1
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Yin C, Zhang MM, Wang GL, Deng XY, Tu Z, Jiang SS, Gao ZD, Hao M, Chen Y, Li Y, Yang SY. Loss of ADAR1 induces ferroptosis of breast cancer cells. Cell Signal 2024; 121:111258. [PMID: 38866351 DOI: 10.1016/j.cellsig.2024.111258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024]
Abstract
Adenosine deaminases acting on RNA 1(ADAR1), an RNA editing enzyme that converts adenosine to inosine by deamination in double-stranded RNAs, plays an important role in occurrence and progression of various types of cancer. Ferroptosis has emerged as a hot topic of cancer research in recent years. We have previously reported that ADAR1 promotes breast cancer progression by regulating miR-335-5p and METTL3. However, whether ADAR1 has effects on ferroptosis in breast cancer cells is largely unknown. In this study, we knocked down ADAR1 using CRISPR-Cas9 technology or over-expressed ADAR1 protein using plasmid expressing ADAR1 in MCF-7 and MDA-MB-231 breast cancer cell lines, then detected cell viability, and levels of ROS, MDA, GSH, Fe2+, GPX4 protein and miR-335-5p. We showed that the cell proliferation was inhibited, levels of ROS, MDA, Fe2+, and miR-335-5p were increased, while GSH and GPX4 levels were decreased after loss of ADAR1, compared to the control group. The opposite effects were observed after ADAR1 overexpression in the cells. Further, we demonstrated that ADAR1-controlled miR-335-5p targeted Sp1 transcription factor of GPX4, a known ferroptosis molecular marker, leading to inhibition of ferroptosis by ADAR1 in breast cancer cells. Moreover, RNA editing activity of ADAR1 is not essential for inducing ferroptosis. Collectively, loss of ADAR1 induces ferroptosis in breast cancer cells by regulating miR-335-5p/Sp1/GPX4 pathway. The findings may provide insights into the mechanism by which ADAR1 promotes breast cancer progression via inhibiting ferroptosis.
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Affiliation(s)
- Chuan Yin
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Meng-Meng Zhang
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Guo-Liang Wang
- Department of General Surgery, Union Hospital of Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiao-Yan Deng
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zeng Tu
- Department of Pathogen Biology, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Shan-Shan Jiang
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zheng-Dan Gao
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Meng Hao
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yong Chen
- Department of Radiology and Intervention, General Hospital of Ningxia Medical University, Yinchuan 750004, China.
| | - Yi Li
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China.
| | - Sheng-Yong Yang
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China.
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2
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Eliad B, Schneider N, Ben-Naim Zgayer O, Amichan Y, Glaser F, Erdmann EA, Rajendren S, Hundley HA, Lamm AT. ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection. Nucleic Acids Res 2024:gkae641. [PMID: 39036970 DOI: 10.1093/nar/gkae641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/05/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a prevalent and conserved RNA modification. While A-to-I RNA editing is essential in mammals, in Caenorhabditis elegans, it is not, making them invaluable for RNA editing research. In C. elegans, ADR-2 is the sole catalytic A-to-I editing enzyme, and ADR-1 is an RNA editing regulator. ADAR localization is well-studied in humans but not well-established in C. elegans. In this study, we examine the cellular and tissue-specific localization of ADR-2. We show that while ADR-2 is present in most cells in the embryo, at later developmental stages, its expression is both tissue- and cell-type-specific. Additionally, both ADARs are mainly in the nucleus. ADR-2 is adjacent to the chromosomes during the cell cycle. We show that the nuclear localization of endogenous ADR-2 depends on ADBP-1, not ADR-1. In adbp-1 mutant worms, ADR-2 is mislocalized, while ADR-1 is not, leading to decreased editing levels and de-novo editing, mostly in exons, suggesting that ADR-2 is also functional in the cytoplasm. Besides, mutated ADBP-1 affects gene expression. Furthermore, we show that ADR-2 targets adenosines with different surrounding nucleotides in exons and introns. Our findings indicate that ADR-2 cellular localization is highly regulated and affects its function.
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Affiliation(s)
- Berta Eliad
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Noa Schneider
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Orna Ben-Naim Zgayer
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Yarden Amichan
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Fabian Glaser
- Technion Center for Structural Biology, Technion Human Health Initiative, Technion, Haifa 32000, Israel
| | - Emily A Erdmann
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Suba Rajendren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ayelet T Lamm
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
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3
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Huang WC, Hsu CH, Albu TV, Yang CN. Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study. J Comput Aided Mol Des 2024; 38:25. [PMID: 39014124 DOI: 10.1007/s10822-024-00565-1] [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: 05/02/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024]
Abstract
Adenosine deaminases acting on RNA (ADARs) are pivotal RNA-editing enzymes responsible for converting adenosine to inosine within double-stranded RNA (dsRNA). Dysregulation of ADAR1 editing activity, often arising from genetic mutations, has been linked to elevated interferon levels and the onset of autoinflammatory diseases. However, understanding the molecular underpinnings of this dysregulation is impeded by the lack of an experimentally determined structure for the ADAR1 deaminase domain. In this computational study, we utilized homology modeling and the AlphaFold2 to construct structural models of the ADAR1 deaminase domain in wild-type and two pathogenic variants, R892H and Y1112F, to decipher the structural impact on the reduced deaminase activity. Our findings illuminate the critical role of structural complementarity between the ADAR1 deaminase domain and dsRNA in enzyme-substrate recognition. That is, the relative position of E1008 and K1120 must be maintained so that they can insert into the minor and major grooves of the substrate dsRNA, respectively, facilitating the flipping-out of adenosine to be accommodated within a cavity surrounding E912. Both amino acid replacements studied, R892H at the orthosteric site and Y1112F at the allosteric site, alter K1120 position and ultimately hinder substrate RNA binding.
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Affiliation(s)
- Wen-Chieh Huang
- Institute of Precision Medicine, National Sun Yat-sen University, No. 70 Lien-Hai Road, Kaohsiung, 80424, Taiwan
| | - Chia-Hung Hsu
- Department of Internal Medicine, Zuoying Armed Forces General Hospital, Kaohsiung, Taiwan
| | - Titus V Albu
- Department of Chemistry and Physics, University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Chia-Ning Yang
- Institute of Precision Medicine, National Sun Yat-sen University, No. 70 Lien-Hai Road, Kaohsiung, 80424, Taiwan.
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4
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Lama-Diaz T, Blanco MG. Alternative translation initiation by ribosomal leaky scanning produces multiple isoforms of the Pif1 helicase. Nucleic Acids Res 2024; 52:6928-6944. [PMID: 38783074 PMCID: PMC11229318 DOI: 10.1093/nar/gkae400] [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: 11/13/2023] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
In budding yeast, the integrity of both the nuclear and mitochondrial genomes relies on dual-targeted isoforms of the conserved Pif1 helicase, generated by alternative translation initiation (ATI) of PIF1 mRNA from two consecutive AUG codons flanking a mitochondrial targeting signal. Here, we demonstrate that ribosomal leaky scanning is the specific ATI mechanism that produces not only these, but also novel, previously uncharacterized Pif1 isoforms. Both in-frame, downstream AUGs as well as near-cognate start codons contribute to the generation of these alternative isoforms. This has crucial implications for the rational design of genuine separation-of-function alleles and provides an explanation for the suboptimal behaviour of the widely employed mitochondrial- (pif1-m1) and nuclear-deficient (pif1-m2) alleles, with mutations in the first or second AUG codon, respectively. We have taken advantage of this refined model to develop improved versions of these alleles, which will serve as valuable tools to elucidate novel functions of this helicase and to disambiguate previously described genetic interactions of PIF1 in the context of nuclear and mitochondrial genome stability.
