101
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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: 40] [Impact Index Per Article: 5.7] [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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102
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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: 5.9] [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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103
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Kung CP, Maggi LB, Weber JD. The Role of RNA Editing in Cancer Development and Metabolic Disorders. Front Endocrinol (Lausanne) 2018; 9:762. [PMID: 30619092 PMCID: PMC6305585 DOI: 10.3389/fendo.2018.00762] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/03/2018] [Indexed: 12/26/2022] Open
Abstract
Numerous human diseases arise from alterations of genetic information, most notably DNA mutations. Thought to be merely the intermediate between DNA and protein, changes in RNA sequence were an afterthought until the discovery of RNA editing 30 years ago. RNA editing alters RNA sequence without altering the sequence or integrity of genomic DNA. The most common RNA editing events are A-to-I changes mediated by adenosine deaminase acting on RNA (ADAR), and C-to-U editing mediated by apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1). Both A-to-I and C-to-U editing were first identified in the context of embryonic development and physiological homeostasis. The role of RNA editing in human disease has only recently started to be understood. In this review, the impact of RNA editing on the development of cancer and metabolic disorders will be examined. Distinctive functions of each RNA editase that regulate either A-to-I or C-to-U editing will be highlighted in addition to pointing out important regulatory mechanisms governing these processes. The potential of developing novel therapeutic approaches through intervention of RNA editing will be explored. As the role of RNA editing in human disease is elucidated, the clinical utility of RNA editing targeted therapies will be needed. This review aims to serve as a bridge of information between past findings and future directions of RNA editing in the context of cancer and metabolic disease.
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Affiliation(s)
- Che-Pei Kung
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Leonard B. Maggi
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Jason D. Weber
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
- Siteman Cancer Center, Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, United States
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104
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Peng L, Zhang H, Su Y, Shen Q, Du C, Xie H, Li H, Yan J, Shen Z, Jiang W, Xia Y, Xu X, Tang W. Lipopolysaccharide enhances ADAR2 which drives Hirschsprung's disease by impairing miR-142-3p biogenesis. J Cell Mol Med 2018; 22:4045-4055. [PMID: 29956457 PMCID: PMC6111854 DOI: 10.1111/jcmm.13652] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/19/2018] [Indexed: 01/04/2023] Open
Abstract
Researches over the past decade suggest that lipopolysaccharide is a dominant driver of gastrointestinal motility and could damage the enteric neuron of rat or porcine. However, it remains poorly defined whether LPS participates in Hirschsprung's disease (HSCR). Here, we discovered that LPS increased in HSCR tissues. Furthermore, LPS treatment suppressed the proliferation and differentiation of neural precursor cells (NPCs) or proliferation and migration of human 293T cells. ADAR2 (adenosine deaminase acting on RNA2)-mediated post-transcriptional adenosine-to-inosine RNA editing promotes cancer progression. We show that increased LPS activates ADAR2 and subsequently regulates the A-to-I RNA editing which suppresses the miR-142 expression. RNA sequencing combined with qRT-PCR suggested that ADAR2 restrain cell migration and proliferation via pri-miR-142 editing and STAU1 up-regulation. In conclusion, the findings illustrate that LPS participates in HSCR through the LPS-ADAR2-miR-142-STAU1 axis.
