf7. Additional inactivation of the cytosolic RNA sensor MDA5 (melanoma differentiation-associated gene 5; encoded by the Ifih1 gene) in Adar1 mutant mice prevented activation of interferon signaling gene and delayed heart failure but did not prevent lethality after 8.5 months. In contrast, compound mutants only expressing catalytically inactive ADAR1 in an Ifih1-mutant background were completely normal. Inactivation of Irf7 attenuated the phenotype of Adar1-deficient cardiomyocytes to a similar extent as Ifih1 depletion, identifying IRF7 as the main mediator of autoinflammatory responses caused by the absence of ADAR1 in cardiomyocytes. CONCLUSIONS Enzymatically active ADAR1 prevents IRF7-mediated autoinflammatory reactions in the heart triggered by endogenous nonedited RNAs. In addition to RNA editing, ADAR1 also serves editing-independent roles in the heart required for long-term cardiac function and survival.
Collapse
Affiliation(s)
- Claudia Garcia-Gonzalez
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.).,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. Del Hospital Universitario, Oviedo, Spain (C.G.-G.)
| | - Christoph Dieterich
- Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, Section of Bioinformatics and Systems Cardiology, University Hospital, Heidelberg, Germany (C.D.)
| | - Giovanni Maroli
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.)
| | - Marion Wiesnet
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.)
| | - Astrid Wietelmann
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.)
| | - Xiang Li
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.)
| | - Xuejun Yuan
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.)
| | - Johannes Graumann
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.).,German Centre for Cardiovascular Research (DZHK), Partner Sites Rhine-Main and Heidelberg/Mannheim, Bad Nauheim and Mannheim, Germany (J.G., K.S., T.B.)
| | - Konstantinos Stellos
- German Centre for Cardiovascular Research (DZHK), Partner Sites Rhine-Main and Heidelberg/Mannheim, Bad Nauheim and Mannheim, Germany (J.G., K.S., T.B.).,Department of Cardiovascular Research, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (K.S.).,Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom (K.S.)
| | - Thomas Kubin
- Department of Cardiac Surgery, Kerckhoff Heart Center, Bad Nauheim, Germany (T.K.)
| | - Andre Schneider
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.)
| | - Thomas Braun
- Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany (C.G.-G., G.M., M.W., A.W., X.L., X.Y., J.G., A.S., T.B.).,German Centre for Cardiovascular Research (DZHK), Partner Sites Rhine-Main and Heidelberg/Mannheim, Bad Nauheim and Mannheim, Germany (J.G., K.S., T.B.)
| |
Collapse
|
10
|
Flores-López BA, Ayala-Madrigal MDLL, Moreno-Ortiz JM, Peregrina-Sandoval J, Trujillo-Rojas MÁ, Venegas-Rodríguez JL, Hernández-Ramírez R, Fernández-Galindo MA, Gutiérrez-Angulo M. Molecular Profiling of Tumor Tissue in Mexican Patients with Colorectal Cancer. Curr Issues Mol Biol 2022; 44:3770-3778. [PMID: 36005154 PMCID: PMC9406459 DOI: 10.3390/cimb44080258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 12/03/2022] Open
Abstract
Colorectal cancer is a heterogeneous disease with multiple genomic changes that influence the clinical management of patients; thus, the search for new molecular targets remains necessary. The aim of this study was to identify genetic variants in tumor tissues from Mexican patients with colorectal cancer, using massive parallel sequencing. A total of 4813 genes were analyzed in tumoral DNA from colorectal cancer patients, using the TruSight One Sequencing panel. From these, 192 variants with clinical associations were found distributed in 168 different genes, of which 46 variants had not been previous reported in the literature or databases, although genes harboring those variants had already been described in colorectal cancer. Enrichment analysis of the affected genes was performed using Reactome software; pathway over-representation showed significance for disease, signal transduction, and immune system subsets in all patients, while exclusive subsets such as DNA repair, autophagy, and RNA metabolism were also found. Those characteristics, whether individual or shared, could give tumors specific capabilities for survival, aggressiveness, or response to treatment. Our results can be useful for future investigations targeting specific characteristics of tumors in colorectal cancer patients. The identification of exclusive or common pathways in colorectal cancer patients could be important for better diagnosis and personalized cancer treatment.
