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Nakamura K, Shigeyasu K, Maki J, Eto E, Masuyama H. The adenosine deaminase family acting on RNA 1 can be a useful diagnostic biomarker in chorioamnionitis. Placenta 2024; 153:53-58. [PMID: 38820942 DOI: 10.1016/j.placenta.2024.05.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
INTRODUCTION Chorioamnionitis (CAM) involves infection and inflammation of the chorion and amniotic membrane, but there are still no effective diagnostic biomarkers for CAM. METHODS We investigated the correlation between RNA editing enzyme Adenosine deaminase family acting on RNA 1 (ADAR1) and CAM in chorion and amniotic membrane specimens derived from premature rupture of the membrane (PROM), CAM (pathologically diagnosed), and clinical CAM (clinically diagnosed) patients using reverse transcription polymerase chain reaction (RT-PCR). RESULTS ADAR1 was upregulated in the chorion and amniotic membrane specimens of CAM and clinical CAM patients (p < 0.001 and p = 0.005). ADAR1 had a significantly higher area under the curve (AUC) (0.735 and 0.828) than markers of inflammation characteristics in diagnosing CAM and clinical CAM patients. ADAR1 also had significantly higher AUC (0.701 and 0.837) than clinical characteristics for CAM and clinical CAM patients. DISCUSSION ADAR1 can be a useful diagnostic biomarker in CAM patients.
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Affiliation(s)
- Keiichiro Nakamura
- Department of Obstetrics and Gynecology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
| | - Kunitoshi Shigeyasu
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Jota Maki
- Department of Obstetrics and Gynecology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Eriko Eto
- Department of Obstetrics and Gynecology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Hisashi Masuyama
- Department of Obstetrics and Gynecology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
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Lin S, Kuang M. RNA modification-mediated mRNA translation regulation in liver cancer: mechanisms and clinical perspectives. Nat Rev Gastroenterol Hepatol 2024; 21:267-281. [PMID: 38243019 DOI: 10.1038/s41575-023-00884-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/21/2024]
Abstract
Malignant liver cancer is characterized by rapid tumour progression and a high mortality rate, whereas the molecular mechanisms underlying liver cancer initiation and progression are still poorly understood. The dynamic and reversible RNA modifications have crucial functions in gene expression regulation by modulating RNA processing and mRNA translation. Emerging evidence has revealed that alterations in RNA modifications facilitate the selective translation of oncogenic transcripts and promote the diverse tumorigenic processes of liver cancer. In this Review, we first highlight the current progress on the functions and mechanisms underlying RNA modifications in the regulation of mRNA translation and then summarize the exciting discoveries on aberrant RNA modification-mediated mRNA translation in the regulation of tumour initiation, metastasis, metabolism, tumour microenvironment, and drug and radiotherapy resistance in liver cancer. Finally, we discuss the diagnostic and therapeutic potentials of targeting RNA modifications and mRNA translation for the clinical management of liver cancer.
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Affiliation(s)
- Shuibin Lin
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Ming Kuang
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
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Feng Q, Wang H, Shao Y, Xu X. Antizyme inhibitor family: biological and translational research implications. Cell Commun Signal 2024; 22:11. [PMID: 38169396 PMCID: PMC10762828 DOI: 10.1186/s12964-023-01445-1] [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: 05/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Metabolism of polyamines is of critical importance to physiological processes. Ornithine decarboxylase (ODC) antizyme inhibitors (AZINs) are capable of interacting with antizymes (AZs), thereby releasing ODC from ODC-AZs complex, and promote polyamine biosynthesis. AZINs regulate reproduction, embryonic development, fibrogenesis and tumorigenesis through polyamine and other signaling pathways. Dysregulation of AZINs has involved in multiple human diseases, especially malignant tumors. Adenosine-to-inosine (A-to-I) RNA editing is the most common type of post-transcriptional nucleotide modification in humans. Additionally, the high frequencies of RNA-edited AZIN1 in human cancers correlates with increase of cancer cell proliferation, enhancement of cancer cell stemness, and promotion of tumor angiogenesis. In this review, we summarize the current knowledge on the various contribution of AZINs related with potential cancer promotion, cancer stemness, microenvironment and RNA modification, especially underlying molecular mechanisms, and furthermore explored its promising implication for cancer diagnosis and treatment.
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Affiliation(s)
- Qiaohui Feng
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110001, PR China
| | - Huijie Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning Province, PR China
| | - Youcheng Shao
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning Province, PR China
| | - Xiaoyan Xu
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning Province, PR China.
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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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Kong FS, Lu Z, Zhou Y, Lu Y, Ren CY, Jia R, Zeng B, Huang P, Wang J, Ma Y, Chen JH. Transcriptome analysis identification of A-to-I RNA editing in granulosa cells associated with PCOS. Front Endocrinol (Lausanne) 2023; 14:1170957. [PMID: 37547318 PMCID: PMC10401594 DOI: 10.3389/fendo.2023.1170957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/06/2023] [Indexed: 08/08/2023] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is a complex, multifactor disorder in women of reproductive age worldwide. Although RNA editing may contribute to a variety of diseases, its role in PCOS remains unclear. Methods A discovery RNA-Seq dataset was obtained from the NCBI Gene Expression Omnibus database of granulosa cells from women with PCOS and women without PCOS (controls). A validation RNA-Seq dataset downloaded from the European Nucleotide Archive Databank was used to validate differential editing. Transcriptome-wide investigation was conducted to analyze adenosine-to-inosine (A-to-I) RNA editing in PCOS and control samples. Results A total of 17,395 high-confidence A-to-I RNA editing sites were identified in 3,644 genes in all GC samples. As for differential RNA editing, there were 545 differential RNA editing (DRE) sites in 259 genes with Nucleoporin 43 (NUP43), Retinoblastoma Binding Protein 4 (RBBP4), and leckstrin homology-like domain family A member 1 (PHLDA) showing the most significant three 3'-untranslated region (3'UTR) editing. Furthermore, we identified 20 DRE sites that demonstrated a significant correlation between editing levels and gene expression levels. Notably, MIR193b-365a Host Gene (MIR193BHG) and Hook Microtubule Tethering Protein 3 (HOOK3) exhibited significant differential expression between PCOS and controls. Functional enrichment analysis showed that these 259 differentially edited genes were mainly related to apoptosis and necroptosis pathways. RNA binding protein (RBP) analysis revealed that RNA Binding Motif Protein 45 (RBM45) was predicted as the most frequent RBP binding with RNA editing sites. Additionally, we observed a correlation between editing levels of differential editing sites and the expression level of the RNA editing enzyme Adenosine Deaminase RNA Specific B1 (ADARB1). Moreover, the existence of 55 common differentially edited genes and nine differential editing sites were confirmed in the validation dataset. Conclusion Our current study highlighted the potential role of RNA editing in the pathophysiology of PCOS as an epigenetic process. These findings could provide valuable insights into the development of more targeted and effective treatment options for PCOS.
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Affiliation(s)
- Fan-Sheng Kong
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Zijing Lu
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yuan Zhou
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yinghua Lu
- Department of Reproductive Medicine, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Ruofan Jia
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Beilei Zeng
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Panwang Huang
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Jihong Wang
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yaping Ma
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
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Mei Y, Liang D, Ai B, Wang T, Guo S, Jin G, Yu D. Genome-wide identification of A-to-I RNA editing events provides the functional implications in PDAC. Front Oncol 2023; 13:1092046. [PMID: 36895481 PMCID: PMC9990869 DOI: 10.3389/fonc.2023.1092046] [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: 11/07/2022] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
Introduction RNA editing, a wide-acknowledged post-transcriptional mechanism, has been reported to be involved in the occurrence and development of cancer, especially the abnormal alteration of adenosine to inosine. However, fewer studies focus on pancreaticcancer. Therefore, we aimed to explore the possible linkages between altered RNA editing events and the development of PDAC. Method We characterized the global A-to-I RNA editing spectrum from RNA and matched whole-genome sequencing data of 41 primary PDAC and adjacent normal tissues. The following analyses were performed: different editing level and RNA expression analysis,pathway analysis, motif analysis, RNA secondary structure analysis, alternative splicing events analysis, and survival analysis.The RNA editing of single-cell RNA public sequencing data was also characterized. Result A large number of adaptive RNA editing events with significant differences in editing levels were identified, which are mainly regulated by ADAR1. Moreover, RNA editing in tumors has a higher editing level and more abundant editing sites in general. 140genes were screened out since they were identified with significantly different RNA editing events and were significantly different in expression level between tumor and matched normal samples. Further analysis showed a preference that in the tumor-specific group, they are mainly enriched in cancer-related signal pathways, while in the normal tissue-specific group, they are mainly enriched in pancreatic secretion. At the same time, we also found positively selected differentially edited sites in a series of cancer immune genes, including EGF, IGF1R, and PIK3CD. RNA editing might participate in pathogenisis of PDAC through regulating the alternative splicing and RNA secondary structure of important genesto further regulate gene expression and protein synthesis, including RAB27B and CERS4. Furthermore, single cell sequencing results showed that type2 ductal cells contributed the most to RNA editing events in tumors. Conclusion RNA editing is an epigenetic mechanism involved in the occurrence and development of pancreatic cancer, which has the potential to diagnose of PDAC and is closely related to the prognosis.