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Affiliation(s)
- Lei Peng
- Department of GastroenterologyFirst Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Hua Zhang
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
- Ministry of EducationKey Laboratory of Modern ToxicologyNanjing Medical UniversityNanjingChina
| | - Yang Su
- Department of Hepatobiliary & Pancreatic SurgeryThe Affiliated Huaian No.1 Peoples Hospital of Nanjing Medical UniversityHuaianChina
| | - Qiyang Shen
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
- Ministry of EducationKey Laboratory of Modern ToxicologyNanjing Medical UniversityNanjingChina
| | - Chunxia Du
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
- Ministry of EducationKey Laboratory of Modern ToxicologyNanjing Medical UniversityNanjingChina
| | - Hua Xie
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
- Ministry of EducationKey Laboratory of Modern ToxicologyNanjing Medical UniversityNanjingChina
| | - Hongxing Li
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
- Ministry of EducationKey Laboratory of Modern ToxicologyNanjing Medical UniversityNanjingChina
| | - Jin Yan
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
| | - Ziyang Shen
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
- Ministry of EducationKey Laboratory of Modern ToxicologyNanjing Medical UniversityNanjingChina
| | - Weiwei Jiang
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
| | - Yankai Xia
- Ministry of EducationKey Laboratory of Modern ToxicologyNanjing Medical UniversityNanjingChina
- State Key Laboratory of Reproductive MedicineInstitute of ToxicologySchool of Public HealthNanjing Medical UniversityNanjingChina
| | - Xiaoqun Xu
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
| | - Weibing Tang
- Department of Pediatric SurgeryChildren's Hospital of Nanjing Medical UniversityNanjingChina
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105
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Huang LY, Wang X, Cui XF, Li H, Zhao J, Wu CC, Min L, Zhou Z, Wan L, Wang YP, Zhang C, Gao WQ, Sun Y, Han ZG. IRTKS is correlated with progression and survival time of patients with gastric cancer. Gut 2018. [PMID: 28647685 DOI: 10.1136/gutjnl-2016-313478] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVES IRTKS functions as a novel regulator of tumour suppressor p53; however, the role of IRTKS in pathogenesis of gastric cancer is unclear. DESIGN We used immunohistochemistry to detect IRTKS levels in 527 human gastric cancer specimens. We generated both IRTKS-deficient and p53-deficient mice to observe survival time of these mice and to isolate mouse embryonic fibroblasts (MEFs) for evaluating in vivo tumorigenicity. Co-immunoprecipitation was used to study the interaction among p53, MDM2 and IRTKS, as well as the ubiquitination of p53. RESULTS IRTKS was significantly overexpressed in human gastric cancer, which was conversely associated with wild-type p53 expression. Among patients with wild-type p53 (n=206), those with high IRTKS expression (n=141) had a shorter survival time than those with low IRTKS (n=65) (p=0.0153). Heterozygous p53+/- mice with IRTKS deficiency exhibited significantly delayed tumorigenesis and an extended tumour-free survival time. p53+/- MEFs without IRTKS exhibited attenuated in vivo tumorigenicity. IRTKS depletion upregulated p53 and its target genes, such as BAX and p21. Intriguingly, IRTKS overexpression promoted p53 ubiquitination and degradation in MEFs and gastric cancer cells. Under DNA damage conditions, IRTKS was phosphorylated at Ser331 by the activated Chk2 kinase and then dissociated from p53, along with the p53-specific E3 ubiquitin ligase MDM2, resulting in attenuated p53 ubiquitination and degradation. CONCLUSION IRTKS overexpression is negatively correlated with progression and overall survival time of patients with gastric cancer with wild-type p53 through promotion of p53 degradation via the ubiquitin/proteasome pathway.
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Affiliation(s)
- Li-Yu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xuefei Wang
- Department of General Surgery, Zhongshan Hospital, General Surgery Research Institute, Fudan University, Shanghai, China
| | - Xiao-Fang Cui
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - He Li
- Department of General Surgery, Zhongshan Hospital, General Surgery Research Institute, Fudan University, Shanghai, China
| | - Junjie Zhao
- Department of General Surgery, Zhongshan Hospital, General Surgery Research Institute, Fudan University, Shanghai, China
| | - Chong-Chao Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lingqiang Min
- Department of General Surgery, Zhongshan Hospital, General Surgery Research Institute, Fudan University, Shanghai, China
| | - Zhicheng Zhou
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Lixin Wan
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, USA
| | - Yu-Ping Wang
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, USA.,Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medical College of Cornell University, New York, USA
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yihong Sun
- Department of General Surgery, Zhongshan Hospital, General Surgery Research Institute, Fudan University, Shanghai, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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106
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Shi L, Yang L, Wu Z, Xu W, Song J, Guan W. Adenosine signaling: Next checkpoint for gastric cancer immunotherapy? Int Immunopharmacol 2018; 63:58-65. [PMID: 30075429 DOI: 10.1016/j.intimp.2018.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/21/2018] [Indexed: 12/11/2022]
Abstract
Adenosine (ADO), generated by the ectonucleotidase CD39 and CD73 from ATP, interacts with its specific G protein-coupled receptors, which can impair anti-tumor immune responses inhibiting the infiltration and function of CD8+ T cell and natural killer cell. Recent studies have also identified that ADO pathway plays a critical role in tumor immune surveillance, especially for some non-solid cancers. In addition, although immune checkpoint therapy targeting ADO pathway in gastric cancer is still in an early phase, encouraging results have come out from some drugs targeting ADO pathway. Therefore, target ADO signaling may be a new promising strategy to treat gastric cancer. In this review, we summarized recent works on the role of ADO in cancer immunotherapy and also discussed relative mechanisms underlying the function of ADO signaling in cancer immune responses.