Collapse
Affiliation(s)
- Beatriz Armida Flores-López
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - María de la Luz Ayala-Madrigal
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - José Miguel Moreno-Ortiz
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Jorge Peregrina-Sandoval
- Departamento de Biología Celular y Molecular, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara 45200, Jalisco, Mexico
| | - Miguel Ángel Trujillo-Rojas
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - José Luis Venegas-Rodríguez
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Rosario Hernández-Ramírez
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Martha Alejandra Fernández-Galindo
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Melva Gutiérrez-Angulo
- Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Departamento de Ciencias de la Salud, Centro Universitario de los Altos, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Correspondence:
| |
Collapse
|
11
|
ADAR2 Protein Is Associated with Overall Survival in GBM Patients and Its Decrease Triggers the Anchorage-Independent Cell Growth Signature. Biomolecules 2022; 12:biom12081142. [PMID: 36009036 PMCID: PMC9405742 DOI: 10.3390/biom12081142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Epitranscriptomic mechanisms, such as A-to-I RNA editing mediated by ADAR deaminases, contribute to cancer heterogeneity and patients’ stratification. ADAR enzymes can change the sequence, structure, and expression of several RNAs, affecting cancer cell behavior. In glioblastoma, an overall decrease in ADAR2 RNA level/activity has been reported. However, no data on ADAR2 protein levels in GBM patient tissues are available; and most data are based on ADARs overexpression experiments. Methods: We performed IHC analysis on GBM tissues and correlated ADAR2 levels and patients’ overall survival. We silenced ADAR2 in GBM cells, studied cell behavior, and performed a gene expression/editing analysis. Results: GBM tissues do not all show a low/no ADAR2 level, as expected by previous studies. Although, different amounts of ADAR2 protein were observed in different patients, with a low level correlating with a poor patient outcome. Indeed, reducing the endogenous ADAR2 protein in GBM cells promotes cell proliferation and migration and changes the cell’s program to an anchorage-independent growth mode. In addition, deep-seq data and bioinformatics analysis indicated multiple RNAs are differently expressed/edited upon siADAR2. Conclusion: ADAR2 protein is an important deaminase in GBM and its amount correlates with patient prognosis.
Collapse
|
12
|
Liu J, Wang F, Zhang Y, Liu J, Zhao B. ADAR1-Mediated RNA Editing and Its Role in Cancer. Front Cell Dev Biol 2022; 10:956649. [PMID: 35898396 PMCID: PMC9309331 DOI: 10.3389/fcell.2022.956649] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
It is well known that the stability of RNA, the interaction between RNA and protein, and the correct translation of protein are significant forces that drive the transition from normal cell to malignant tumor. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that catalyzes the deamination of adenosine to inosine (A-to-I), which is one dynamic modification that in a combinatorial manner can give rise to a very diverse transcriptome. ADAR1-mediated RNA editing is essential for survival in mammals and its dysregulation results in aberrant editing of its substrates that may affect the phenotypic changes in cancer. This overediting phenomenon occurs in many cancers, such as liver, lung, breast, and esophageal cancers, and promotes tumor progression in most cases. In addition to its editing role, ADAR1 can also play an editing-independent role, although current research on this mechanism is relatively shallowly explored in tumors. In this review, we summarize the nature of ADAR1, mechanisms of ADAR1 editing-dependent and editing-independent and implications for tumorigenesis and prognosis, and pay special attention to effects of ADAR1 on cancers by regulating non-coding RNA formation and function.
Collapse
Affiliation(s)
- Jizhe Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Yindan Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Jingfeng Liu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
| |
Collapse
|
13
|
Shoaib Y, Usman B, Kang H, Jung KH. Epitranscriptomics: An Additional Regulatory Layer in Plants' Development and Stress Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:1033. [PMID: 35448761 PMCID: PMC9027318 DOI: 10.3390/plants11081033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Epitranscriptomics has added a new layer of regulatory machinery to eukaryotes, and the advancement of sequencing technology has revealed more than 170 post-transcriptional modifications in various types of RNAs, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Among these, N6-methyladenosine (m6A) and N5-methylcytidine (m5C) are the most prevalent internal mRNA modifications. These regulate various aspects of RNA metabolism, mainly mRNA degradation and translation. Recent advances have shown that regulation of RNA fate mediated by these epitranscriptomic marks has pervasive effects on a plant's development and responses to various biotic and abiotic stresses. Recently, it was demonstrated that the removal of human-FTO-mediated m6A from transcripts in transgenic rice and potatoes caused a dramatic increase in their yield, and that the m6A reader protein mediates stress responses in wheat and apple, indicating that regulation of m6A levels could be an efficient strategy for crop improvement. However, changing the overall m6A levels might have unpredictable effects; therefore, the identification of precise m6A levels at a single-base resolution is essential. In this review, we emphasize the roles of epitranscriptomic modifications in modulating molecular, physiological, and stress responses in plants, and provide an outlook on epitranscriptome engineering as a promising tool to ensure food security by editing specific m6A and m5C sites through robust genome-editing technology.