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Affiliation(s)
- Tomas Lama-Diaz
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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5
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Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
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Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
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6
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Weidle UH, Nopora A. CircRNAs in Pancreatic Cancer: New Tools for Target Identification and Therapeutic Intervention. Cancer Genomics Proteomics 2024; 21:327-349. [PMID: 38944427 PMCID: PMC11215428 DOI: 10.21873/cgp.20451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/01/2024] Open
Abstract
We have reviewed the literature for circular RNAs (circRNAs) with efficacy in preclinical pancreatic-cancer related in vivo models. The identified circRNAs target chemoresistance mechanisms (n=5), secreted proteins and transmembrane receptors (n=15), transcription factors (n=9), components of the signaling- (n=11), ubiquitination- (n=2), autophagy-system (n=2), and others (n=9). In addition to identifying targets for therapeutic intervention, circRNAs are potential new entities for treatment of pancreatic cancer. Up-regulated circRNAs can be inhibited by antisense oligonucleotides (ASO), small interfering RNAs (siRNAs), short hairpin RNAs (shRNAs) or clustered regularly interspaced short-palindromic repeats-CRISPR associated protein (CRISPR-CAS)-based intervention. The function of down-regulated circRNAs can be reconstituted by replacement therapy using plasmids or virus-based vector systems. Target validation experiments and the development of improved delivery systems for corresponding agents were examined.
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Affiliation(s)
- Ulrich H Weidle
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | - Adam Nopora
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
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7
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Chen H, Li T, Gao R, Cheng M, Zhang Q, Liu X, Chen M, Liao X, Qin L. RNA editing landscape of adipose tissue in polycystic ovary syndrome provides insight into the obesity-related immune responses. Front Endocrinol (Lausanne) 2024; 15:1379293. [PMID: 38978626 PMCID: PMC11229675 DOI: 10.3389/fendo.2024.1379293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is the most common reproductive-endocrine disorder with wide-ranging metabolic implications, including obesity. RNA editing, a post-transcriptional modification, can fine-tune protein function and introduce heterogeneity. However, the role of RNA editing and its impact on adipose tissue function in PCOS remain poorly understood. Methods This study aimed to comprehensively analyze RNA-editing events in abdominal and subcutaneous adipose tissue of PCOS patients and healthy controls using high-throughput whole-genome sequencing (WGS) and RNA sequencing. Results Our results revealed that PCOS patients exhibited more RNA-editing sites, with adenosine-to-inosine (A-to-I) editing being prevalent. The expression of ADAR genes, responsible for A-to-I editing, was also higher in PCOS. Aberrant RNA-editing sites in PCOS adipose tissue was enriched in immune responses, and interleukin-12 biosynthetic process. Tumor necrosis factor (TNF) signaling, nuclear factor kappa B (NF-κB) signaling, Notch signaling, terminal uridylyl transferase 4 (TUT4), hook microtubule tethering protein 3 (HOOK3), and forkhead box O1 (FOXO1) were identified to be of significant differences. Differentially expressed genes (DEGs) in PCOS adipose tissue were enriched in immune responses compared with controls, and the DEGs between subcutaneous and abdominal adipose tissue were also enriched in immune responses suggesting the important role of subcutaneous adipose tissue. Furthermore, we identified the correlations between RNA editing levels and RNA expression levels of specific genes, such as ataxia-telangiectasia mutated (ATM) and mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) in inflammation pathways and ATM, TUT4, and YTH N6-methyladenosine RNA-binding protein C2 (YTHDC2) in oocyte development pathway. Conclusions These findings suggest that RNA-editing dysregulation in PCOS adipose tissue may contribute to inflammatory dysregulations. Understanding the interplay between RNA editing and adipose tissue function may unveil potential therapeutic targets for PCOS management. However, further research and validation are required to fully elucidate the molecular mechanisms underlying these associations.
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Affiliation(s)
- Hanxiao Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Tongtong Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Department of Physiology School of Basic Medical Sciences, Cheeloo College of Medicine Shandong University, Jinan, Shandong, China
| | - Rui Gao
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- The Reproductive Medical Center, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Meng Cheng
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qiong Zhang
- Department of Obstetrics and Gynecology, Sichuan Province Ziyang Maternal and Child Health Care Hospital, Ziyang, China
| | - Xiumei Liu
- Department of Obstetrics and Gynecology, Sichuan Province Ziyang Maternal and Child Health Care Hospital, Ziyang, China
| | - Mingli Chen
- Department of Obstetrics and Gynecology, Sichuan Province Ziyang Maternal and Child Health Care Hospital, Ziyang, China
| | - Xin Liao
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Operation Room, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lang Qin
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- The Reproductive Medical Center, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
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8
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Eliad B, Schneider N, Zgayer OBN, Amichan Y, Glaser F, Erdmann EA, Rajendren S, Hundley HA, Lamm AT. ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.14.540679. [PMID: 38895382 PMCID: PMC11185548 DOI: 10.1101/2023.05.14.540679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a prevalent and conserved RNA modification. While A-to-I RNA editing is essential in mammals, in Caenorhabditis elegans , it is not, making them invaluable for RNA editing research. In C. elegans , ADR-2 is the sole catalytic A-to-I editing enzyme, and ADR-1 is an RNA editing regulator. ADAR localization is well-studied in humans but not well-established in C. elegans . In this study, we examine the cellular and tissue-specific localization of ADR-2. We show that while ADR-2 is present in most cells in the embryo, at later developmental stages, its expression is both tissue- and cell-type-specific. Additionally, both ADARs are mainly in the nucleus. ADR-2 is adjacent to the chromosomes during the cell cycle. We show that the nuclear localization of endogenous ADR-2 depends on ADBP-1, not ADR-1. In adbp-1 mutant worms, ADR-2 is mislocalized, while ADR-1 is not, leading to decreased editing levels and de-novo editing, mostly in exons, suggesting that ADR-2 is also functional in the cytoplasm. Besides, mutated ADBP-1 affects gene expression. Furthermore, we show that ADR-2 targets adenosines with different surrounding nucleotides in exons and introns. Our findings indicate that ADR-2 cellular localization is highly regulated and affects its function.
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9
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Wernaart D, Fumagalli A, Agami R. Molecular mechanisms of non-genetic aberrant peptide production in cancer. Oncogene 2024; 43:2053-2062. [PMID: 38802646 DOI: 10.1038/s41388-024-03069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024]
Abstract
The cancer peptidome has long been known to be altered by genetic mutations. However, more recently, non-genetic polypeptide mutations have also been related to cancer cells. These non-genetic mutations occur post-t30ranscriptionally, leading to the modification of the peptide primary structure, while the corresponding genes remain unchanged. Three main processes participate in the production of these aberrant proteins: mRNA alternative splicing, mRNA editing, and mRNA aberrant translation. In this review, we summarize the molecular mechanisms underlying these processes and the recent findings on the functions of the aberrant proteins, as well as their exploitability as new therapeutic targets due to their specific enrichment in cancer cells. These non-genetic aberrant polypeptides represent a source of novel cancer cell targets independent from their level of mutational burden, still to be exhaustively explored.
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Affiliation(s)
- Demi Wernaart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Amos Fumagalli
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Erasmus MC, Department of Genetics, Rotterdam University, Rotterdam, The Netherlands.
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10
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Yang M, Jiang J, Ren R, Gao N, He J, Zhang Y. Role of ADAR1 on Proliferation and Differentiation in Porcine Preadipocytes. Animals (Basel) 2024; 14:1201. [PMID: 38672349 PMCID: PMC11047480 DOI: 10.3390/ani14081201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/30/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Recent research has identified ADAR1 as a participant in the regulation of lipid accumulation in mice. However, there are no reports on the roles of ADAR1 in proliferation, apoptosis and differentiation of porcine preadipocytes. In this study, we investigated the role of ADAR1 in differentiation, proliferation and apoptosis of porcine preadipocytes using CCK-8, EdU staining, cell cycle detection, RT-qPCR, Western blot, a triglyceride assay and Oil Red O staining. The over-expression of ADAR1 significantly promoted proliferation but inhibited the differentiation and apoptosis of porcine preadipocytes. The inhibition of ADAR1 had the opposite effect on the proliferation, differentiation and apoptosis of porcine preadipocytes with over-expressed ADAR1. Then, the regulation mechanisms of ADAR1 on preadipocyte proliferation were identified using RNA-seq, and 197 DEGs in response to ADAR1 knockdown were identified. The MAPK signaling pathway is significantly enriched, indicating its importance in mediating fat accumulation regulated by ADAR1. The study's findings will aid in uncovering the mechanisms that regulate fat accumulation through ADAR1.