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Affiliation(s)
- Yue Mei
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Dong Liang
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Bin Ai
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Tengjiao Wang
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Shiwei Guo
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Gang Jin
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Dong Yu
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
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Wang Z, Zhu Y, Xia L, Li J, Song M, Yang C. Exercise-Induced ADAR2 Protects against Nonalcoholic Fatty Liver Disease through miR-34a. Nutrients 2022; 15:nu15010121. [PMID: 36615779 PMCID: PMC9824461 DOI: 10.3390/nu15010121] [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: 11/14/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a growing health problem that is closely associated with insulin resistance and hereditary susceptibility. Exercise is a beneficial approach to NAFLD. However, the relief mechanism of exercise training is still unknown. In this study, mice on a normal diet or a high-fat diet (HFD), combined with Nω-nitro-L-arginine methyl ester, hydrochloride (L-NAME) mice, were either kept sedentary or were subjected to a 12-week exercise running scheme. We found that exercise reduced liver steatosis in mice with diet-induced NAFLD. The hepatic adenosine deaminases acting on RNA 2 (ADAR2) were downregulated in NAFLD and were upregulated in the liver after 12-week exercise. Next, overexpression of ADAR2 inhibited and suppression promoted lipogenesis in HepG2 cells treated with oleic acid (OA), respectively. We found that ADAR2 could down-regulate mature miR-34a in hepatocytes. Functional reverse experiments further proved that miR-34a mimicry eliminated the suppression of ADAR2 overexpression in lipogenesis in vitro. Moreover, miR-34a inhibition and mimicry could also affect lipogenesis in hepatocytes. In conclusion, exercise-induced ADAR2 protects against lipogenesis during NAFLD by editing miR-34a. RNA editing mediated by ADAR2 may be a promising therapeutic candidate for NAFLD.
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Affiliation(s)
- Zhijing Wang
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yaru Zhu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Lu Xia
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jing Li
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
- Correspondence: (J.L.); (M.S.); (C.Y.)
| | - Meiyi Song
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
- Correspondence: (J.L.); (M.S.); (C.Y.)
| | - Changqing Yang
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200092, China
- Correspondence: (J.L.); (M.S.); (C.Y.)
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8
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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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ADAR1 and AZIN1 RNA editing function as an oncogene and contributes to immortalization in endometrial cancer. Gynecol Oncol 2022; 166:326-333. [PMID: 35697535 DOI: 10.1016/j.ygyno.2022.05.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Adenosine-to-inosine (A-to-I) RNA editing is a recently described epigenetic modification, which is believed to constitute a key oncogenic mechanism in human cancers. However, its functional role and clinical significance in endometrial cancer (EC) remain unclear. METHODS Adenosine Deaminase family Acting on RNA1 (ADAR1) expression and Antizyme inhibitor 1 (AZIN1) RNA editing were examined to clarify the correlation with clinicopathological parameters and prognosis in EC patients. The biological functions and inhibitory effects of ADAR1 knockdown were investigated in JHUCS-1 and TU-ECS-1 EC cell lines. RESULTS ADAR1 showed significant association with worse histology (P = 0.006), and lymph vascular space involvement (P = 0.049) in EC. The level of AZIN1 RNA editing was also significantly associated with worse histology (P = 0.012). ADAR1 expression was significantly correlated with AZIN1 RNA editing level (R = 0.729, R2 = 0.547, P < 0.001). Multivariate analysis indicated that higher ADAR1 expression along with AZIN1 RNA editing is an independent predictor of prognosis in EC patients (P = 0.015). Knockdown of ADAR1 led to increased MDA-5, RIG-I, PKR, and IRF-7 expression, which in turn resulted in increased levels of Bak and apoptosis in EC cells. CONCLUSIONS High ADAR1 expression along with AZIN1 RNA editing could be a predictor of worse prognosis in EC. ADAR1 could be a potential therapeutic target in EC patients.
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Dynamic Variations of 3'UTR Length Reprogram the mRNA Regulatory Landscape. Biomedicines 2021; 9:biomedicines9111560. [PMID: 34829789 PMCID: PMC8615635 DOI: 10.3390/biomedicines9111560] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/10/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022] Open
Abstract
This paper concerns 3′-untranslated regions (3′UTRs) of mRNAs, which are non-coding regulatory platforms that control stability, fate and the correct spatiotemporal translation of mRNAs. Many mRNAs have polymorphic 3′UTR regions. Controlling 3′UTR length and sequence facilitates the regulation of the accessibility of functional effectors (RNA binding proteins, miRNAs or other ncRNAs) to 3′UTR functional boxes and motifs and the establishment of different regulatory landscapes for mRNA function. In this context, shortening of 3′UTRs would loosen miRNA or protein-based mechanisms of mRNA degradation, while 3′UTR lengthening would strengthen accessibility to these effectors. Alterations in the mechanisms regulating 3′UTR length would result in widespread deregulation of gene expression that could eventually lead to diseases likely linked to the loss (or acquisition) of specific miRNA binding sites. Here, we will review the mechanisms that control 3′UTR length dynamics and their alterations in human disorders. We will discuss, from a mechanistic point of view centered on the molecular machineries involved, the generation of 3′UTR variability by the use of alternative polyadenylation and cleavage sites, of mutually exclusive terminal alternative exons (exon skipping) as well as by the process of exonization of Alu cassettes to generate new 3′UTRs with differential functional features.
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Ramírez-Moya J, Miliotis C, Baker AR, Gregory RI, Slack FJ, Santisteban P. An ADAR1-dependent RNA editing event in the cyclin-dependent kinase CDK13 promotes thyroid cancer hallmarks. Mol Cancer 2021; 20:115. [PMID: 34496885 PMCID: PMC8424981 DOI: 10.1186/s12943-021-01401-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Adenosine deaminases acting on RNA (ADARs) modify many cellular RNAs by catalyzing the conversion of adenosine to inosine (A-to-I), and their deregulation is associated with several cancers. We recently showed that A-to-I editing is elevated in thyroid tumors and that ADAR1 is functionally important for thyroid cancer cell progression. The downstream effectors regulated or edited by ADAR1 and the significance of ADAR1 deregulation in thyroid cancer remain, however, poorly defined. Methods We performed whole transcriptome sequencing to determine the consequences of ADAR1 deregulation for global gene expression, RNA splicing and editing. The effects of gene silencing or RNA editing were investigated by analyzing cell viability, proliferation, invasion and subnuclear localization, and by protein and gene expression analysis. Results We report an oncogenic function for CDK13 in thyroid cancer and identify a new ADAR1-dependent RNA editing event that occurs in the coding region of its transcript. CDK13 was significantly over-edited (c.308A > G) in tumor samples and functional analysis revealed that this editing event promoted cancer cell hallmarks. Finally, we show that CDK13 editing increases the nucleolar abundance of the protein, and that this event might explain, at least partly, the global change in splicing produced by ADAR1 deregulation. Conclusions Overall, our data support A-to-I editing as an important pathway in cancer progression and highlight novel mechanisms that might be used therapeutically in thyroid and other cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01401-y.