Collapse
Affiliation(s)
- Yasira Shoaib
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Babar Usman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| |
Collapse
|
14
|
Kotar A, Ma S, Keane SC. pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31. Biophys Chem 2022; 283:106763. [DOI: 10.1016/j.bpc.2022.106763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022]
|
15
|
Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
Collapse
|
16
|
Park E, Jiang Y, Hao L, Hui J, Xing Y. Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes. Genome Biol 2021; 22:77. [PMID: 33685485 PMCID: PMC7942016 DOI: 10.1186/s13059-021-02287-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND A-to-I RNA editing diversifies the transcriptome and has multiple downstream functional effects. Genetic variation contributes to RNA editing variability between individuals and has the potential to impact phenotypic variability. RESULTS We analyze matched genetic and transcriptomic data in 49 tissues across 437 individuals to identify RNA editing events that are associated with genetic variation. Using an RNA editing quantitative trait loci (edQTL) mapping approach, we identify 3117 unique RNA editing events associated with a cis genetic polymorphism. Fourteen percent of these edQTL events are also associated with genetic variation in their gene expression. A subset of these events are associated with genome-wide association study signals of complex traits or diseases. We determine that tissue-specific levels of ADAR and ADARB1 are able to explain a subset of tissue-specific edQTL events. We find that certain microRNAs are able to differentiate between the edited and unedited isoforms of their targets. Furthermore, microRNAs can generate an expression quantitative trait loci (eQTL) signal from an edQTL locus by microRNA-mediated transcript degradation in an editing-specific manner. By integrative analyses of edQTL, eQTL, and microRNA expression profiles, we computationally discover and experimentally validate edQTL-microRNA pairs for which the microRNA may generate an eQTL signal from an edQTL locus in a tissue-specific manner. CONCLUSIONS Our work suggests a mechanism in which RNA editing variability can influence the phenotypes of complex traits and diseases by altering the stability and steady-state level of critical RNA molecules.
Collapse
Affiliation(s)
- Eddie Park
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Yan Jiang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Lili Hao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| |
Collapse
|
17
|
Görücü Yilmaz S. Genome editing technologies: CRISPR, LEAPER, RESTORE, ARCUT, SATI, and RESCUE. EXCLI JOURNAL 2021; 20:19-45. [PMID: 33510590 PMCID: PMC7838830 DOI: 10.17179/excli2020-3070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022]
Abstract
Genome editing technologies include techniques used for desired genetic modifications and allow the insertion, modification or deletion of specific DNA fragments. Recent advances in genome biology offer unprecedented promise for interdisciplinary collaboration and applications in gene editing. New genome editing technologies enable specific and efficient genome modifications. The sources that inspire these modifications and already exist in the genome are DNA degradation enzymes and DNA repair pathways. Six of these recent technologies are the clustered regularly interspaced short palindromic repeats (CRISPR), leveraging endogenous ADAR for programmable editing of RNA (LEAPER), recruiting endogenous ADAR to specific transcripts for oligonucleotide-mediated RNA editing (RESTORE), chemistry-based artificial restriction DNA cutter (ARCUT), single homology arm donor mediated intron-targeting integration (SATI), RNA editing for specific C-to-U exchange (RESCUE). These technologies are widely used from various biomedical researches to clinics, agriculture, and allow you to rearrange genomic sequences, create cell lines and animal models to solve human diseases. This review emphasizes the characteristics, superiority, limitations, also whether each technology can be used in different biological systems and the potential application of these systems in the treatment of several human diseases.