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Affiliation(s)
- Menghuan Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Ruimin Ren
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
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11
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Mendoza HG, Beal PA. Structural and functional effects of inosine modification in mRNA. RNA (NEW YORK, N.Y.) 2024; 30:512-520. [PMID: 38531652 PMCID: PMC11019749 DOI: 10.1261/rna.079977.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Inosine (I), resulting from the deamination of adenosine (A), is a prominent modification in the human transcriptome. The enzymes responsible for the conversion of adenosine to inosine in human mRNAs are the ADARs (adenosine deaminases acting on RNA). Inosine modification introduces a layer of complexity to mRNA processing and function, as it can impact various aspects of RNA biology, including mRNA stability, splicing, translation, and protein binding. The relevance of this process is emphasized in the growing number of human disorders associated with dysregulated A-to-I editing pathways. Here, we describe the impact of the A-to-I conversion on the structure and stability of duplex RNA and on the consequences of this modification at different locations in mRNAs. Furthermore, we highlight specific open questions regarding the interplay between inosine formation in duplex RNA and the innate immune response.
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Affiliation(s)
- Herra G Mendoza
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, California 95616, USA
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Wang Z, Zhang D, Qiu X, Inuzuka H, Xiong Y, Liu J, Chen L, Chen H, Xie L, Kaniskan HÜ, Chen X, Jin J, Wei W. Structurally Specific Z-DNA Proteolysis Targeting Chimera Enables Targeted Degradation of Adenosine Deaminase Acting on RNA 1. J Am Chem Soc 2024; 146:7584-7593. [PMID: 38469801 PMCID: PMC10988290 DOI: 10.1021/jacs.3c13646] [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] [Indexed: 03/13/2024]
Abstract
Given the prevalent advancements in DNA- and RNA-based PROTACs, there remains a significant need for the exploration and expansion of more specific DNA-based tools, thus broadening the scope and repertoire of DNA-based PROTACs. Unlike conventional A- or B-form DNA, Z-form DNA is a configuration that exclusively manifests itself under specific stress conditions and with specific target sequences, which can be recognized by specific reader proteins, such as ADAR1 or ZBP1, to exert downstream biological functions. The core of our innovation lies in the strategic engagement of Z-form DNA with ADAR1 and its degradation is achieved by leveraging a VHL ligand conjugated to Z-form DNA to recruit the E3 ligase. This ingenious construct engendered a series of Z-PROTACs, which we utilized to selectively degrade the Z-DNA-binding protein ADAR1, a molecule that is frequently overexpressed in cancer cells. This meticulously orchestrated approach triggers a cascade of PANoptotic events, notably encompassing apoptosis and necroptosis, by mitigating the blocking effect of ADAR1 on ZBP1, particularly in cancer cells compared with normal cells. Moreover, the Z-PROTAC design exhibits a pronounced predilection for ADAR1, as opposed to other Z-DNA readers, such as ZBP1. As such, Z-PROTAC likely elicits a positive immunological response, subsequently leading to a synergistic augmentation of cancer cell death. In summary, the Z-DNA-based PROTAC (Z-PROTAC) approach introduces a modality generated by the conformational change from B- to Z-form DNA, which harnesses the structural specificity intrinsic to potentiate a selective degradation strategy. This methodology is an inspiring conduit for the advancement of PROTAC-based therapeutic modalities, underscoring its potential for selectivity within the therapeutic landscape of PROTACs to target undruggable proteins.
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Affiliation(s)
- Zhen Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Dingpeng Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Xing Qiu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Li Chen
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - He Chen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ling Xie
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 United States
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xian Chen
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
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Zhang D, Zhu L, Gao Y, Wang Y, Li P. RNA editing enzymes: structure, biological functions and applications. Cell Biosci 2024; 14:34. [PMID: 38493171 PMCID: PMC10944622 DOI: 10.1186/s13578-024-01216-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
With the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ubiquitous modification in mammalian transcriptomes and is an important co/posttranscriptional modification that plays a crucial role in various cellular processes. There are two main types of RNA editing events: adenosine to inosine (A-to-I) editing, catalyzed by ADARs on double-stranded RNA or ADATs on tRNA, and cytosine to uridine (C-to-U) editing catalyzed by APOBECs. This article provides an overview of the structure, function, and applications of RNA editing enzymes. We discuss the structural characteristics of three RNA editing enzyme families and their catalytic mechanisms in RNA editing. We also explain the biological role of RNA editing, particularly in innate immunity, cancer biogenesis, and antiviral activity. Additionally, this article describes RNA editing tools for manipulating RNA to correct disease-causing mutations, as well as the potential applications of RNA editing enzymes in the field of biotechnology and therapy.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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14
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Li W, Li X, Gao Y, Xiong C, Tang Z. Emerging roles of RNA binding proteins in intervertebral disc degeneration and osteoarthritis. Orthop Surg 2023; 15:3015-3025. [PMID: 37803912 PMCID: PMC10694020 DOI: 10.1111/os.13851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 10/08/2023] Open
Abstract
The etiology of intervertebral disc degeneration (IDD) and osteoarthritis (OA) is complex and multifactorial. Both predisposing genes and environmental factors are involved in the pathogenesis of IDD and OA. Moreover, epigenetic modifications affect the development of IDD and OA. Dysregulated phenotypes of nucleus pulposus (NP) cells and OA chondrocytes, including apoptosis, extracellular matrix disruption, inflammation, and angiogenesis, are involved at all developmental stages of IDD and OA. RNA binding proteins (RBPs) have recently been recognized as essential post-transcriptional regulators of gene expression. RBPs are implicated in many cellular processes, such as proliferation, differentiation, and apoptosis. Recently, several RBPs have been reported to be associated with the pathogenesis of IDD and OA. This review briefly summarizes the current knowledge on the RNA-regulatory networks controlled by RBPs and their potential roles in the pathogenesis of IDD and OA. These initial findings support the idea that specific modulation of RBPs represents a promising approach for managing IDD and OA.
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Affiliation(s)
- Wen Li
- Department of EmergencyGeneral Hospital of Central Theater Command of PLAWuhanChina
| | - Xing‐Hua Li
- Department of EmergencyGeneral Hospital of Central Theater Command of PLAWuhanChina
| | - Yang Gao
- Department of OrthopaedicGeneral Hospital of Central Theater Command of PLAWuhanChina
| | - Cheng‐Jie Xiong
- Department of OrthopaedicGeneral Hospital of Central Theater Command of PLAWuhanChina
| | - Zhong‐Zhi Tang
- Department of EmergencyGeneral Hospital of Central Theater Command of PLAWuhanChina
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15
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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.