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Affiliation(s)
- Julia Ramírez-Moya
- Instituto, de Investigaciones Biomédicas "Alberto Sols"; Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Department of Pathology, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Departments of Biological Chemistry and Molecular Pharmacology, and Pediatrics, Harvard Medical School, Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Christos Miliotis
- Department of Pathology, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Allison R Baker
- Department of Pathology, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Departments of Biological Chemistry and Molecular Pharmacology, and Pediatrics, Harvard Medical School, Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
| | - Frank J Slack
- Department of Pathology, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Pilar Santisteban
- Instituto, de Investigaciones Biomédicas "Alberto Sols"; Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
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12
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Hämetoja H, Andersson LC, Mäkitie A, Bäck L, Hagström J, Haglund C. Antizyme inhibitor 2 (AZIN2) associates with better prognosis of head and neck minor salivary gland adenoid cystic carcinoma. APMIS 2021; 129:503-511. [PMID: 34046926 DOI: 10.1111/apm.13158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/17/2021] [Indexed: 11/28/2022]
Abstract
The key regulator of the polyamine biosynthetic pathway is ornithine decarboxylase (ODC). ODC is activated by antizyme inhibitor 1 (AZIN1) and 2 (AZIN2). AZIN1 and recently AZIN2 have been related to cancer; however, their functions in adenoid cystic carcinoma (ACC) have not been studied. We performed immunohistochemical study on minor salivary and mucous gland ACC tissue samples of patients treated at the Helsinki University Hospital (Helsinki, Finland) during 1974-2012. We scored AZIN1 and 2 immunoexpression in 42 and 45 tumor tissue samples, respectively, and correlated them with clinicopathological factors and survival. Enhanced AZIN2 expression was associated with better survival. In addition, both AZINs were seen more commonly in cribriform and tubular than in solid growth patterns. AZIN1 expression did not correlate with the studied clinicopathological factors. It seems that AZIN2 expression is higher in cancer tissue with secretory functions. In ACC tissue, high AZIN2 expression could be related to well-differentiated histological type which still has a functioning vesicle transportation system. Thus, AZIN2 could be a prognostic factor for better survival of ACC patients.
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Affiliation(s)
- Hanna Hämetoja
- Department of Pathology, Helsinki, Finland.,Department of Oral Pathology and Radiology, University of Turku, and Turku University Hospital, Turku, Finland
| | | | - Antti Mäkitie
- Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Leif Bäck
- Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jaana Hagström
- Department of Pathology, Helsinki, Finland.,Department of Oral Pathology and Radiology, University of Turku, and Turku University Hospital, Turku, Finland.,Research Programs Unit, Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland
| | - Caj Haglund
- Research Programs Unit, Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland.,Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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13
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Ding HY, Yang WY, Zhang LH, Li L, Xie F, Li HY, Chen XY, Tu Z, Li Y, Chen Y, Yang SY. 8-Chloro-Adenosine Inhibits Proliferation of MDA-MB-231 and SK-BR-3 Breast Cancer Cells by Regulating ADAR1/p53 Signaling Pathway. Cell Transplant 2021; 29:963689720958656. [PMID: 32907379 PMCID: PMC7784596 DOI: 10.1177/0963689720958656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
8-Chloro-adenosine (8-Cl-Ado) has been shown to exhibit its antitumor activity by inducing apoptosis in human lung cancer A549 and H1299 cells or autophagy in chronic lymphocytic leukemia, and MDA-MB-231 and MCF-7 breast cancer cells. Adenosine deaminases acting on RNA 1 (ADAR1) is tightly associated with cancer development and progression. The aim of this study was to investigate the role of ADAR1 in the proliferation of MDA-MB-231 and SK-BR-3 breast cancer cell lines after 8-Cl-Ado exposure and its possible mechanisms. After 8-Cl-Ado exposure, CCK-8 assay was performed to determine the cell proliferation; flow cytometry was used to analyze the cell cycle profiles and apoptosis; and the protein levels of ADAR1, p53, p21, and cyclin D1 were measured by western blotting. The results showed that the cell proliferation was greatly inhibited, G1 cell cycle was arrested, and apoptosis was induced after 8-Cl-Ado exposure. ADAR1 and cyclin D1 protein levels were dramatically decreased, while p53 and p21 levels were increased after 8-Cl-Ado exposure. Moreover, the cell growth inhibition was rescued, apoptosis was reduced, and p53 and p21 protein levels were downregulated, while cyclin D1 was upregulated when cells were transfected with plasmids expressing ADAR1 proteins. More importantly, RNA-binding domain of ADAR1 is critical to the cell growth inhibition of breast cancer cells exposed to 8-Cl-Ado. Together, 8-Cl-Ado inhibits the cell proliferation, induces G1 phase arrest and apoptosis at least by targeting ADAR1/p53/p21 signaling pathway. The findings may provide us with insights into the role of ADAR1 in breast cancer progression and help us better understand the effects of 8-Cl-Ado in the treatment of breast cancer.
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Affiliation(s)
- Hong-Yue Ding
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Wan-Yong Yang
- Dongguan Waterfront Zone Central Hospital, Dongguan, Guangdong, China
| | - Li-Hong Zhang
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Li Li
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Feng Xie
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Hua-Yi Li
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Xiao-Yu Chen
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Zeng Tu
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Yi Li
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Yong Chen
- Department of Radiology and Intervention, The General Hospital of Ningxia Medical University, Yinchuan, China
| | - Sheng-Yong Yang
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
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14
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RNA editing contributes to epitranscriptome diversity in chronic lymphocytic leukemia. Leukemia 2020; 35:1053-1063. [PMID: 32728184 PMCID: PMC8024191 DOI: 10.1038/s41375-020-0995-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
RNA editing-primarily conversion of adenosine to inosine (A > I)-is a widespread posttranscriptional mechanism, mediated by Adenosine Deaminases acting on RNA (ADAR) enzymes to alter the RNA sequence of primary transcripts. Hence, in addition to somatic mutations and alternative RNA splicing, RNA editing can be a further source for recoding events. Although RNA editing has been detected in many solid cancers and normal tissue, RNA editing in chronic lymphocytic leukemia (CLL) has not been addressed so far. We determined global RNA editing and recurrent, recoding RNA editing events from matched RNA-sequencing and whole exome sequencing data in CLL samples from 45 untreated patients. RNA editing was verified in a validation cohort of 98 CLL patients and revealed substantially altered RNA editing profiles in CLL compared with normal B cells. We further found that RNA editing patterns were prognostically relevant. Finally, we showed that ADAR knockout decreased steady state viability of MEC1 cells and made them more susceptible to treatment with fludarabine and ibrutinib in vitro. We propose that RNA editing contributes to the pathophysiology of CLL and targeting the RNA editing machinery could be a future strategy to maximize treatment efficacy.
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15
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Kong XY, Vik ES, Nawaz MS, Berges N, Dahl TB, Vågbø C, Suganthan R, Segers F, Holm S, Quiles-Jiménez A, Gregersen I, Fladeby C, Aukrust P, Bjørås M, Klungland A, Halvorsen B, Alseth I. Deletion of Endonuclease V suppresses chemically induced hepatocellular carcinoma. Nucleic Acids Res 2020; 48:4463-4479. [PMID: 32083667 PMCID: PMC7192598 DOI: 10.1093/nar/gkaa115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/08/2020] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Endonuclease V (EndoV) is a conserved inosine-specific ribonuclease with unknown biological function. Here, we present the first mouse model lacking EndoV, which is viable without visible abnormalities. We show that endogenous murine EndoV cleaves inosine-containing RNA in vitro, nevertheless a series of experiments fails to link an in vivo function to processing of such transcripts. As inosine levels and adenosine-to-inosine editing often are dysregulated in hepatocellular carcinoma (HCC), we chemically induced HCC in mice. All mice developed liver cancer, however, EndoV−/− tumors were significantly fewer and smaller than wild type tumors. Opposed to human HCC, adenosine deaminase mRNA expression and site-specific editing were unaltered in our model. Loss of EndoV did not affect editing levels in liver tumors, however mRNA expression of a selection of cancer related genes were reduced. Inosines are also found in certain tRNAs and tRNAs are cleaved during stress to produce signaling entities. tRNA fragmentation was dysregulated in EndoV−/− livers and apparently, inosine-independent. We speculate that the inosine-ribonuclease activity of EndoV is disabled in vivo, but RNA binding allowed to promote stabilization of transcripts or recruitment of proteins to fine-tune gene expression. The EndoV−/− tumor suppressive phenotype calls for related studies in human HCC.