Collapse
Affiliation(s)
- Senay Görücü Yilmaz
- Department of Nutrition and Dietetics, Gaziantep University, Gaziantep, Turkey 27310
| |
Collapse
|
18
|
Erdmann EA, Mahapatra A, Mukherjee P, Yang B, Hundley HA. To protect and modify double-stranded RNA - the critical roles of ADARs in development, immunity and oncogenesis. Crit Rev Biochem Mol Biol 2020; 56:54-87. [PMID: 33356612 DOI: 10.1080/10409238.2020.1856768] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) are present in all animals and function to both bind double-stranded RNA (dsRNA) and catalyze the deamination of adenosine (A) to inosine (I). As inosine is a biological mimic of guanosine, deamination by ADARs changes the genetic information in the RNA sequence and is commonly referred to as RNA editing. Millions of A-to-I editing events have been reported for metazoan transcriptomes, indicating that RNA editing is a widespread mechanism used to generate molecular and phenotypic diversity. Loss of ADARs results in lethality in mice and behavioral phenotypes in worm and fly model systems. Furthermore, alterations in RNA editing occur in over 35 human pathologies, including several neurological disorders, metabolic diseases, and cancers. In this review, a basic introduction to ADAR structure and target recognition will be provided before summarizing how ADARs affect the fate of cellular RNAs and how researchers are using this knowledge to engineer ADARs for personalized medicine. In addition, we will highlight the important roles of ADARs and RNA editing in innate immunity and cancer biology.
Collapse
Affiliation(s)
- Emily A Erdmann
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Priyanka Mukherjee
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
| | - Boyoon Yang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
| |
Collapse
|
19
|
Rajendren S, Dhakal A, Vadlamani P, Townsend J, Deffit SN, Hundley HA. Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development. Genome Res 2020; 31:27-39. [PMID: 33355311 PMCID: PMC7849389 DOI: 10.1101/gr.267575.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022]
Abstract
Adenosine (A) to inosine (I) RNA editing contributes to transcript diversity and modulates gene expression in a dynamic, cell type–specific manner. During mammalian brain development, editing of specific adenosines increases, whereas the expression of A-to-I editing enzymes remains unchanged, suggesting molecular mechanisms that mediate spatiotemporal regulation of RNA editing exist. Herein, by using a combination of biochemical and genomic approaches, we uncover a molecular mechanism that regulates RNA editing in a neural- and development-specific manner. Comparing editomes during development led to the identification of neural transcripts that were edited only in one life stage. The stage-specific editing is largely regulated by differential gene expression during neural development. Proper expression of nearly one-third of the neurodevelopmentally regulated genes is dependent on adr-2, the sole A-to-I editing enzyme in C. elegans. However, we also identified a subset of neural transcripts that are edited and expressed throughout development. Despite a neural-specific down-regulation of adr-2 during development, the majority of these sites show increased editing in adult neural cells. Biochemical data suggest that ADR-1, a deaminase-deficient member of the adenosine deaminase acting on RNA (ADAR) family, is competing with ADR-2 for binding to specific transcripts early in development. Our data suggest a model in which during neural development, ADR-2 levels overcome ADR-1 repression, resulting in increased ADR-2 binding and editing of specific transcripts. Together, our findings reveal tissue- and development-specific regulation of RNA editing and identify a molecular mechanism that regulates ADAR substrate recognition and editing efficiency.
Collapse
Affiliation(s)
- Suba Rajendren
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Alfa Dhakal
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| | - Jack Townsend
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| | - Sarah N Deffit
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| |
Collapse
|
20
|
Competing Endogenous RNA Networks as Biomarkers in Neurodegenerative Diseases. Int J Mol Sci 2020; 21:ijms21249582. [PMID: 33339180 PMCID: PMC7765627 DOI: 10.3390/ijms21249582] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
Protein aggregation is classically considered the main cause of neuronal death in neurodegenerative diseases (NDDs). However, increasing evidence suggests that alteration of RNA metabolism is a key factor in the etiopathogenesis of these complex disorders. Non-coding RNAs are the major contributor to the human transcriptome and are particularly abundant in the central nervous system, where they have been proposed to be involved in the onset and development of NDDs. Interestingly, some ncRNAs (such as lncRNAs, circRNAs and pseudogenes) share a common functionality in their ability to regulate gene expression by modulating miRNAs in a phenomenon known as the competing endogenous RNA mechanism. Moreover, ncRNAs are found in body fluids where their presence and concentration could serve as potential non-invasive biomarkers of NDDs. In this review, we summarize the ceRNA networks described in Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and spinocerebellar ataxia type 7, and discuss their potential as biomarkers of these NDDs. Although numerous studies have been carried out, further research is needed to validate these complex interactions between RNAs and the alterations in RNA editing that could provide specific ceRNET profiles for neurodegenerative disorders, paving the way to a better understanding of these diseases.