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Affiliation(s)
- Linsen Shi
- Departments of Gastrointestinal surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, PR China; The Affiliated Drum Tower Clinical College of NanJing Medical University, Nanjing, PR China
| | - Lin Yang
- XuZhou Medical University, Xuzhou, PR China
| | - Zhaoyin Wu
- XuZhou Medical University, Xuzhou, PR China
| | - Wei Xu
- Departments of Gastrointestinal surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, PR China
| | - Jun Song
- Departments of Gastrointestinal surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, PR China.
| | - Wenxian Guan
- Departments of Gastrointestinal surgery, the Affiliated Drum Tower hospital of NanJing Medical University, Nanjing, PR China.
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107
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Cho CJ, Jung J, Jiang L, Lee EJ, Kim DS, Kim BS, Kim HS, Jung HY, Song HJ, Hwang SW, Park Y, Jung MK, Pack CG, Myung SJ, Chang S. Combinatory RNA-Sequencing Analyses Reveal a Dual Mode of Gene Regulation by ADAR1 in Gastric Cancer. Dig Dis Sci 2018; 63:1835-1850. [PMID: 29691780 DOI: 10.1007/s10620-018-5081-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/16/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND Adenosine deaminase acting on RNA 1 (ADAR1) is known to mediate deamination of adenosine-to-inosine through binding to double-stranded RNA, the phenomenon known as RNA editing. Currently, the function of ADAR1 in gastric cancer is unclear. AIMS This study was aimed at investigating RNA editing-dependent and editing-independent functions of ADAR1 in gastric cancer, especially focusing on its influence on editing of 3' untranslated regions (UTRs) and subsequent changes in expression of messenger RNAs (mRNAs) as well as microRNAs (miRNAs). METHODS RNA-sequencing and small RNA-sequencing were performed on AGS and MKN-45 cells with a stable ADAR1 knockdown. Changed frequencies of editing and mRNA and miRNA expression were then identified by bioinformatic analyses. Targets of RNA editing were further validated in patients' samples. RESULTS In the Alu region of both gastric cell lines, editing was most commonly of the A-to-I type in 3'-UTR or intron. mRNA and protein levels of PHACTR4 increased in ADAR1 knockdown cells, because of the loss of seed sequences in 3'-UTR of PHACTR4 mRNA that are required for miRNA-196a-3p binding. Immunohistochemical analyses of tumor and paired normal samples from 16 gastric cancer patients showed that ADAR1 expression was higher in tumors than in normal tissues and inversely correlated with PHACTR4 staining. On the other hand, decreased miRNA-148a-3p expression in ADAR1 knockdown cells led to increased mRNA and protein expression of NFYA, demonstrating ADAR1's editing-independent function. CONCLUSIONS ADAR1 regulates post-transcriptional gene expression in gastric cancer through both RNA editing-dependent and editing-independent mechanisms.