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Affiliation(s)
- Xiang Yi Kong
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Erik Sebastian Vik
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Meh Sameen Nawaz
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Natalia Berges
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Tuva Børresdatter Dahl
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Cathrine Vågbø
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Rajikala Suganthan
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Filip Segers
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Ana Quiles-Jiménez
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Cathrine Fladeby
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway.,Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, NO-0424 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway.,Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University ofOslo, NO-0317 Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
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16
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Shen B, Tong Y, Li Z, Yan H, Ye F, Wang Y, XCai X. C1GALT1C1/COSMC is a novel prognostic biomarker for hepatocellular carcinoma. Clin Res Hepatol Gastroenterol 2020; 44:310-320. [PMID: 31471227 DOI: 10.1016/j.clinre.2019.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/25/2019] [Accepted: 07/23/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND/AIMS The aim of this study is to explore the effects of COSMC on the prognosis of hepatocellular carcinoma (HCC), and establish a novel model with improved predictive capacity. METHODS Ninety-two patients diagnosed with HCC from 2006 to 2010 in our hospital were recruited to analyze the correlation between COSMC expression and prognosis. Cellular experiments were performed to verify the anti-tumor effects of COSMC. A predictive model was established based on the risk factors from multiple COX regression analysis. After validation, the novel model was compared with the conventional model in terms of capacity of predicting the prognosis. RESULTS The expression of COSMC was lower in tumor tissues than in normal tissues and inhibited HCC migration in cells. Besides the expression of COSMC was significantly negatively correlated with overall survival (OS) in HCC, regression analysis showed that COSMC expression, vascular invasion, and TNM stage were prognostic risk factors. Our novel model comprising these three elements was established and validated. Besides the good fit of the calibration curves, a higher concordance index (C-index) for OS (P=0.011) as well as better decision curve analysis (DCA) and survival curves for both disease-free survival (DFS) and OS suggested the superiority of this novel model compared with conventional TNM staging in predicting the prognosis of HCC patients. CONCLUSIONS We established a novel model by integrating the expression of COSMC, vascular invasion, and TNM stage, and found that it was better able to predict survival in patients with HCC compared with conventional TNM staging.
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Affiliation(s)
- Bo Shen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China; Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China
| | - Yifan Tong
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China; Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China
| | - Zheyong Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China; Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China
| | - Han Yan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China; Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China
| | - Fang Ye
- Department of Children Preventive Medicine, Children's Hospital, School of Medicine, Zhejiang University, China
| | - Yifan Wang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China; Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China
| | - Xiujun XCai
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China; Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China.
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17
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ADAR1-mediated RNA editing is a novel oncogenic process in thyroid cancer and regulates miR-200 activity. Oncogene 2020; 39:3738-3753. [PMID: 32157211 PMCID: PMC7190574 DOI: 10.1038/s41388-020-1248-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 01/08/2023]
Abstract
Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA. A-to-I editing of RNA is a widespread posttranscriptional process that has recently emerged as an important mechanism in cancer biology. A-to-I editing levels are high in several human cancers, including thyroid cancer, but ADAR1 editase-dependent mechanisms governing thyroid cancer progression are unexplored. To address the importance of RNA A-to-I editing in thyroid cancer, we examined the role of ADAR1. Loss-of-function analysis showed that ADAR1 suppression profoundly repressed proliferation, invasion, and migration in thyroid tumor cell models. These observations were validated in an in vivo xenograft model, which showed that ADAR1-silenced cells had a diminished ability to form tumors. RNA editing of miRNAs has the potential to markedly alter target recognition. According to TCGA data, the tumor suppressor miR-200b is overedited in thyroid tumors, and its levels of editing correlate with a worse progression-free survival and disease stage. We confirmed miR-200b overediting in thyroid tumors and we showed that edited miR-200b has weakened activity against its target gene ZEB1 in thyroid cancer cells, likely explaining the reduced aggressiveness of ADAR1-silenced cells. We also found that RAS, but not BRAF, modulates ADAR1 levels, an effect mediated predominantly by PI3K and in part by MAPK. Lastly, pharmacological inhibition of ADAR1 activity with the editing inhibitor 8-azaadenosine reduced cancer cell aggressiveness. Overall, our data implicate ADAR1-mediated A-to-I editing as an important pathway in thyroid cancer progression, and highlight RNA editing as a potential therapeutic target in thyroid cancer.
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18
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Chen J, Wang L, Wang F, Liu J, Bai Z. Genomic Identification of RNA Editing Through Integrating Omics Datasets and the Clinical Relevance in Hepatocellular Carcinoma. Front Oncol 2020; 10:37. [PMID: 32117713 PMCID: PMC7033493 DOI: 10.3389/fonc.2020.00037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
RNA editing is a widespread post-transcriptional mechanism to introduce single nucleotide changes to RNA in human cancers. Here, we characterized the global RNA editing profiles of 373 hepatocellular carcinoma (HCC) and 50 adjacent normal liver samples from The Cancer Genome Atlas (TCGA) and revealed that most editing events tend to occur in minor percentage of samples with moderate editing degrees (20–30%). Moreover, these RNA editing prefer to be A-to-I RNA editing in protein coding genes, especially in 3′UTR regions. Considering the association between DNA mutation and RNA editing, our analysis found that RNA editing maybe a complementary event for DNA mutation of HCC risk genes in HCC patients. We next identified 454 HCC-related editing sites, and many locate on the same genes with the same editing patterns. The functional consequences of editing revealed 2,086 functional editing sites and demonstrated that most editing in coding regions are non-synonymous variations. Furthermore, our results showed that editing in the 3′UTR regions tend to influence miRNA–target binding, and the editing degree seems to be negatively correlated with gene expression. Finally, we found that 46 HCC-related editing sites with consequence are able to distinguish the prognosis differences of HCC patients, suggesting their clinical relevance. Together, our results highlight RNA editing as a valuable molecular resource for investigating HCC mechanisms and clinical treatments.
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Affiliation(s)
- Juan Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Fangbin Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Jian Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China.,Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei, China
| | - Zhenyu Bai
- Department of Laboratory, General Hospital of Pingmei Shenma Medical Group, Pingdingshan, China
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19
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Wolfe AD, Arnold DB, Chen XS. Comparison of RNA Editing Activity of APOBEC1-A1CF and APOBEC1-RBM47 Complexes Reconstituted in HEK293T Cells. J Mol Biol 2019; 431:1506-1517. [PMID: 30844405 PMCID: PMC6443457 DOI: 10.1016/j.jmb.2019.02.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 12/15/2022]
Abstract
RNA editing is an important form of regulating gene expression and activity. APOBEC1 cytosine deaminase was initially characterized as pairing with a cofactor, A1CF, to form an active RNA editing complex that specifically targets APOB RNA in regulating lipid metabolism. Recent studies revealed that APOBEC1 may be involved in editing other potential RNA targets in a tissue-specific manner, and another protein, RBM47, appears to instead be the main cofactor of APOBEC1 for editing APOB RNA. In this report, by expressing APOBEC1 with either A1CF or RBM47 from human or mouse in an HEK293T cell line with no intrinsic APOBEC1/A1CF/RBM47 expression, we have compared direct RNA editing activity on several known cellular target RNAs. By using a sensitive cell-based fluorescence assay that enables comparative quantification of RNA editing through subcellular localization changes of eGFP, the two APOBEC1 cofactors, A1CF and RBM47, showed clear differences for editing activity on APOB and several other tested RNAs, and clear differences were observed when mouse versus human genes were tested. In addition, we have determined the minimal domain requirement of RBM47 needed for activity. These results provide useful functional characterization of RBM47 and direct biochemical evidence for the differential editing selectivity on a number of RNA targets.