Collapse
|
21
|
Kong XY, Vik ES, Nawaz MS, Berges N, Dahl TB, Vågbø C, Suganthan R, Segers F, Holm S, Quiles-Jiménez A, Gregersen I, Fladeby C, Aukrust P, Bjørås M, Klungland A, Halvorsen B, Alseth I. Deletion of Endonuclease V suppresses chemically induced hepatocellular carcinoma. Nucleic Acids Res 2020; 48:4463-4479. [PMID: 32083667 PMCID: PMC7192598 DOI: 10.1093/nar/gkaa115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/08/2020] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Endonuclease V (EndoV) is a conserved inosine-specific ribonuclease with unknown biological function. Here, we present the first mouse model lacking EndoV, which is viable without visible abnormalities. We show that endogenous murine EndoV cleaves inosine-containing RNA in vitro, nevertheless a series of experiments fails to link an in vivo function to processing of such transcripts. As inosine levels and adenosine-to-inosine editing often are dysregulated in hepatocellular carcinoma (HCC), we chemically induced HCC in mice. All mice developed liver cancer, however, EndoV−/− tumors were significantly fewer and smaller than wild type tumors. Opposed to human HCC, adenosine deaminase mRNA expression and site-specific editing were unaltered in our model. Loss of EndoV did not affect editing levels in liver tumors, however mRNA expression of a selection of cancer related genes were reduced. Inosines are also found in certain tRNAs and tRNAs are cleaved during stress to produce signaling entities. tRNA fragmentation was dysregulated in EndoV−/− livers and apparently, inosine-independent. We speculate that the inosine-ribonuclease activity of EndoV is disabled in vivo, but RNA binding allowed to promote stabilization of transcripts or recruitment of proteins to fine-tune gene expression. The EndoV−/− tumor suppressive phenotype calls for related studies in human HCC.
Collapse
Affiliation(s)
- Xiang Yi Kong
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Erik Sebastian Vik
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Meh Sameen Nawaz
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Natalia Berges
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Tuva Børresdatter Dahl
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Cathrine Vågbø
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Rajikala Suganthan
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Filip Segers
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Ana Quiles-Jiménez
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Cathrine Fladeby
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway.,Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, NO-0424 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway.,Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University ofOslo, NO-0317 Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| |
Collapse
|
22
|
Suardi GAM, Haddad LA. FMRP ribonucleoprotein complexes and RNA homeostasis. ADVANCES IN GENETICS 2020; 105:95-136. [PMID: 32560791 DOI: 10.1016/bs.adgen.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Fragile Mental Retardation 1 gene (FMR1), at Xq27.3, encodes the fragile mental retardation protein (FMRP), and displays in its 5'-untranslated region a series of polymorphic CGG triplet repeats that may undergo dynamic mutation. Fragile X syndrome (FXS) is the leading cause of inherited intellectual disability among men, and is most frequently due to FMR1 full mutation and consequent transcription repression. FMR1 premutations may associate with at least two other clinical conditions, named fragile X-associated primary ovarian insufficiency (FXPOI) and tremor and ataxia syndrome (FXTAS). While FXPOI and FXTAS appear to be mediated by FMR1 mRNA accumulation, relative reduction of FMRP, and triplet repeat translation, FXS is due to the lack of the RNA-binding protein FMRP. Besides its function as mRNA translation repressor in neuronal and stem/progenitor cells, RNA editing roles have been assigned to FMRP. In this review, we provide a brief description of FMR1 transcribed microsatellite and associated clinical disorders, and discuss FMRP molecular roles in ribonucleoprotein complex assembly and trafficking, as well as aspects of RNA homeostasis affected in FXS cells.