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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
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Wang H, Yang L, Liu R, He H, Zhang M, Xu Y. ADAR1 affects gastric cancer cell metastasis and reverses cisplatin resistance through AZIN1. Anticancer Drugs 2023; 34:1132-1145. [PMID: 37104086 PMCID: PMC10569681 DOI: 10.1097/cad.0000000000001516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/30/2022] [Indexed: 04/28/2023]
Abstract
Adenosine deaminases acting on RNA1 (ADAR1) are involved in the occurrence and development of cancers. Although the role of ADAR1 in gastric cancer metastasis has been reported, the role of ADAR1 in the mechanism of cisplatin resistance in gastric cancer is not clear. In this study, human gastric cancer tissue specimens were used to construct cisplatin-resistant gastric cancer cells; the results indicated that the mechanism underlying the inhibition of gastric cancer metastasis and reversal of cisplatin-resistant gastric cancer by ADAR1 inhibits gastric cancer occurs through the antizyme inhibitor 1 (AZIN1) pathway. We assessed ADAR1 and AZIN1 expression in the tissues of patients with low to moderately differentiated gastric cancer. Gastric cancer cells (human gastric adenocarcinoma cell line [AGS] and HGC-27 cells) and gastric cancer cisplatin-resistant cells (AGS CDDP and HGC-27 CDDP ) were selected, and the protein expression of ADAR1 and AZIN1 was detected using immunocytochemistry and immunocytofluorescence. The effects of ADAR1 small interfering RNA (siRNA) on the invasion, migration and proliferation of cisplatin-resistant gastric cancer cells were investigated. Western blot assays were used to assess the protein expression levels of ADAR1, AZIN1 and epithelial-mesenchymal transition (EMT)-related markers. In-vivo experiments, a subcutaneous tumor formation model of nude mice was established, and the effects of ADAR1 on tumor growth and AZIN1 expression level were detected by hematoxylin and eosin, immunohistochemistry and western blot. The expression of ADAR1 and AZIN1 in human gastric cancer tissue was significantly higher than that in paracancerous tissues. The colocalization of ADAR1, AZIN1 and E-cadherin expression in immunofluorescence assays indicated a significant correlation between the three. In in-vitro experiments, ADAR1 knockout not only reduced the invasion and migration ability of AGS and HGC-27 cells but also reduced that of cisplatin-resistant gastric cancer cells. ADAR1 siRNA inhibited the proliferation and decreased the colony number of cisplatin-resistant gastric cancer cells. ADAR1 siRNA decreased the expression of AZIN1 and EMT-related marker proteins (vimentin, N-cadherin, β-catenin, MMP9, MMP2 and TWIST). The effect of ADAR1 siRNA combined with AZIN1 siRNA was more significant. In-vivo, the knockdown of ADAR1 significantly inhibited tumor growth and AZIN1 expression. ADAR1 and AZIN1 are antimetastatic targets of gastric cancer, and AZIN1 is a downstream regulatory target of ADAR1. ADAR1 knockout can inhibit the metastasis of gastric cancer cells and reverse the cisplatin resistance of gastric cancer cells by downregulating the expression of AZIN1, potentially resulting in increased treatment efficacy.
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Affiliation(s)
- Honghong Wang
- Department of Pathology, People’s Hospital of Ningxia Hui Autonomous Region
| | - Lina Yang
- Department of Pathology, People’s Hospital of Ningxia Hui Autonomous Region
| | - Rui Liu
- Department of Pathology, People’s Hospital of Ningxia Hui Autonomous Region
| | - Haiyan He
- Department of Pathology, People’s Hospital of Ningxia Hui Autonomous Region
| | - Miao Zhang
- Department of Pathology, People’s Hospital of Ningxia Hui Autonomous Region
| | - Yuanyi Xu
- Department of Pathology, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China
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17
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Sun H, Li K, Liu C, Yi C. Regulation and functions of non-m 6A mRNA modifications. Nat Rev Mol Cell Biol 2023; 24:714-731. [PMID: 37369853 DOI: 10.1038/s41580-023-00622-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Nucleobase modifications are prevalent in eukaryotic mRNA and their discovery has resulted in the emergence of epitranscriptomics as a research field. The most abundant internal (non-cap) mRNA modification is N6-methyladenosine (m6A), the study of which has revolutionized our understanding of post-transcriptional gene regulation. In addition, numerous other mRNA modifications are gaining great attention because of their major roles in RNA metabolism, immunity, development and disease. In this Review, we focus on the regulation and function of non-m6A modifications in eukaryotic mRNA, including pseudouridine (Ψ), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), inosine, 5-methylcytidine (m5C), N4-acetylcytidine (ac4C), 2'-O-methylated nucleotide (Nm) and internal N7-methylguanosine (m7G). We highlight their regulation, distribution, stoichiometry and known roles in mRNA metabolism, such as mRNA stability, translation, splicing and export. We also discuss their biological consequences in physiological and pathological processes. In addition, we cover research techniques to further study the non-m6A mRNA modifications and discuss their potential future applications.
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Affiliation(s)
- Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Kai Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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18
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Ivanišević V, Žilić L, Čunko M, Fadiga H, Munitić I, Jurak I. RNA Editing-Dependent and -Independent Roles of Adenosine Deaminases Acting on RNA Proteins in Herpesvirus Infection-Hints on Another Layer of Complexity. Viruses 2023; 15:2007. [PMID: 37896783 PMCID: PMC10611208 DOI: 10.3390/v15102007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The Adenosine Deaminases Acting on RNA (ADAR) catalyze the posttranscriptional deamination of adenosine residues to inosine in double-stranded RNAs (dsRNAs, A-to-I editing), preventing the overactivation of dsRNA sensor molecules and interferons. RNA editing is the cornerstone of innate immunity that distinguishes between self and non-self (virus), and it is essential for normal regulation of cellular homeostasis. Although much is already known about the role of ADAR proteins in RNA virus infection, the role of ADAR proteins in herpesvirus infection remains largely unexplored. In this review, we provide several lines of evidence from studies of different herpesviruses for another level of complexity in regulating the already intricate biphasic life cycle of herpesviruses.
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Affiliation(s)
| | | | | | | | | | - Igor Jurak
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia (L.Ž.)
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19
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Mendoza HG, Beal PA. Chemical Modifications in RNA: Elucidating the Chemistry of dsRNA-Specific Adenosine Deaminases (ADARs). Acc Chem Res 2023; 56:2489-2499. [PMID: 37665999 PMCID: PMC10826463 DOI: 10.1021/acs.accounts.3c00390] [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] [Indexed: 09/06/2023]
Abstract
The term RNA editing refers to any structural change in an RNA molecule (e.g. insertion, deletion, or base modification) that changes its coding properties and is not a result of splicing. An important class of enzymes involved in RNA editing is the ADAR family (adenosine deaminases acting on RNA), which facilitate the deamination of adenosine (A) to inosine (I) in double-stranded RNA (dsRNA). Inosines are decoded as guanosines (G) in most cellular processes; hence, A-to-I editing can be considered an A-to-G substitution. Among the RNA editing enzymes, ADARs are of particular interest because a large portion of RNA editing events are due to A-to-I editing by the two catalytically active human ADARs (ADAR1 and ADAR2). ADARs have diverse roles in RNA processing, gene expression regulation, and innate immunity; and mutations in the ADAR genes and dysregulated ADAR activity have been associated with cancer, autoimmune diseases, and neurological disorders. A-to-I editing is also currently being explored for correcting disease-causing mutations in the RNA, where therapeutic guide oligonucleotides complementary to the target transcript are used to form a dsRNA substrate and site-specifically direct ADAR editing. Knowledge of the mechanism of ADAR-catalyzed reaction and the origin of its substrate selectivity will allow understanding of ADAR’s role in disease biology and expedite the process of developing ADAR-targeted therapeutics. Chemically modified oligonucleotides provide a versatile platform for modulating the activity and interrogating the structure, function, and selectivity of nucleic acid binding or modifying proteins. In this account, we provide an overview of oligonucleotide modifications that have allowed us to gain deeper understanding of ADAR’s molecular mechanisms, which we utilize in the rational design and optimization of ADAR activity modulators. First, we describe the use of the nucleoside analog 8-azanebularine (8-azaN) to generate high-affinity ADAR-RNA complexes for biochemical and biophysical studies with ADARs, with particular emphasis on X-ray crystallography. We then discuss key observations derived from the crystal structures of ADAR bound to 8-azaN-modified RNA duplexes and describe how these findings provided insight into ADAR editing optimization by introducing nucleoside modifications at various positions in synthetic guide strands. We also present the informed design of 8-azaN-modified RNA duplexes that selectively bind and inhibit ADAR1 but not the closely-related ADAR2 enzyme. Finally, we conclude with some open questions on ADAR structure and substrate recognition and share our current endeavors in the development of ADAR guide oligonucleotides and inhibitors.