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Affiliation(s)
- Aaron D Wolfe
- Molecular and Computational Biology, Department of Biological Sciences, Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Don B Arnold
- Molecular and Computational Biology, Department of Biological Sciences, Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences, Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
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20
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Jiang Q, Isquith J, Zipeto MA, Diep RH, Pham J, Delos Santos N, Reynoso E, Chau J, Leu H, Lazzari E, Melese E, Ma W, Fang R, Minden M, Morris S, Ren B, Pineda G, Holm F, Jamieson C. Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation. Cancer Cell 2019; 35:81-94.e7. [PMID: 30612940 PMCID: PMC6333511 DOI: 10.1016/j.ccell.2018.11.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 10/20/2018] [Accepted: 11/26/2018] [Indexed: 12/26/2022]
Abstract
Adenosine deaminase associated with RNA1 (ADAR1) deregulation contributes to therapeutic resistance in many malignancies. Here we show that ADAR1-induced hyper-editing in normal human hematopoietic progenitors impairs miR-26a maturation, which represses CDKN1A expression indirectly via EZH2, thereby accelerating cell-cycle transit. However, in blast crisis chronic myeloid leukemia progenitors, loss of EZH2 expression and increased CDKN1A oppose cell-cycle transit. Moreover, A-to-I editing of both the MDM2 regulatory microRNA and its binding site within the 3' UTR region stabilizes MDM2 transcripts, thereby enhancing blast crisis progenitor propagation. These data reveal a dual mechanism governing malignant transformation of progenitors that is predicated on hyper-editing of cell-cycle-regulatory miRNAs and the 3' UTR binding site of tumor suppressor miRNAs.
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Affiliation(s)
- Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
| | - Jane Isquith
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Maria Anna Zipeto
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Raymond H Diep
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Jessica Pham
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Nathan Delos Santos
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Eduardo Reynoso
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Julisia Chau
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Heather Leu
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Elisa Lazzari
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Etienne Melese
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wenxue Ma
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Minden
- Princess Margaret Hospital, Toronto, ON M5T 2M9, Canada
| | - Sheldon Morris
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gabriel Pineda
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Health Sciences, School of Health and Human Services, National University, San Diego, CA, USA
| | - Frida Holm
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Catriona Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
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21
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Takeda S, Shigeyasu K, Okugawa Y, Yoshida K, Mori Y, Yano S, Noma K, Umeda Y, Kondo Y, Kishimoto H, Teraishi F, Nagasaka T, Tazawa H, Kagawa S, Fujiwara T, Goel A. Activation of AZIN1 RNA editing is a novel mechanism that promotes invasive potential of cancer-associated fibroblasts in colorectal cancer. Cancer Lett 2018; 444:127-135. [PMID: 30583079 DOI: 10.1016/j.canlet.2018.12.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/03/2018] [Accepted: 12/11/2018] [Indexed: 12/31/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a recently described epigenetic modification, which is believed to constitute a key oncogenic mechanism in human cancers. However, its functional role in cancer-associated fibroblasts (CAFs) within the tumor microenvironment (TME) and its clinical significance remains unclear. Herein, we systematically analyzed a large cohort of 627 colorectal cancer (CRC) specimens, and investigated the expression pattern of ADAR1 and its biological significance on the antizyme inhibitor 1 (AZIN1) RNA editing levels. Both ADAR1 expression and AZIN1 RNA editing levels were significantly elevated in CRC tissues vs. normal mucosa, and these findings correlated with the increased expression of mesenchymal markers, Vimentin (ρ = 0.44) and Fibroblast activation protein (ρ = 0.38). Intriguingly, ADAR1 expression was specifically upregulated in both cancer cells and fibroblasts from cancerous lesions. Conditioned medium from cancer cells led to induction of ADAR1 expression and activation of AZIN1 RNA editing in fibroblasts (p < 0.05). Additionally, edited AZIN1 enhanced the invasive potential of fibroblasts. In conclusion, we provide novel evidence that hyper-editing of AZIN1 enhances the invasive potential of CAFs within the TME in colon and is an important predictor of tumor invasiveness in CRC.
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Affiliation(s)
- Sho Takeda
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Kunitoshi Shigeyasu
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan; Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, TX, USA
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, TX, USA; Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Kazuhiro Yoshida
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan; Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, TX, USA
| | - Yoshiko Mori
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Shuya Yano
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Kazuhiro Noma
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yuzo Umeda
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshitaka Kondo
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroyuki Kishimoto
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Fuminori Teraishi
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Takeshi Nagasaka
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroshi Tazawa
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Shunsuke Kagawa
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, TX, USA.
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22
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Okugawa Y, Toiyama Y, Shigeyasu K, Yamamoto A, Shigemori T, Yin C, Ichikawa T, Yasuda H, Fujikawa H, Yoshiyama S, Hiro J, Ohi M, Araki T, Kusunoki M, Goel A. Enhanced AZIN1 RNA editing and overexpression of its regulatory enzyme ADAR1 are important prognostic biomarkers in gastric cancer. J Transl Med 2018; 16:366. [PMID: 30563560 PMCID: PMC6299520 DOI: 10.1186/s12967-018-1740-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/07/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Adenosine-to-inosine (A-to-I) RNA editing is catalyzed by adenosine deaminases acting on RNA (ADAR) enzymes. Recent evidence suggests that RNA editing of antizyme inhibitor 1 (AZIN1) RNA is emerging as a key epigenetic alteration underlying cancer pathogenesis. METHODS We evaluated AZIN1 RNA editing levels, and the expression of its regulator, ADAR1, in 280 gastric tissues from 140 patients, using a RNA editing site-specific quantitative polymerase chain reaction assays. We also analyzed the clinical significance of these results as disease biomarkers in gastric cancer (GC) patients. RESULTS Both AZIN1 RNA editing levels and ADAR1 expression were significantly elevated in GC tissues compared with matched normal mucosa (P < 0.0001, 0.0008, respectively); and AZIN1 RNA editing was positively correlated with ADAR1 expression. Elevated expression of ADAR1 significantly correlated with poor overall survival (P = 0.034), while hyper-edited AZIN1 emerged as an independent prognostic factor for OS and disease-free survival in GC patients [odds ratio (OR):1.98, 95% CI 1.17-3.35, P = 0.011, OR: 4.55, 95% CI 2.12-9.78, P = 0.0001, respectively]. Increased AZIN1 RNA editing and ADAR1 over-expression were significantly correlated with key clinicopathological factors, such as advanced T stage, presence of lymph node metastasis, distant metastasis, and higher TNM stages in GC patients. Logistic regression analysis revealed that hyper-editing status of AZIN1 RNA was an independent risk factor for lymph node metastasis in GC patients [hazard ratio (HR):3.03, 95% CI 1.19-7.71, P = 0.02]. CONCLUSIONS AZIN1 RNA editing levels may be an important prognostic biomarker in GC patients, and may serve as a key clinical decision-making tool for determining preoperative treatment strategies in GC patients.
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Affiliation(s)
- Yoshinaga Okugawa
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Kunitoshi Shigeyasu
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Okayama Japan
| | - Akira Yamamoto
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Tsunehiko Shigemori
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Chengzeng Yin
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Takashi Ichikawa
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Hiromi Yasuda
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Hiroyuki Fujikawa
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Shigeyuki Yoshiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Junichiro Hiro
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Masaki Ohi
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Toshimitsu Araki
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Masato Kusunoki
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Tsu, Mie Japan
| | - Ajay Goel
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, 3410 Worth Street, Suite 610, Dallas, TX 75246 USA
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23
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Wang M, Yu F, Li P. Circular RNAs: Characteristics, Function and Clinical Significance in Hepatocellular Carcinoma. Cancers (Basel) 2018; 10:cancers10080258. [PMID: 30072625 PMCID: PMC6116001 DOI: 10.3390/cancers10080258] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/27/2018] [Accepted: 07/31/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. HCC patients are commonly diagnosed at an advanced stage, for which highly effective therapies are limited. Moreover, the five-year survival rate of HCC patients remains poor due to high frequency of tumor metastasis and recurrence. These challenges give rise to the emergent need to discover promising biomarkers for HCC diagnosis and identify novel targets for HCC therapy. Circular RNAs (circRNAs), a class of long-overlook non-coding RNA, have been revealed as multi-functional RNAs in recent years. Growing evidence indicates that circRNA expression alterations have a broad impact in biological characteristics of HCC. Most of these circRNAs regulate HCC progression by acting as miRNA sponges, suggesting that circRNAs may function as promising diagnostic biomarkers and ideal therapeutic targets for HCC. In this review, we summarize the current progress in studying the functional role of circRNAs in HCC pathogenesis and present their potential values as diagnostic biomarkers and therapeutic targets. In-depth investigations on the function and mechanism of circRNAs in HCC will enrich our knowledge of HCC pathogenesis and contribute to the development of effective diagnostic biomarkers and therapeutic targets for HCC.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Dengzhou Road 38, Qingdao 266021, China.
| | - Fei Yu
- Institute for Translational Medicine, Medical College of Qingdao University, Dengzhou Road 38, Qingdao 266021, China.
| | - Peifeng Li
- Institute for Translational Medicine, Medical College of Qingdao University, Dengzhou Road 38, Qingdao 266021, China.