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Affiliation(s)
- Charles J Cho
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Jaeeun Jung
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Lushang Jiang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Eun Ji Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Dae-Soo Kim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Byung Sik Kim
- Department of Gastric Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Hee Sung Kim
- Department of Gastric Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Hwoon-Yong Jung
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Ho-June Song
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Sung Wook Hwang
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Yangsoon Park
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Min Kyo Jung
- Department of Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Chan Gi Pack
- Department of Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Seung-Jae Myung
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea. .,Department of Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea. .,Department of Gastroenterology and Convergence Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea.
| | - Suhwan Chang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Korea.
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108
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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: 93] [Impact Index Per Article: 13.3] [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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109
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Tusup M, Kundig T, Pascolo S. Epitranscriptomics of cancer. World J Clin Oncol 2018; 9:42-55. [PMID: 29900123 PMCID: PMC5997933 DOI: 10.5306/wjco.v9.i3.42] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/18/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
The functional impact of modifications of cellular RNAs, including mRNAs, miRNAs and lncRNAs, is a field of intense study. The role of such modifications in cancer has started to be elucidated. Diverse and sometimes opposite effects of RNA modifications have been reported. Some RNA modifications promote, while others decrease the growth and invasiveness of cancer. The present manuscript reviews the current knowledge on the potential impacts of N6-Methyladenosine, Pseudouridine, Inosine, 2’O-methylation or methylcytidine in cancer’s RNA. It also highlights the remaining questions and provides hints on research avenues and potential therapeutic applications, whereby modulating dynamic RNA modifications may be a new method to treat cancer.
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Affiliation(s)
- Marina Tusup
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
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110
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Shevchenko G, Morris KV. All I's on the RADAR: role of ADAR in gene regulation. FEBS Lett 2018; 592:2860-2873. [PMID: 29770436 DOI: 10.1002/1873-3468.13093] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/26/2018] [Accepted: 05/05/2018] [Indexed: 12/12/2022]
Abstract
Adenosine to inosine (A-to-I) editing is the most abundant form of RNA modification in mammalian cells, which is catalyzed by adenosine deaminase acting on the double-stranded RNA (ADAR) protein family. A-to-I editing is currently known to be involved in the regulation of the immune system, RNA splicing, protein recoding, microRNA biogenesis, and formation of heterochromatin. Editing occurs within regions of double-stranded RNA, particularly within inverted Alu repeats, and is associated with many diseases including cancer, neurological disorders, and metabolic syndromes. However, the significance of RNA editing in a large portion of the transcriptome remains unknown. Here, we review the current knowledge about the prevalence and function of A-to-I editing by the ADAR protein family, focusing on its role in the regulation of gene expression. Furthermore, RNA editing-independent regulation of cellular processes by ADAR and the putative role(s) of this process in gene regulation will be discussed.
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Affiliation(s)
- Galina Shevchenko
- Hematological Malignancy and Stem Cell Transplantation Institute, Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - Kevin V Morris
- Hematological Malignancy and Stem Cell Transplantation Institute, Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
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111
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Peng X, Xu X, Wang Y, Hawke DH, Yu S, Han L, Zhou Z, Mojumdar K, Jeong KJ, Labrie M, Tsang YH, Zhang M, Lu Y, Hwu P, Scott KL, Liang H, Mills GB. A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer. Cancer Cell 2018; 33:817-828.e7. [PMID: 29706454 PMCID: PMC5953833 DOI: 10.1016/j.ccell.2018.03.026] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/05/2018] [Accepted: 03/26/2018] [Indexed: 01/30/2023]
Abstract
Adenosine (A) to inosine (I) RNA editing introduces many nucleotide changes in cancer transcriptomes. However, due to the complexity of post-transcriptional regulation, the contribution of RNA editing to proteomic diversity in human cancers remains unclear. Here, we performed an integrated analysis of TCGA genomic data and CPTAC proteomic data. Despite limited site diversity, we demonstrate that A-to-I RNA editing contributes to proteomic diversity in breast cancer through changes in amino acid sequences. We validate the presence of editing events at both RNA and protein levels. The edited COPA protein increases proliferation, migration, and invasion of cancer cells in vitro. Our study suggests an important contribution of A-to-I RNA editing to protein diversity in cancer and highlights its translational potential.