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Affiliation(s)
- Herra G. Mendoza
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, CA 95616 USA
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20
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Datta R, Adamska JZ, Bhate A, Li JB. A-to-I RNA editing by ADAR and its therapeutic applications: From viral infections to cancer immunotherapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1817. [PMID: 37718249 PMCID: PMC10947335 DOI: 10.1002/wrna.1817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
ADAR deaminases catalyze adenosine-to-inosine (A-to-I) editing on double-stranded RNA (dsRNA) substrates that regulate an umbrella of biological processes. One of the two catalytically active ADAR enzymes, ADAR1, plays a major role in innate immune responses by suppression of RNA sensing pathways which are orchestrated through the ADAR1-dsRNA-MDA5 axis. Unedited immunogenic dsRNA substrates are potent ligands for the cellular sensor MDA5. Upon activation, MDA5 leads to the induction of interferons and expression of hundreds of interferon-stimulated genes with potent antiviral activity. In this way, ADAR1 acts as a gatekeeper of the RNA sensing pathway by striking a fine balance between innate antiviral responses and prevention of autoimmunity. Reduced editing of immunogenic dsRNA by ADAR1 is strongly linked to the development of common autoimmune and inflammatory diseases. In viral infections, ADAR1 exhibits both antiviral and proviral effects. This is modulated by both editing-dependent and editing-independent functions, such as PKR antagonism. Several A-to-I RNA editing events have been identified in viruses, including in the insidious viral pathogen, SARS-CoV-2 which regulates viral fitness and infectivity, and could play a role in shaping viral evolution. Furthermore, ADAR1 is an attractive target for immuno-oncology therapy. Overexpression of ADAR1 and increased dsRNA editing have been observed in several human cancers. Silencing ADAR1, especially in cancers that are refractory to immune checkpoint inhibitors, is a promising therapeutic strategy for cancer immunotherapy in conjunction with epigenetic therapy. The mechanistic understanding of dsRNA editing by ADAR1 and dsRNA sensing by MDA5 and PKR holds great potential for therapeutic applications. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Rohini Datta
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia Z Adamska
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amruta Bhate
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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21
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Zhong Y, Zhong X, Qiao L, Wu H, Liu C, Zhang T. Zα domain proteins mediate the immune response. Front Immunol 2023; 14:1241694. [PMID: 37771585 PMCID: PMC10523160 DOI: 10.3389/fimmu.2023.1241694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023] Open
Abstract
The Zα domain has a compact α/β architecture containing a three-helix bundle flanked on one side by a twisted antiparallel β sheet. This domain displays a specific affinity for double-stranded nucleic acids that adopt a left-handed helical conformation. Currently, only three Zα-domain proteins have been identified in eukaryotes, specifically ADAR1, ZBP1, and PKZ. ADAR1 is a double-stranded RNA (dsRNA) binding protein that catalyzes the conversion of adenosine residues to inosine, resulting in changes in RNA structure, function, and expression. In addition to its editing function, ADAR1 has been shown to play a role in antiviral defense, gene regulation, and cellular differentiation. Dysregulation of ADAR1 expression and activity has been associated with various disease states, including cancer, autoimmune disorders, and neurological disorders. As a sensing molecule, ZBP1 exhibits the ability to recognize nucleic acids with a left-handed conformation. ZBP1 harbors a RIP homotypic interaction motif (RHIM), composed of a highly charged surface region and a leucine-rich hydrophobic core, enabling the formation of homotypic interactions between proteins with similar structure. Upon activation, ZBP1 initiates a downstream signaling cascade leading to programmed cell death, a process mediated by RIPK3 via the RHIM motif. PKZ was identified in fish, and contains two Zα domains at the N-terminus. PKZ is essential for normal growth and development and may contribute to the regulation of immune system function in fish. Interestingly, some pathogenic microorganisms also encode Zα domain proteins, such as, Vaccinia virus and Cyprinid Herpesvirus. Zα domain proteins derived from pathogenic microorganisms have been demonstrated to be pivotal contributors in impeding the host immune response and promoting virus replication and spread. This review focuses on the mammalian Zα domain proteins: ADAR1 and ZBP1, and thoroughly elucidates their functions in the immune response.
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Affiliation(s)
- Yuhan Zhong
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao Zhong
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Liangjun Qiao
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Hong Wu
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Chang Liu
- Division of Liver, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Zhang
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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22
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Garland KM, Kwiatkowski AJ, Tossberg JT, Crooke PS, Aune TM, Wilson JT. Nanoparticle Delivery of Immunostimulatory Alu RNA for Cancer Immunotherapy. CANCER RESEARCH COMMUNICATIONS 2023; 3:1800-1809. [PMID: 37691856 PMCID: PMC10487107 DOI: 10.1158/2767-9764.crc-22-0354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
It was recently found that patients with relapsing remitting multiple sclerosis exhibit widespread loss of adenosine-to-inosine (A-to-I) RNA editing, which contributes to the accumulation of immunostimulatory double-stranded Alu RNA in circulating leukocytes and an attendant increase in levels of proinflammatory cytokines (e.g., type I IFNs). A specific Alu RNA (i.e., AluJb RNA) was implicated in activating multiple RNA-sensing pathways and found to be a potent innate immune agonist. Here, we have performed a bioinformatic analysis of A-to-I RNA editing in human melanoma samples and determined that pre-therapy levels of A-to-I RNA editing negatively correlate with survival times, suggesting that an accumulation of endogenous double-stranded Alu RNA might contribute to cancer patient survival. Furthermore, we demonstrated that immunostimulatory Alu RNA can be leveraged pharmacologically for cancer immunotherapy. AluJb RNA was in vitro transcribed and then formulated with endosome-destabilizing polymer nanoparticles to improve intracellular delivery of the RNA and enable activation of RNA-sensing pathways. AluJb RNA/polymer complexes (i.e., Alu-NPs) were engineered to form colloidally stable nanoparticles that exhibited immunostimulatory activity in vitro and in vivo. Finally, the therapeutic potential of Alu-NPs for the treatment of cancer was demonstrated by attenuated tumor growth and prolonged survival in the B16.F10 murine melanoma tumor model. Thus, these data collectively implicate intratumoral Alu RNA as a potentiator of antitumor innate immunity and identify AluJb RNA as a novel nucleic acid immunotherapeutic for cancer. Significance Loss of A-to-I editing leads to accumulation of unedited Alu RNAs that activate innate immunity via RNA-sensing pattern recognition receptors. When packaged into endosome-releasing polymer nanoparticles, AluJB RNA becomes highly immunostimulatory and can be used pharmacologically to inhibit tumor growth in mouse melanoma models. These findings identify Alu RNAs as a new class of nucleic acid innate immune agonists for cancer immunotherapy.
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Affiliation(s)
- Kyle M. Garland
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee
| | - Alexander J. Kwiatkowski
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee
| | - John T. Tossberg
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Philip S. Crooke
- Department of Mathematics, Vanderbilt University, Nashville, Tennessee
| | - Thomas M. Aune
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John T. Wilson
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee
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23
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Yu H, Bai K, Cheng Y, Lv J, Song Q, Yang H, Lu Q, Yang X. Clinical significance, tumor immune landscape and immunotherapy responses of ADAR in pan-cancer and its association with proliferation and metastasis of bladder cancer. Aging (Albany NY) 2023; 15:6302-6330. [PMID: 37414093 PMCID: PMC10373965 DOI: 10.18632/aging.204853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND ADAR is an enzyme involved in adenosine-inosine RNA editing. However, the role of ADAR in tumorigenesis, progression, and immunotherapy has not been fully elucidated. METHODS The TCGA, GTEx and GEO databases were extensively utilized to explore the expression level of ADAR across cancers. Combined with the clinical information of patients, the risk profile of ADAR in various cancers was delineated. We identified pathways enriched in ADAR and their related genes and explored the association between ADAR expression and the cancer immune microenvironment score and response to immunotherapy. Finally, we specifically explored the potential value of ADAR in the treatment of the bladder cancer immune response and verified the critical role of ADAR in the development and progression of bladder cancer through experiments. RESULTS ADAR is highly expressed in most cancers at both the RNA and protein level. ADAR is associated with the aggressiveness of some cancers, especially bladder cancer. In addition, ADAR is associated with immune-related genes, especially immune checkpoint genes, in the tumor immune microenvironment. Moreover, ADAR expression is positively correlated with tumor mutation burden and microsatellite instability in a variety of cancers, indicating that ADAR could be used as a biomarker of immunotherapy. Finally, we demonstrated that ADAR is a key pathogenic factor in bladder cancer. ADAR promoted proliferation and metastasis of bladder cancer cells. CONCLUSION ADAR regulates the tumor immune microenvironment and can be used as a biomarker of the tumor immunotherapy response, providing a novel strategy for the treatment of tumors, especially bladder cancer.