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24
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Czermak P, Amman F, Jantsch MF, Cimatti L. Organ-wide profiling in mouse reveals high editing levels of Filamin B mRNA in the musculoskeletal system. RNA Biol 2018; 15:877-885. [PMID: 30064337 PMCID: PMC6161736 DOI: 10.1080/15476286.2018.1480252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/15/2018] [Indexed: 01/24/2023] Open
Abstract
Adenosine to inosine RNA editing in protein-coding messenger RNAs (mRNAs) potentially leads to changes in the amino acid composition of the encoded proteins. The mRNAs encoding the ubiquitously expressed actin-crosslinking proteins Filamin A and Filamin B undergo RNA editing leading to a highly conserved glutamine to arginine exchange at the identical position in either protein. Here, by targeted amplicon sequencing we analysed the RNA editing of Filamin B across several mouse tissues during post-natal development. We find highest filamin B editing levels in skeletal muscles, cartilage and bones, tissues where Filamin B function seems most important. Through the analysis of Filamin B editing in mice deficient in either ADAR1 or 2, we identified ADAR2 as the enzyme responsible for Filamin B RNA editing. We show that in neuronal tissues Filamin B editing drops in spliced transcripts indicating regulated maturation of edited transcripts. We show further that the variability of Filamin B editing across several organs correlates with its mRNA expression.
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Affiliation(s)
- Philipp Czermak
- Center of Anatomy and Cell Biology, Division of Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute of Theoretical Biochemistry, University of Vienna, Vienna, Austria
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna, Vienna, Austria
| | - Michael F. Jantsch
- Center of Anatomy and Cell Biology, Division of Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Laura Cimatti
- Center of Anatomy and Cell Biology, Division of Cell Biology, Medical University of Vienna, Vienna, Austria
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna, Vienna, Austria
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25
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Shigeyasu K, Okugawa Y, Toden S, Miyoshi J, Toiyama Y, Nagasaka T, Takahashi N, Kusunoki M, Takayama T, Yamada Y, Fujiwara T, Chen L, Goel A. AZIN1 RNA editing confers cancer stemness and enhances oncogenic potential in colorectal cancer. JCI Insight 2018; 3:99976. [PMID: 29925690 PMCID: PMC6124399 DOI: 10.1172/jci.insight.99976] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/17/2018] [Indexed: 12/30/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, a process mediated by adenosine deaminases that act on the RNA (ADAR) gene family, is a recently discovered epigenetic modification dysregulated in human cancers. However, the clinical significance and the functional role of RNA editing in colorectal cancer (CRC) remain unclear. We have systematically and comprehensively investigated the significance of the expression status of ADAR1 and of the RNA editing levels of antizyme inhibitor 1 (AZIN1), one of the most frequently edited genes in cancers, in 392 colorectal tissues from multiple independent CRC patient cohorts. Both ADAR1 expression and AZIN1 RNA editing levels were significantly elevated in CRC tissues when compared with corresponding normal mucosa. High levels of AZIN1 RNA editing emerged as a prognostic factor for overall survival and disease-free survival and were an independent risk factor for lymph node and distant metastasis. Furthermore, elevated AZIN1 editing identified high-risk stage II CRC patients. Mechanistically, edited AZIN1 enhances stemness and appears to drive the metastatic processes. We have demonstrated that edited AZIN1 functions as an oncogene and a potential therapeutic target in CRC. Moreover, AZIN1 RNA editing status could be used as a clinically relevant prognostic indicator in CRC patients.
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Affiliation(s)
- Kunitoshi Shigeyasu
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Shusuke Toden
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
| | - Jinsei Miyoshi
- Department of Gastroenterology and Oncology, University of Tokushima, Tokushima, Japan
| | - Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Takeshi Nagasaka
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | | | - Masato Kusunoki
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Tetsuji Takayama
- Department of Gastroenterology and Oncology, University of Tokushima, Tokushima, Japan
| | | | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ajay Goel
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Baylor Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
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26
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Rayon-Estrada V, Harjanto D, Hamilton CE, Berchiche YA, Gantman EC, Sakmar TP, Bulloch K, Gagnidze K, Harroch S, McEwen BS, Papavasiliou FN. Epitranscriptomic profiling across cell types reveals associations between APOBEC1-mediated RNA editing, gene expression outcomes, and cellular function. Proc Natl Acad Sci U S A 2017; 114:13296-13301. [PMID: 29167373 PMCID: PMC5740640 DOI: 10.1073/pnas.1714227114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epitranscriptomics refers to posttranscriptional alterations on an mRNA sequence that are dynamic and reproducible, and affect gene expression in a similar way to epigenetic modifications. However, the functional relevance of those modifications for the transcript, the cell, and the organism remain poorly understood. Here, we focus on RNA editing and show that Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-1 (APOBEC1), together with its cofactor RBM47, mediates robust editing in different tissues. The majority of editing events alter the sequence of the 3'UTR of targeted transcripts, and we focus on one cell type (monocytes) and on a small set of highly edited transcripts within it to show that editing alters gene expression by modulating translation (but not RNA stability or localization). We further show that specific cellular processes (phagocytosis and transendothelial migration) are enriched for transcripts that are targets of editing and that editing alters their function. Finally, we survey bone marrow progenitors and demonstrate that common monocyte progenitor cells express high levels of APOBEC1 and are susceptible to loss of the editing enzyme. Overall, APOBEC1-mediated transcriptome diversification is required for the fine-tuning of protein expression in monocytes, suggesting an epitranscriptomic mechanism for the proper maintenance of homeostasis in innate immune cells.
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Affiliation(s)
- Violeta Rayon-Estrada
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
- The Rockefeller Graduate Program, The Rockefeller University, New York, NY 10065
| | - Dewi Harjanto
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
| | - Claire E Hamilton
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065
- The Rockefeller Graduate Program, The Rockefeller University, New York, NY 10065
- The Tri-Institutional MD-PhD Program, The Rockefeller University, New York, NY 10065
| | - Yamina A Berchiche
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY 10065
| | - Emily Conn Gantman
- The Rockefeller Graduate Program, The Rockefeller University, New York, NY 10065
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, NY 10065
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY 10065
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Karen Bulloch
- The Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY 10065
| | - Khatuna Gagnidze
- The Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY 10065
| | - Sheila Harroch
- Division of Immune Diversity, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Bruce S McEwen
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY 10065
| | - F Nina Papavasiliou
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10065;
- Division of Immune Diversity, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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27
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Circular RNA expression is suppressed by androgen receptor (AR)-regulated adenosine deaminase that acts on RNA (ADAR1) in human hepatocellular carcinoma. Cell Death Dis 2017; 8:e3171. [PMID: 29144509 PMCID: PMC5775411 DOI: 10.1038/cddis.2017.556] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/05/2017] [Accepted: 09/18/2017] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is a heterogeneous malignancy as a result of complex genetic and epigenetic alterations. HCC is characterized by a clear gender disparity for which there is lack of a clear mechanistic understanding. Androgen receptor (AR) is thought to be critical for such bias. Meanwhile, the potential function of circular RNA (circRNA), regulated by RNA editing enzyme, remained largely unknown in malignancy till now. By utilizing circRNA microarray survey coupled with in vitro analysis, we analyzed the influence of AR on circRNA expression in HCC. Our results indicated that AR could suppress circRNA expression by upregulating ADAR1 p110. Such effect is because AR served as a transcriptional activator of ADAR1 promoter. More significantly, data collected from our center strongly suggest that ADAR1 expression can effectively predict HCC patients' prognosis and an abnormal overexpression of ADAR1 is positively correlated with AR in HCC. In addition, we found CircARSP91 (hsa_circ_0085154), one of the circRNAs downregulated by AR in an ADAR1-dependent manner, could inhibit HCC tumor growth both in vitro and in vivo. These findings highlight the fact that AR as a contributing factor for gender disparity in HCC can cause complex consequences though regulation of circRNA expression. Better understanding of the roles of circRNA during HCC initiation and progression will provide a novel angle to develop potential HCC therapies.