Collapse
Affiliation(s)
- Gabriela Aparecida Marcondes Suardi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luciana Amaral Haddad
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| |
Collapse
|
23
|
Piazzi M, Bavelloni A, Gallo A, Blalock WL. AKT-Dependent Phosphorylation of ADAR1p110 and ADAR2 Represents a New and Important Link Between Cell Signaling and RNA Editing. DNA Cell Biol 2020; 39:343-348. [PMID: 31999481 DOI: 10.1089/dna.2020.5351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
RNA editing is a process by which nascent RNA transcripts are covalently modified, thus enhancing the complexity of the transcriptome. The most common modifications are deaminations of adenosine to inosine at sites of complex RNA secondary structure, a process that is carried out by the adenosine deaminase acting on double-strand RNA (ADAR) family of RNA editases. Although much has been learned about the ADAR family members since their discovery, very little information on their post-transcriptional regulation has been reported. Similar to most proteins, the ADAR family members are post-translationally modified at multiple sites. We recently reported that members of the AKT kinase family directly phosphorylate ADAR1p110 and ADAR2 on a conserved threonine within the catalytic domain of the protein. Phosphorylation was observed to differentially inhibit the enzymatic activity of the ADAR proteins toward known RNA substrates. The direct downstream involvement of the AKT kinases in multiple major signaling pathways associated with cell survival, growth, glucose metabolism (insulin signaling), and differentiation is well established; thus, the AKT kinases represent a link between ADAR-dependent A-to-I editing and major signal transduction pathways that are necessary for cell maintenance and development.
Collapse
Affiliation(s)
- Manuela Piazzi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza," Consiglio Nazionale delle Ricerca (IGM-CNR) Bologna, Italy.,IRCCS, Istituto Ortopedico Rizzoli, Bologna Italy
| | - Alberto Bavelloni
- Laboratory of Experimental Oncology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Dipartimento di Oncoematologia, IRCCS, Ospedale Pediatrica Bambino Gesù, Rome, Italy
| | - William L Blalock
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza," Consiglio Nazionale delle Ricerca (IGM-CNR) Bologna, Italy.,IRCCS, Istituto Ortopedico Rizzoli, Bologna Italy
| |
Collapse
|
24
|
Arribas-Hernández L, Brodersen P. Occurrence and Functions of m 6A and Other Covalent Modifications in Plant mRNA. PLANT PHYSIOLOGY 2020; 182:79-96. [PMID: 31748418 PMCID: PMC6945878 DOI: 10.1104/pp.19.01156] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/13/2019] [Indexed: 05/07/2023]
Abstract
Posttranscriptional control of gene expression is indispensable for the execution of developmental programs and environmental adaptation. Among the many cellular mechanisms that regulate mRNA fate, covalent nucleotide modification has emerged as a major way of controlling the processing, localization, stability, and translatability of mRNAs. This powerful mechanism is conserved across eukaryotes and controls the cellular events that lead to development and growth. As in other eukaryotes, N 6-methylation of adenosine is the most abundant and best studied mRNA modification in flowering plants. It is essential for embryonic and postembryonic plant development and it affects growth rate and stress responses, including susceptibility to plant RNA viruses. Although the mRNA modification field is young, the intense interest triggered by its involvement in stem cell differentiation and cancer has led to rapid advances in understanding how mRNA modifications control gene expression in mammalian systems. An equivalent effort from plant molecular biologists has been lagging behind, but recent work in Arabidopsis (Arabidopsis thaliana) and other plant species is starting to give insights into how this essential layer of posttranscriptional regulation works in plants, and both similarities and differences with other eukaryotes are emerging. In this Update, we summarize, connect, and evaluate the experimental work that supports our current knowledge of the biochemistry, molecular mechanisms, and biological functions of mRNA modifications in plants. We devote particular attention to N 6-methylation of adenosine and attempt to place the knowledge gained from plant studies within the context of a more general framework derived from studies in other eukaryotes.
Collapse
Affiliation(s)
| | - Peter Brodersen
- University of Copenhagen, Department of Biology, DK-2200 Copenhagen N, Denmark
| |
Collapse
|
25
|
Wang W, Xie Y, Chen F, Liu X, Zhong LL, Wang HQ, Li QC. LncRNA MEG3 acts a biomarker and regulates cell functions by targeting ADAR1 in colorectal cancer. World J Gastroenterol 2019; 25:3972-3984. [PMID: 31413531 PMCID: PMC6689807 DOI: 10.3748/wjg.v25.i29.3972] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/07/2019] [Accepted: 06/26/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most prevalent malignancy and has the fourth highest global cancer mortality rate. Early diagnosis and prompt medical attention can improve quality of life and the prognosis of CRC patients. Accumulating evidence reveals that long non-coding RNAs (lncRNAs) function as oncogenes or anti-oncogenes, as well as biomarkers in various cancers.