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Affiliation(s)
- Hao Yu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
- Institute of Urology and Andrology, Nanjing Medical University, Nanjing 210029, PR China
| | - Kexin Bai
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
- Institute of Urology and Andrology, Nanjing Medical University, Nanjing 210029, PR China
| | - Yidong Cheng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Jiancheng Lv
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
- Institute of Urology and Andrology, Nanjing Medical University, Nanjing 210029, PR China
| | - Qiang Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
- Institute of Urology and Andrology, Nanjing Medical University, Nanjing 210029, PR China
| | - Qiang Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Xiao Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
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24
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Park MJ, Jeong E, Lee EJ, Choi HJ, Moon BH, Kang K, Chang S. RNA Editing Enzyme ADAR1 Suppresses the Mobility of Cancer Cells via ARPIN. Mol Cells 2023; 46:351-359. [PMID: 36921992 PMCID: PMC10258462 DOI: 10.14348/molcells.2023.2174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/15/2023] [Indexed: 03/17/2023] Open
Abstract
Deamination of adenine or cytosine in RNA, called RNA editing, is a constitutively active and common modification. The primary role of RNA editing is tagging RNA right after its synthesis so that the endogenous RNA is recognized as self and distinguished from exogenous RNA, such as viral RNA. In addition to this primary function, the direct or indirect effects on gene expression can be utilized in cancer where a high level of RNA editing activity persists. This report identified actin-related protein 2/3 complex inhibitor (ARPIN) as a target of ADAR1 in breast cancer cells. Our comparative RNA sequencing analysis in MCF7 cells revealed that the expression of ARPIN was decreased upon ADAR1 depletion with altered editing on its 3'UTR. However, the expression changes of ARPIN were not dependent on 3'UTR editing but relied on three microRNAs acting on ARPIN. As a result, we found that the migration and invasion of cancer cells were profoundly increased by ADAR1 depletion, and this cellular phenotype was reversed by the exogenous ARPIN expression. Altogether, our data suggest that ADAR1 suppresses breast cancer cell mobility via the upregulation of ARPIN.
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Affiliation(s)
- Min Ji Park
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Eunji Jeong
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Eun Ji Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Hyeon Ji Choi
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Bo Hyun Moon
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Suhwan Chang
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
- Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
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25
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Turk A, Lee S, Yeon SW, Ryu SH, Han YK, Kim YJ, Ko SM, Kim BS, Hwang BY, Lee KY, Lee MK. Adenosine Deaminase Inhibitory Activity of Medicinal Plants: Boost the Production of Cordycepin in Cordyceps militaris. Antioxidants (Basel) 2023; 12:1260. [PMID: 37371990 DOI: 10.3390/antiox12061260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Cordycepin, also known as 3'-deoxyadenosine, is a major active ingredient of Cordyceps militaris with diverse pharmacological effects. Due to its limited supply, many attempts have been conducted to enhance the cordycepin content. As part of this study, eight medicinal plants were supplemented with cultivation substrates of Cordyceps to increase the cordycepin content. Cordyceps cultivated on brown rice supplemented with Mori Folium, Curcumae Rhizoma, Saururi Herba, and Angelicae Gigantis Radix exhibited increased cordycepin content compared to a brown rice control. Among them, the addition of 25% Mori Folium increased the cordycepin content up to 4 times. Adenosine deaminase (ADA) modulates the deamination of adenosine and deoxyadenosine, and the inhibitors have therapeutic potential with anti-proliferative and anti-inflammatory properties. As ADA is also known to be involved in converting cordycepin to 3'-deoxyinosine, the inhibitory activity of medicinal plants on ADA was measured by spectrophotometric analysis using cordycepin as a substrate. As expected, Mori Folium, Curcumae Rhizoma, Saururi Herba, and Angelicae Gigas Radix strongly inhibited ADA activity. Molecular docking analysis also showed the correlation between ADA and the major components of these medicinal plants. Conclusively, our research suggests a new strategy of using medicinal plants to enhance cordycepin production in C. militaris.
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Affiliation(s)
- Ayman Turk
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Solip Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Sang Won Yeon
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Se Hwan Ryu
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Yoo Kyong Han
- College of Pharmacy, Korea University, Sejong 47236, Republic of Korea
| | - Young Jun Kim
- College of Pharmacy, Korea University, Sejong 47236, Republic of Korea
| | - Sung Min Ko
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
- C&G Agricultural Association, Sejong 30067, Republic of Korea
| | - Beom Seok Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
- C&G Agricultural Association, Sejong 30067, Republic of Korea
| | - Bang Yeon Hwang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Ki Yong Lee
- College of Pharmacy, Korea University, Sejong 47236, Republic of Korea
| | - Mi Kyeong Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
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26
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Bölük A, Yavuz M, Takanlou MS, Avcı ÇB, Demircan T. In vitro anti-carcinogenic effect of andarine as a selective androgen receptor modulator on MIA-PaCa-2 cells by decreased proliferation and cell-cycle arrest at G0/G1 phase. Biochem Biophys Res Commun 2023; 671:132-139. [PMID: 37302286 DOI: 10.1016/j.bbrc.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 05/25/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
Pancreatic cancer (PC) continues to be devastating due to its highly malignant nature and poor prognosis. The limited benefits of the chemotherapeutic drugs and increasing resistance pose a critical challenge to overcome and warrant investigations for new therapeutic agents. Several preclinical and clinical studies have suggested a possible role of the androgen receptor (AR) signaling pathway in PC development and progression. Nevertheless, the studies are limited and inconclusive in explaining the molecular link between AR signaling and PC. Selective androgen receptor modulators (SARMs) are small molecule drugs with high affinity for the androgen receptor. SARMs elicit selective anabolic activities while abrogating undesired androgenic side effects. There is no study focusing on the utility of SARMs as inhibitors of PC. Here, we report the first study evaluating the possible anti-carcinogenic influences of andarine, a member of the SARMs, on PC. The data we presented here has illustrated that andarine repressed PC cell growth and proliferation via cell cycle arrest at G0/G1 phase. Gene expression analysis revealed that it downregulates CDKN1A expression level accordingly. Furthermore, we established that the anti-carcinogenic activity of andarine is not mediated by the PI3K/AKT/mTOR signaling pathway, a crucial regulator of cell survival. Our findings suggest that andarine might be considered as a prospective drug for PC.
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Affiliation(s)
- Aydın Bölük
- School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Mervenur Yavuz
- Institute of Natural Sciences, Department of Molecular Biology and Genetics, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Maryam Sabour Takanlou
- Institute of Health Sciences, Department of Medical Biology, Ege University, İzmir, Turkey
| | - Çığır Biray Avcı
- Medical Biology Department, School of Medicine, Ege University, İzmir, Turkey
| | - Turan Demircan
- Medical Biology Department, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey.