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28
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Qi L, Song Y, Chan THM, Yang H, Lin CH, Tay DJT, Hong H, Tang SJ, Tan KT, Huang XX, Lin JS, Ng VHE, Maury JJP, Tenen DG, Chen L. An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer. Nucleic Acids Res 2017; 45:10436-10451. [PMID: 28985428 PMCID: PMC5737565 DOI: 10.1093/nar/gkx667] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 07/19/2017] [Indexed: 12/16/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by Adenosine DeAminases acting on double-stranded RNA(dsRNA) (ADAR), occurs predominantly in the 3′ untranslated regions (3′UTRs) of spliced mRNA. Here we uncover an unanticipated link between ADARs (ADAR1 and ADAR2) and the expression of target genes undergoing extensive 3′UTR editing. Using METTL7A (Methyltransferase Like 7A), a novel tumor suppressor gene with multiple editing sites at its 3′UTR, we demonstrate that its expression could be repressed by ADARs beyond their RNA editing and double-stranded RNA (dsRNA) binding functions. ADARs interact with Dicer to augment the processing of pre-miR-27a to mature miR-27a. Consequently, mature miR-27a targets the METTL7A 3′UTR to repress its expression level. In sum, our study unveils that the extensive 3′UTR editing of METTL7A is merely a footprint of ADAR binding, and there are a subset of target genes that are equivalently regulated by ADAR1 and ADAR2 through their non-canonical RNA editing and dsRNA binding-independent functions, albeit maybe less common. The functional significance of ADARs is much more diverse than previously appreciated and this gene regulatory function of ADARs is most likely to be of high biological importance beyond the best-studied editing function. This non-editing side of ADARs opens another door to target cancer.
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Affiliation(s)
- Lihua Qi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Chi Ho Lin
- Centre for Genomic Sciences, the University of Hong Kong, Hong Kong
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - HuiQi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Kar Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xi Xiao Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jaymie Siqi Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Anatomy, National University of Singapore, Singapore
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29
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Ye LQ, Zhao H, Zhou HJ, Ren XD, Liu LL, Otecko NO, Wang ZB, Yang MM, Zeng L, Hu XT, Yao YG, Zhang YP, Wu DD. The RNA editome of Macaca mulatta and functional characterization of RNA editing in mitochondria. Sci Bull (Beijing) 2017; 62:820-830. [PMID: 36659315 DOI: 10.1016/j.scib.2017.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/09/2017] [Accepted: 05/16/2017] [Indexed: 01/21/2023]
Abstract
RNA editing was first discovered in mitochondrial RNA molecular. However, whether adenosine-to-inosine (A-to-I) RNA editing has functions in nuclear genes involved in mitochondria remains elusive. Here, we retrieved 707,246 A-to-I RNA editing sites in Macaca mulatta leveraging massive transcriptomes of 30 different tissues and genomes of nine tissues, together with the reported data, and found that A-to-I RNA editing occurred frequently in nuclear genes that have functions in mitochondria. The mitochondrial structure, the level of ATP production, and the expression of some key genes involved in mitochondrial function were dysregulated after knocking down the expression of ADAR1 and ADAR2, the key genes encoding the enzyme responsible for RNA editing. When investigating dynamic changes of RNA editing during brain development, an amino-acid-changing RNA editing site (I234/V) in MFN1, a mediator of mitochondrial fusion, was identified to be significantly correlated with age, and could influence the function of MFN1. When studying transcriptomes of brain disorder, we found that dysregulated RNA editing sites in autism were also enriched within genes having mitochondrial functions. These data indicated that RNA editing had a significant function in mitochondria via their influence on nuclear genes.
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Affiliation(s)
- Ling-Qun Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Hui Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - He-Jiang Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Die Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Lin-Lin Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Zheng-Bo Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xin-Tian Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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Jiang Q, Crews LA, Holm F, Jamieson CHM. RNA editing-dependent epitranscriptome diversity in cancer stem cells. Nat Rev Cancer 2017; 17:381-392. [PMID: 28416802 PMCID: PMC5665169 DOI: 10.1038/nrc.2017.23] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer stem cells (CSCs) can regenerate all facets of a tumour as a result of their stem cell-like capacity to self-renew, survive and become dormant in protective microenvironments. CSCs evolve during tumour progression in a manner that conforms to Charles Darwin's principle of natural selection. Although somatic DNA mutations and epigenetic alterations promote evolution, post-transcriptional RNA modifications together with RNA binding protein activity (the 'epitranscriptome') might also contribute to clonal evolution through dynamic determination of RNA function and gene expression diversity in response to environmental stimuli. Deregulation of these epitranscriptomic events contributes to CSC generation and maintenance, which governs cancer progression and drug resistance. In this Review, we discuss the role of malignant RNA processing in CSC generation and maintenance, including mechanisms of RNA methylation, RNA editing and RNA splicing, and the functional consequences of their aberrant regulation in human malignancies. Finally, we highlight the potential of these events as novel CSC biomarkers as well as therapeutic targets.
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Affiliation(s)
- Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Leslie A Crews
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Frida Holm
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, USA
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31
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Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM. Precancer Atlas to Drive Precision Prevention Trials. Cancer Res 2017; 77:1510-1541. [PMID: 28373404 PMCID: PMC6681830 DOI: 10.1158/0008-5472.can-16-2346] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 02/07/2023]
Abstract
Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA - an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510-41. ©2017 AACR.
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Affiliation(s)
- Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ludmil Alexandrov
- Theoretical Division, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Rafael Bejar
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Olivera J Finn
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Madhav Dhodapkar
- Department of Hematology and Immunology, Yale Cancer Center, New Haven, Connecticut
| | - Neil E Kay
- Department of Hematology, Mayo Clinic Hospital, Rochester, Minnesota
| | - Esteban Braggio
- Department of Hematology, Mayo Clinic Hospital, Phoenix, Arizona
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah A Mazzilli
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Timothy R Rebbeck
- Division of Hematology and Oncology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor E Velculescu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
- Department of Pathology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Mary L Disis
- Department of Medicine, Center for Translational Medicine in Women's Health, University of Washington, Seattle, Washington
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott M Lippman
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California.
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32
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Chan THM, Qamra A, Tan KT, Guo J, Yang H, Qi L, Lin JS, Ng VHE, Song Y, Hong H, Tay ST, Liu Y, Lee J, Rha SY, Zhu F, So JBY, Teh BT, Yeoh KG, Rozen S, Tenen DG, Tan P, Chen L. ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer. Gastroenterology 2016; 151:637-650.e10. [PMID: 27373511 PMCID: PMC8286172 DOI: 10.1053/j.gastro.2016.06.043] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUD & AIMS Gastric cancer (GC) is the third leading cause of global cancer mortality. Adenosine-to-inosine RNA editing is a recently described novel epigenetic mechanism involving sequence alterations at the RNA but not DNA level, primarily mediated by ADAR (adenosine deaminase that act on RNA) enzymes. Emerging evidence suggests a role for RNA editing and ADARs in cancer, however, the relationship between RNA editing and GC development and progression remains unknown. METHODS In this study, we leveraged on the next-generation sequencing transcriptomics to demarcate the GC RNA editing landscape and the role of ADARs in this deadly malignancy. RESULTS Relative to normal gastric tissues, almost all GCs displayed a clear RNA misediting phenotype with ADAR1/2 dysregulation arising from the genomic gain and loss of the ADAR1 and ADAR2 gene in primary GCs, respectively. Clinically, patients with GCs exhibiting ADAR1/2 imbalance demonstrated extremely poor prognoses in multiple independent cohorts. Functionally, we demonstrate in vitro and in vivo that ADAR-mediated RNA misediting is closely associated with GC pathogenesis, with ADAR1 and ADAR2 playing reciprocal oncogenic and tumor suppressive roles through their catalytic deaminase domains, respectively. Using an exemplary target gene PODXL (podocalyxin-like), we demonstrate that the ADAR2-regulated recoding editing at codon 241 (His to Arg) confers a loss-of-function phenotype that neutralizes the tumorigenic ability of the unedited PODXL. CONCLUSIONS Our study highlights a major role for RNA editing in GC disease and progression, an observation potentially missed by previous next-generation sequencing analyses of GC focused on DNA alterations alone. Our findings also suggest new GC therapeutic opportunities through ADAR1 enzymatic inhibition or the potential restoration of ADAR2 activity.