AIM To investigate the levels and molecular mechanism of the lncRNA maternally expressed gene 3 (MEG3) in CRC.
METHODS The levels of lncRNA MEG3 in CRC tissue, serum and cell line samples were explored via qRT-PCR. The relationship between MEG3 levels and clinicopathological features in CRC was investigated. The diagnostic and prognostic values of serum MEG3 levels were analyzed with ROC curves and Kaplan‑Meier survival curves, respectively.
RESULTS Significant decreased levels of MEG3 existed in CRC tissue, cell lines and serum. CRC patients with down-regulated serum MEG3 levels had larger tumor sizes, and advanced clinical stages. The sensitivity and specificity of serum MEG3 levels in CRC detection was 0.667 and 0.875, respectively. Tumor size, T stages, and serum MEG3 levels are indie factors that produce an effect on CRC patients' prognosis. Kaplan‑Meier survival curves suggested that CRC patients with high levels of MEG3 had a remarkably better overall survival rate.
CONCLUSION LncRNA MEG3 is down-regulated in CRC, and regulates cell functions by targeting adenosine deaminase’s effect on RNA 1 in CRC.
Collapse
Affiliation(s)
- Wei Wang
- College of Basic Medical Sciences, China medical University and Department of Pathology, the First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
- Teaching and Research Department of Pathology, Basic Medical College, Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Ying Xie
- Department of Synopsis of The Golden Chamber, School of Basic Medical Sciences, Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Fei Chen
- Department of Synopsis of The Golden Chamber, School of Basic Medical Sciences, Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Xu Liu
- Experiment and Training Center, Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Li-Li Zhong
- Department of Pathology, the First Clinical Medical College, Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Hai-Qiang Wang
- Department of Gastroenterology, the First Clinical Medical College, Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Qing-Chang Li
- College of Basic Medical Sciences, China medical University and Department of Pathology, the First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| |
Collapse
|
26
|
Rosani U, Bai CM, Maso L, Shapiro M, Abbadi M, Domeneghetti S, Wang CM, Cendron L, MacCarthy T, Venier P. A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks. BMC Evol Biol 2019; 19:149. [PMID: 31337330 PMCID: PMC6651903 DOI: 10.1186/s12862-019-1472-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
Background Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. Results We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets. Conclusions We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1472-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 32121, Padova, Italy. .,Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute (AWI), Wadden Sea Station, 25992, List auf Sylt, Germany.
| | - Chang-Ming Bai
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Lorenzo Maso
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Miriam Abbadi
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, Italy
| | | | - Chong-Ming Wang
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Laura Cendron
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Paola Venier
- Department of Biology, University of Padova, 32121, Padova, Italy.
| |
Collapse
|
27
|
Tassinari V, Cesarini V, Silvestris DA, Gallo A. The adaptive potential of RNA editing-mediated miRNA-retargeting in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:291-300. [PMID: 30605729 DOI: 10.1016/j.bbagrm.2018.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
A-to-I RNA editing is a post-transcriptional mechanism that converts the genomically coded Adenosine (A) into Inosine (I) at the RNA level. This type of RNA editing is the most frequent in humans and is mediated by the ADAR enzymes. RNA editing can alter the genetic code of mRNAs, but also affect the functions of noncoding RNAs such as miRNAs. Recent studies have identified thousands of microRNA editing events in different cancer types. However, the important role played by miRNA-editing in cancer has been reported for just a few microRNAs. Herein, we recapitulate the current studies on cancer-related microRNA editing and discuss their importance in tumor growth and progression. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
Collapse
Affiliation(s)
- Valentina Tassinari
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Valeriana Cesarini
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Domenico Alessandro Silvestris
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy.
| |
Collapse
|
28
|
Zavolan M, Gerber AP. Mirroring the multifaceted role of
RNA
and its partners in gene expression. FEBS Lett 2018; 592:2825-2827. [DOI: 10.1002/1873-3468.13230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - André P. Gerber
- Faculty of Health and Medical Sciences Department of Microbial Sciences School of Biosciences and Medicine University of Surrey Guildford UK
| |
Collapse
|