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27
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Booth BJ, Nourreddine S, Katrekar D, Savva Y, Bose D, Long TJ, Huss DJ, Mali P. RNA editing: Expanding the potential of RNA therapeutics. Mol Ther 2023; 31:1533-1549. [PMID: 36620962 PMCID: PMC9824937 DOI: 10.1016/j.ymthe.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
RNA therapeutics have had a tremendous impact on medicine, recently exemplified by the rapid development and deployment of mRNA vaccines to combat the COVID-19 pandemic. In addition, RNA-targeting drugs have been developed for diseases with significant unmet medical needs through selective mRNA knockdown or modulation of pre-mRNA splicing. Recently, RNA editing, particularly antisense RNA-guided adenosine deaminase acting on RNA (ADAR)-based programmable A-to-I editing, has emerged as a powerful tool to manipulate RNA to enable correction of disease-causing mutations and modulate gene expression and protein function. Beyond correcting pathogenic mutations, the technology is particularly well suited for therapeutic applications that require a transient pharmacodynamic effect, such as the treatment of acute pain, obesity, viral infection, and inflammation, where it would be undesirable to introduce permanent alterations to the genome. Furthermore, transient modulation of protein function, such as altering the active sites of enzymes or the interface of protein-protein interactions, opens the door to therapeutic avenues ranging from regenerative medicine to oncology. These emerging RNA-editing-based toolsets are poised to broadly impact biotechnology and therapeutic applications. Here, we review the emerging field of therapeutic RNA editing, highlight recent laboratory advancements, and discuss the key challenges on the path to clinical development.
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Affiliation(s)
| | - Sami Nourreddine
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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28
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Abstract
Our defenses against infection rely on the ability of the immune system to distinguish invading pathogens from self. This task is exceptionally challenging, if not seemingly impossible, in the case of retroviruses that have integrated almost seamlessly into the host. This review examines the limits of innate and adaptive immune responses elicited by endogenous retroviruses and other retroelements, the targets of immune recognition, and the consequences for host health and disease. Contrary to theoretical expectation, endogenous retroelements retain substantial immunogenicity, which manifests most profoundly when their epigenetic repression is compromised, contributing to autoinflammatory and autoimmune disease and age-related inflammation. Nevertheless, recent evidence suggests that regulated immune reactivity to endogenous retroelements is integral to immune system development and function, underpinning cancer immunosurveillance, resistance to infection, and responses to the microbiota. Elucidation of the interaction points with endogenous retroelements will therefore deepen our understanding of immune system function and contribution to disease.
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Affiliation(s)
- George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, United Kingdom;
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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29
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Chen L, Ou L, Jing X, Kong Y, Xie B, Zhang N, Shi H, Qin H, Li X, Hao P. DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing. Genome Biol 2023; 24:75. [PMID: 37069604 PMCID: PMC10108526 DOI: 10.1186/s13059-023-02921-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/28/2023] [Indexed: 04/19/2023] Open
Abstract
Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA sequencing offers a great opportunity for direct RNA editing detection. Here, we develop a neural network model, DeepEdit, that not only recognizes A-to-I editing events in single reads of Oxford Nanopore direct RNA sequencing, but also resolves the phasing of RNA editing events on transcripts. We illustrate the robustness of DeepEdit by applying it to Schizosaccharomyces pombe and Homo sapiens transcriptome data. We anticipate DeepEdit to be a powerful tool for the study of RNA editing from a new perspective.
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Affiliation(s)
- Longxian Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Liang Ou
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xinyun Jing
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yimeng Kong
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bingran Xie
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Niubing Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Han Shi
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hang Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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30
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Gong Y, Liu Y. R-Loops at Chromosome Ends: From Formation, Regulation, and Cellular Consequence. Cancers (Basel) 2023; 15:cancers15072178. [PMID: 37046839 PMCID: PMC10093737 DOI: 10.3390/cancers15072178] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Telomeric repeat containing RNA (TERRA) is transcribed from subtelomeric regions to telomeres. TERRA RNA can invade telomeric dsDNA and form telomeric R-loop structures. A growing body of evidence suggests that TERRA-mediated R-loops are critical players in telomere length homeostasis. Here, we will review current knowledge on the regulation of R-loop levels at telomeres. In particular, we will discuss how the central player TERRA and its binding proteins modulate R-loop levels through various mechanisms. We will further provide an overview of the consequences of TERRA-mediated persistent or unscheduled R-loops at telomeres in human ALT cancers and other organisms, with a focus on telomere length regulation after replication interference-induced damage and DNA homologous recombination-mediated repair.
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Affiliation(s)
- Yi Gong
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Yie Liu
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
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31
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Yang Q, Xu P, Liu Q, Hu F, Xie X, Jiang L, Bi R, Wang L, Ding F, Xiao H. Depleting DDX1 sensitizes non-small cell lung cancer cells to chemotherapy by attenuating cancer stem cell traits. Life Sci 2023; 323:121592. [PMID: 36934972 DOI: 10.1016/j.lfs.2023.121592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023]
Abstract
AIMS DEAD-box helicase 1 (DDX1) has oncogenic properties in several human cancers. However, the clinical significance and biological role of DDX1 in non-small cell lung cancer (NSCLC) remain elusive. Here, we examined the chemotherapeutic relevance of DDX1 in NSCLC. MAIN METHODS We used the UALCAN database, Western blot analysis, and immunohistochemical and RT-qPCR assays to assess DDX1 expression in NSCLC cell lines (H1650 and A549) and patient tissues. The role of DDX1 in the chemosensitivity of NSCLC cells and the underlying mechanisms were determined using colony formation, CCK-8, flow cytometry, wound healing, Transwell, tumor sphere formation, and immunostaining assays, together with a xenograft tumor model in nude mice. KEY FINDINGS Our study revealed that DDX1 was overexpressed in NSCLC cell lines and tissues. We further found that depleting DDX1 increased the sensitivity of NSCLC cells to the chemotherapy drug cisplatin, increased cell apoptosis, and inhibited cell migration and invasion. Co-immunoprecipitation assays revealed that DDX1 bound to ADAR1, and increased ADAR1 protein expression. Furthermore, we found that ADAR1 mediated cancer-promoting effects, independent of deaminase activity, by binding to RAC3 mRNA. Our findings not only show that DDX1 mediates chemosensitivity to cisplatin via the ADAR1/RAC3 axis but also highlight the importance of ADARs as essential RNA-binding proteins for cell homeostasis, as well as cancer progression. SIGNIFICANCE Our results suggest that DDX1 plays an important role in the development and progression of human NSCLC and that DDX1 may serve as a therapeutic target in NSCLC patients.
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Affiliation(s)
- Qi Yang
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Pei Xu
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Qingtao Liu
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Fengqing Hu
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Xiao Xie
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Lianyong Jiang
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Rui Bi
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China
| | - Lei Wang
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China.
| | - Fangbao Ding
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China.
| | - Haibo Xiao
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated to, Shanghai Jiao Tong University, School of medicine, Shanghai 200092, PR China.
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32
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Cao Y, Huang C, Zhao X, Yu J. Regulation of SUMOylation on RNA metabolism in cancers. Front Mol Biosci 2023; 10:1137215. [PMID: 36911524 PMCID: PMC9998694 DOI: 10.3389/fmolb.2023.1137215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Post-translational modifications of proteins play very important roles in regulating RNA metabolism and affect many biological pathways. Here we mainly summarize the crucial functions of small ubiquitin-like modifier (SUMO) modification in RNA metabolism including transcription, splicing, tailing, stability and modification, as well as its impact on the biogenesis and function of microRNA (miRNA) in particular. This review also highlights the current knowledge about SUMOylation regulation in RNA metabolism involved in many cellular processes such as cell proliferation and apoptosis, which is closely related to tumorigenesis and cancer progression.