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Affiliation(s)
- Xinxin Peng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoyan Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Pathophysiology, College of Basic Medicine, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - David H Hawke
- The Proteomics and Metabolomics Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shuangxing Yu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Zhicheng Zhou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kamalika Mojumdar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kang Jin Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marilyne Labrie
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Minying Zhang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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112
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Accurate identification of RNA editing sites from primitive sequence with deep neural networks. Sci Rep 2018; 8:6005. [PMID: 29662087 PMCID: PMC5902551 DOI: 10.1038/s41598-018-24298-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/27/2018] [Indexed: 12/18/2022] Open
Abstract
RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations. DeepRed achieved 98.1% and 97.9% area under the curve (AUC) in training and test sets, respectively. We further validated DeepRed using experimentally verified U87 cell RNA-seq data, achieving 97.9% positive predictive value (PPV). We demonstrated that DeepRed offers better prediction accuracy and computational efficiency than current methods with large-scale, mass RNA-seq data. We used DeepRed to assess the impact of multiple factors on editing identification with RNA-seq data from the Association of Biomolecular Resource Facilities and Sequencing Quality Control projects. We explored developmental RNA editing pattern changes during human early embryogenesis and evolutionary patterns in Drosophila species and the primate lineage using DeepRed. Our work illustrates DeepRed’s state-of-the-art performance; it may decipher the hidden principles behind RNA editing, making editing detection convenient and effective.
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113
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Dou N, Yu S, Ye X, Yang D, Li Y, Gao Y. Aberrant overexpression of ADAR1 promotes gastric cancer progression by activating mTOR/p70S6K signaling. Oncotarget 2018; 7:86161-86173. [PMID: 27863387 PMCID: PMC5349904 DOI: 10.18632/oncotarget.13354] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/08/2016] [Indexed: 12/24/2022] Open
Abstract
ADAR1, one of adenosine deaminases acting on RNA, modulates RNA transcripts through converting adenosine (A) to inosine (I) by deamination. Emerging evidence has implicated that ADAR1 plays an important role in a few of human cancers, however, its expression and physiological significance in gastric cancer remain undefined. In the present study, we demonstrated that ADAR1 was frequently overexpressed in gastric cancer samples by quantitative real-time PCR analysis. In a gastric cancer tissue microarray, ADAR1 staining was closely correlated with tumor stage (P < 0.001) and N classification (P < 0.001). Functional analysis indicated that ADAR1 overexpression promoted cell proliferation and migration in vitro, whereas ADAR1 knockdown resulted in an opposite phenotypes. Furthermore, ADAR1 knockdown also inhibited tumorigenicity and lung metastasis potential of gastric cancer cells in nude mice models. Mechanistically, ADAR1 expression had a significant effect on phosphorylation level of mTOR, p70S kinase, and S6 ribosomal protein, implying its involvement in the regulation of mTOR signaling pathway. We conclude that ADAR1 contributes to gastric cancer development and progression via activating mTOR/p70S6K/S6 ribosomal protein signaling axis. Our findings suggest that ADAR1 may be a valuable biomarker for GC diagnosis and prognosis and may represent a new novel therapeutic opportunities.
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Affiliation(s)
- Ning Dou
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Shijun Yu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaojuan Ye
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Dong Yang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
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114
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Verma R, Sharma PC. Next generation sequencing-based emerging trends in molecular biology of gastric cancer. Am J Cancer Res 2018; 8:207-225. [PMID: 29511593 PMCID: PMC5835690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer related mortality in the world. Being asymptomatic in nature till advanced stage, diagnosis of gastric cancer becomes difficult in early stages of the disease. The onset and progression of gastric cancer has been attributed to multiple factors including genetic alterations, epigenetic modifications, Helicobacter pylori and Epstein-Barr Virus (EBV) infection, and dietary habits. Next Generation Sequencing (NGS) based approaches viz. Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-Seq, and targeted sequencing have expanded the knowledge base of molecular pathogenesis of gastric cancer. In this review, we highlight recent NGS-based advances covering various genetic alterations (Microsatellite Instability, Single Nucleotide Variations, and Copy Number Variations), epigenetic changes (DNA methylation, histone modification, microRNAs) and differential gene expression during gastric tumorigenesis. We also briefly discuss the current and future potential biomarkers, drugs and therapeutic approaches available for the management of gastric cancer.