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Affiliation(s)
- Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Aditi Qamra
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kar Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jing Guo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lihua Qi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jaymie Siqi Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Huiqi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore
| | - Yujing Liu
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Singapore–Massachusetts Institute of Technology Alliance, Singapore
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sun Yong Rha
- Yonsei Cancer Center, Seodaemun-gu, Seoul, South Korea
| | - Feng Zhu
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jimmy Bok Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bin Tean Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore,Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Department of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Steve Rozen
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Centre for Computational Biology, Duke–National University of Singapore Graduate Medical School, Singapore
| | - Daniel G. Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore,Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore; Genome Institute of Singapore, Singapore.
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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33
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Zipeto MA, Court AC, Sadarangani A, Delos Santos NP, Balaian L, Chun HJ, Pineda G, Morris SR, Mason CN, Geron I, Barrett C, Goff DJ, Wall R, Pellecchia M, Minden M, Frazer KA, Marra MA, Crews LA, Jiang Q, Jamieson CHM. ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis. Cell Stem Cell 2016; 19:177-191. [PMID: 27292188 PMCID: PMC4975616 DOI: 10.1016/j.stem.2016.05.004] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 04/12/2016] [Accepted: 05/06/2016] [Indexed: 12/17/2022]
Abstract
Post-transcriptional adenosine-to-inosine RNA editing mediated by adenosine deaminase acting on RNA1 (ADAR1) promotes cancer progression and therapeutic resistance. However, ADAR1 editase-dependent mechanisms governing leukemia stem cell (LSC) generation have not been elucidated. In blast crisis chronic myeloid leukemia (BC CML), we show that increased JAK2 signaling and BCR-ABL1 amplification activate ADAR1. In a humanized BC CML mouse model, combined JAK2 and BCR-ABL1 inhibition prevents LSC self-renewal commensurate with ADAR1 downregulation. Lentiviral ADAR1 wild-type, but not an editing-defective ADAR1(E912A) mutant, induces self-renewal gene expression and impairs biogenesis of stem cell regulatory let-7 microRNAs. Combined RNA sequencing, qRT-PCR, CLIP-ADAR1, and pri-let-7 mutagenesis data suggest that ADAR1 promotes LSC generation via let-7 pri-microRNA editing and LIN28B upregulation. A small-molecule tool compound antagonizes ADAR1's effect on LSC self-renewal in stromal co-cultures and restores let-7 biogenesis. Thus, ADAR1 activation represents a unique therapeutic vulnerability in LSCs with active JAK2 signaling.
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Affiliation(s)
- Maria Anna Zipeto
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angela C Court
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anil Sadarangani
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathaniel P Delos Santos
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Larisa Balaian
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hye-Jung Chun
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Gabriel Pineda
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sheldon R Morris
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cayla N Mason
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ifat Geron
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christian Barrett
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel J Goff
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Russell Wall
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maurizio Pellecchia
- School of Medicine, University of California Riverside, Riverside, CA 92521, USA
| | - Mark Minden
- Princess Margaret Hospital, Toronto, ON M5G 2M9, Canada
| | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Leslie A Crews
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Patil KM, Chen G. Recognition of RNA Sequence and Structure by Duplex and Triplex Formation: Targeting miRNA and Pre-miRNA. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-34175-0_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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35
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ZHANG XIUJUAN, WU CHANGLI, XIONG WEI, CHEN CHUNLING, LI RONG, ZHOU GUANGJI. Knockdown of p54nrb inhibits migration, invasion and TNF-α release of human acute monocytic leukemia THP1 cells. Oncol Rep 2016; 35:3742-8. [DOI: 10.3892/or.2016.4756] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/22/2016] [Indexed: 11/06/2022] Open
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36
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Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2015; 6:391-6. [PMID: 26656153 PMCID: PMC4751558 DOI: 10.1534/g3.115.024471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
RNA editing usually affects only a fraction of expressed transcripts and there is a vast amount of variation in editing levels of ADAR (adenosine deaminase, RNA-specific) targets. Here we explore natural genetic variation affecting editing levels of particular sites in 81 natural strains of Drosophila melanogaster. The analysis of associations between editing levels and single-nucleotide polymorphisms allows us to map putative cis-regulatory regions affecting editing of 16 A-to-I editing sites (cis-RNA editing quantitative trait loci or cis-edQTLs, P < 10(-8)). The observed changes in editing levels are validated by independent molecular technique. All identified regulatory variants are located in close proximity of modulated editing sites. Moreover, colocalized editing sites are often regulated by same loci. Similar to expression and splicing QTL studies, the characterization of edQTLs will greatly expand our understanding of cis-regulatory evolution of gene expression.
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37
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Karpova MA, Karpov DS, Ivanov MV, Pyatnitskiy MA, Chernobrovkin AL, Lobas AA, Lisitsa AV, Archakov AI, Gorshkov MV, Moshkovskii SA. Exome-driven characterization of the cancer cell lines at the proteome level: the NCI-60 case study. J Proteome Res 2014; 13:5551-60. [PMID: 25333775 DOI: 10.1021/pr500531x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cancer genome deviates significantly from the reference human genome, and thus a search against standard genome databases in cancer cell proteomics fails to identify cancer-specific protein variants. The goal of this Article is to combine high-throughput exome data [Abaan et al. Cancer Res. 2013] and shotgun proteomics analysis [Modhaddas Gholami et al. Cell Rep. 2013] for cancer cell lines from NCI-60 panel to demonstrate further that the cell lines can be effectively recognized using identified variant peptides. To achieve this goal, we generated a database containing mutant protein sequences of NCI-60 panel of cell lines. The proteome data were searched using Mascot and X!Tandem search engines against databases of both reference and mutant protein sequences. The identification quality was further controlled by calculating a fraction of variant peptides encoded by the own exome sequence for each cell line. We found that up to 92.2% peptides identified by both search engines are encoded by the own exome. Further, we used the identified variant peptides for cell line recognition. The results of the study demonstrate that proteome data supported by exome sequence information can be effectively used for distinguishing between different types of cancer cell lines.
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Affiliation(s)
- Maria A Karpova
- Orekhovich Institute of Biomedical Chemistry , 119121, Moscow, Russia
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38
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Snider NT, Altshuler PJ, Wan S, Welling TH, Cavalcoli J, Omary MB. Alternative splicing of human NT5E in cirrhosis and hepatocellular carcinoma produces a negative regulator of ecto-5'-nucleotidase (CD73). Mol Biol Cell 2014; 25:4024-33. [PMID: 25298403 PMCID: PMC4263446 DOI: 10.1091/mbc.e14-06-1167] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing of human NT5E generates CD73S, an endoplasmic reticulum–associated and dimerization-deficient glycoprotein that lacks enzymatic activity. CD73S functions as a negative regulator of canonical CD73 by promoting its proteasomal degradation, which may have significance in chronic liver disease and liver cancer. Ecto-5′-nucleotidase (CD73), encoded by NT5E, is the major enzymatic source of extracellular adenosine. CD73 controls numerous pathophysiological responses and is a potential disease target, but its regulation is poorly understood. We examined NT5E regulation by alternative splicing. Genomic database analysis of human transcripts led us to identify NT5E-2, a novel splice variant that was expressed at low abundance in normal human tissues but was significantly up-regulated in cirrhosis and hepatocellular carcinoma (HCC). NT5E-2 encodes a shorter CD73 isoform we named CD73S. The presence of CD73S protein, which lacks 50 amino acids, was detected in HCC using an isoform-specific antibody. A noncanonical mouse mRNA, similar to human CD73S, was observed, but the corresponding protein was undetectable. The two human isoforms exhibited functional differences, such that ectopic expression of canonical CD73 (CD73L) in human HepG2 cells was associated with decreased expression of the proliferation marker Ki67, whereas CD73S expression did not have an effect on Ki67 expression. CD73S was glycosylated, catalytically inactive, unable to dimerize, and complexed intracellularly with the endoplasmic reticulum chaperone calnexin. Furthermore, CD73S complexed with CD73L and promoted proteasome-dependent CD73L degradation. The findings reveal species-specific CD73 regulation, with potential significance to cancer, fibrosis, and other diseases characterized by changes in CD73 expression and function.
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Affiliation(s)
- Natasha T Snider
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
| | - Peter J Altshuler
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
| | - Shanshan Wan
- Departments of Surgery, University of Michigan, Ann Arbor, MI 48109
| | | | - James Cavalcoli
- Departments of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
| | - M Bishr Omary
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109 Departments of Medicine, University of Michigan, Ann Arbor, MI 48109
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