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Affiliation(s)
- Yingting Cao
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Caihu Huang
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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33
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Li M, Yan C, Jiao Y, Xu Y, Bai C, Miao R, Jiang J, Liu J. Site-directed RNA editing by harnessing ADARs: advances and challenges. Funct Integr Genomics 2022; 22:1089-1103. [DOI: 10.1007/s10142-022-00910-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]
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Hajji K, Sedmík J, Cherian A, Amoruso D, Keegan LP, O'Connell MA. ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations. RNA (NEW YORK, N.Y.) 2022; 28:1281-1297. [PMID: 35863867 PMCID: PMC9479739 DOI: 10.1261/rna.079266.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes are essential for neuronal function and innate immune control. ADAR1 RNA editing prevents aberrant activation of antiviral dsRNA sensors through editing of long, double-stranded RNAs (dsRNAs). In this review, we focus on the ADAR2 proteins involved in the efficient, highly site-specific RNA editing to recode open reading frames first discovered in the GRIA2 transcript encoding the key GLUA2 subunit of AMPA receptors; ADAR1 proteins also edit many of these sites. We summarize the history of ADAR2 protein research and give an up-to-date review of ADAR2 structural studies, human ADARBI (ADAR2) mutants causing severe infant seizures, and mouse disease models. Structural studies on ADARs and their RNA substrates facilitate current efforts to develop ADAR RNA editing gene therapy to edit disease-causing single nucleotide polymorphisms (SNPs). Artificial ADAR guide RNAs are being developed to retarget ADAR RNA editing to new target transcripts in order to correct SNP mutations in them at the RNA level. Site-specific RNA editing has been expanded to recode hundreds of sites in CNS transcripts in Drosophila and cephalopods. In Drosophila and C. elegans, ADAR RNA editing also suppresses responses to self dsRNA.
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Affiliation(s)
- Khadija Hajji
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Jiří Sedmík
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Anna Cherian
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | | | - Liam P Keegan
- CEITEC Masaryk University, Brno 62500, Czech Republic
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RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
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Hao Y, Yang B, Yang J, Shi X, Yang X, Zhang D, Zhao D, Yan W, Chen L, Zheng H, Zhang K, Liu X. ZBP1: A Powerful Innate Immune Sensor and Double-Edged Sword in Host Immunity. Int J Mol Sci 2022; 23:ijms231810224. [PMID: 36142136 PMCID: PMC9499459 DOI: 10.3390/ijms231810224] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Z-conformation nucleic acid binding protein 1 (ZBP1), a powerful innate immune sensor, has been identified as the important signaling initiation factor in innate immune response and the multiple inflammatory cell death known as PANoptosis. The initiation of ZBP1 signaling requires recognition of left-handed double-helix Z-nucleic acid (includes Z-DNA and Z-RNA) and subsequent signaling transduction depends on the interaction between ZBP1 and its adapter proteins, such as TANK-binding kinase 1 (TBK1), interferon regulatory factor 3 (IRF3), receptor-interacting serine/threonine-protein kinase 1 (RIPK1), and RIPK3. ZBP1 activated innate immunity, including type-I interferon (IFN-I) response and NF-κB signaling, constitutes an important line of defense against pathogenic infection. In addition, ZBP1-mediated PANoptosis is a double-edged sword in anti-infection, auto-inflammatory diseases, and tumor immunity. ZBP1-mediated PANoptosis is beneficial for eliminating infected cells and tumor cells, but abnormal or excessive PANoptosis can lead to a strong inflammatory response that is harmful to the host. Thus, pathogens and host have each developed multiplex tactics targeting ZBP1 signaling to maintain strong virulence or immune homeostasis. In this paper, we reviewed the mechanisms of ZBP1 signaling, the effects of ZBP1 signaling on host immunity and pathogen infection, and various antagonistic strategies of host and pathogen against ZBP1. We also discuss existent gaps regarding ZBP1 signaling and forecast potential directions for future research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Haixue Zheng
- Correspondence: (H.Z.); (K.Z.); Tel.: +86-15214078335 (K.Z.)
| | - Keshan Zhang
- Correspondence: (H.Z.); (K.Z.); Tel.: +86-15214078335 (K.Z.)
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RNA Editing Enzyme ADAR1 Regulates METTL3 in an Editing Dependent Manner to Promote Breast Cancer Progression via METTL3/ARHGAP5/YTHDF1 Axis. Int J Mol Sci 2022; 23:ijms23179656. [PMID: 36077054 PMCID: PMC9456332 DOI: 10.3390/ijms23179656] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
A-to-I RNA editing and m6A modification are two of the most prevalent types of RNA modifications controlling gene expression in mammals and play very important roles in tumorigenesis and tumor progression. However, the functional roles and correlations of these two RNA modifications remain to be further investigated in cancer. Herein, we show that ADAR1, an A-to-I RNA-editing enzyme, interacts with METTL3 and increases its protein level to promote the proliferation, migration and invasion of breast cancer cells through a mechanism connecting ADAR1, METTL3 and YTHDF1. We show that both ADAR1 and METTL3 are upregulated in breast cancer samples, and ADAR1 positively correlates with METTL3; ADAR1 edits METTL3 mRNA and changes its binding site to miR532-5p, leading to increased METTL3 protein, which further targets ARHGAP5, recognized by YTHDF1. Additionally, we show that loss of ADAR1 significantly inhibits breast cancer growth in vivo. Collectively, our findings identify the ADAR1–METTL3 axis as a novel, important pathway that connects A-to-I editing and m6A RNA modifications during breast cancer progression.
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Liu J, Wang F, Zhang Y, Liu J, Zhao B. ADAR1-Mediated RNA Editing and Its Role in Cancer. Front Cell Dev Biol 2022; 10:956649. [PMID: 35898396 PMCID: PMC9309331 DOI: 10.3389/fcell.2022.956649] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
It is well known that the stability of RNA, the interaction between RNA and protein, and the correct translation of protein are significant forces that drive the transition from normal cell to malignant tumor. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that catalyzes the deamination of adenosine to inosine (A-to-I), which is one dynamic modification that in a combinatorial manner can give rise to a very diverse transcriptome. ADAR1-mediated RNA editing is essential for survival in mammals and its dysregulation results in aberrant editing of its substrates that may affect the phenotypic changes in cancer. This overediting phenomenon occurs in many cancers, such as liver, lung, breast, and esophageal cancers, and promotes tumor progression in most cases. In addition to its editing role, ADAR1 can also play an editing-independent role, although current research on this mechanism is relatively shallowly explored in tumors. In this review, we summarize the nature of ADAR1, mechanisms of ADAR1 editing-dependent and editing-independent and implications for tumorigenesis and prognosis, and pay special attention to effects of ADAR1 on cancers by regulating non-coding RNA formation and function.
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Affiliation(s)
- Jizhe Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Yindan Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Jingfeng Liu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
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RNA editing enzyme ADAR1 controls miR-381-3p-mediated expression of multidrug resistance protein MRP4 via regulation of circRNA in human renal cells. J Biol Chem 2022; 298:102184. [PMID: 35753353 PMCID: PMC9293778 DOI: 10.1016/j.jbc.2022.102184] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/14/2022] [Accepted: 06/18/2022] [Indexed: 12/28/2022] Open
Abstract
Multidrug resistance–associated protein 4 (MRP4), a member of the C subfamily of ATP-binding cassette transporters, is highly expressed in the kidneys of mammals and is responsible for renal elimination of numerous drugs. Adenosine deaminase acting on RNA 1 (ADAR1) has been reported to regulate gene expression by catalyzing adenosine-to-inosine RNA editing reactions; however, potential roles of ADAR1 in the regulation of MRP4 expression have not been investigated. In this study, we found that downregulation of ADAR1 increased the expression of MRP4 in human renal cells at the posttranscriptional level. Luciferase reporter assays and microarray analysis revealed that downregulation of ADAR1 reduced the levels of microRNA miR-381-3p, which led to the corresponding upregulation of MPR4 expression. Circular RNAs (circRNAs) are a type of closed-loop endogenous noncoding RNAs that play an essential role in gene expression by acting as miRNA sponges. We demonstrate that ADAR1 repressed the biogenesis of circRNA circHIPK3 through its adenosine-to-inosine RNA editing activity, which altered the secondary structure of the precursor of circHIPK3. Furthermore, in silico analysis suggested that circHIPK3 acts as a sponge of miR-381-3p. Indeed, we found overexpression of circHIPK3 induced the expression of MRP4 through its interference with miR-381-3p. Taken together, our study provides novel insights into regulation of the expression of xenobiotic transporters through circRNA expression by the RNA editing enzyme ADAR1.
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