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Affiliation(s)
- Renu Verma
- University School of Biotechnology, Guru Gobind Singh Indraprastha UniversityNew Delhi 110078, India
| | - Prakash C Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha UniversityNew Delhi 110078, India
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115
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Regulatory RNA Editing Sites in Cancer: Prediction and Beyond. EBioMedicine 2017; 27:7-8. [PMID: 29273357 PMCID: PMC5828464 DOI: 10.1016/j.ebiom.2017.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 11/22/2022] Open
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116
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Sharpnack MF, Chen B, Aran D, Kosti I, Sharpnack DD, Carbone DP, Mallick P, Huang K. Global Transcriptome Analysis of RNA Abundance Regulation by ADAR in Lung Adenocarcinoma. EBioMedicine 2017; 27:167-175. [PMID: 29273356 PMCID: PMC5828651 DOI: 10.1016/j.ebiom.2017.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/27/2017] [Accepted: 12/05/2017] [Indexed: 01/13/2023] Open
Abstract
Despite tremendous advances in targeted therapies against lung adenocarcinoma, the majority of patients do not benefit from personalized treatments. A deeper understanding of potential therapeutic targets is crucial to increase the survival of patients. One promising target, ADAR, is amplified in 13% of lung adenocarcinomas and in-vitro studies have demonstrated the potential of its therapeutic inhibition to inhibit tumor growth. ADAR edits millions of adenosines to inosines within the transcriptome, and while previous studies of ADAR in cancer have solely focused on protein-coding edits, > 99% of edits occur in non-protein coding regions. Here, we develop a pipeline to discover the regulatory potential of RNA editing sites across the entire transcriptome and apply it to lung adenocarcinoma tumors from The Cancer Genome Atlas. This method predicts that 1413 genes contain regulatory edits, predominantly in non-coding regions. Genes with the largest numbers of regulatory edits are enriched in both apoptotic and innate immune pathways, providing a link between these known functions of ADAR and its role in cancer. We further show that despite a positive association between ADAR RNA expression and apoptotic and immune pathways, ADAR copy number is negatively associated with apoptosis and several immune cell types' signatures. ADAR potentially regulates the mRNA abundance of thousands of genes. Editing of the APOL1 3′ UTR is associated with its upregulation and patient poor overall survival. ADAR-regulated genes are enriched for apoptosis and immune pathways.
Lung cancer is the most deadly cancer globally and current targeted treatments only benefit a minority of patients. Inhibiting the ADAR oncogene has shown promising preclinical results; however, little is known about ADAR's functions in cancer. We investigate a key function of ADAR, mRNA regulation via RNA editing, and provide evidence that it is linked to tumor immunity and cell death in human lung adenocarcinoma. Our results provide a motivation to explore combination immunotherapies that include ADAR inhibition.
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Affiliation(s)
- Michael F Sharpnack
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Bin Chen
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Dvir Aran
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Idit Kosti
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States
| | | | - David P Carbone
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Parag Mallick
- Canary Center for Cancer Early Detection, Stanford University, Palo Alto, CA, United States.
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States; Current Address: Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.
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117
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Fritzell K, Xu LD, Lagergren J, Öhman M. ADARs and editing: The role of A-to-I RNA modification in cancer progression. Semin Cell Dev Biol 2017; 79:123-130. [PMID: 29146145 DOI: 10.1016/j.semcdb.2017.11.018] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/08/2017] [Accepted: 11/12/2017] [Indexed: 11/17/2022]
Abstract
Cancer arises when pathways that control cell functions such as proliferation and migration are dysregulated to such an extent that cells start to divide uncontrollably and eventually spread throughout the body, ultimately endangering the survival of an affected individual. It is well established that somatic mutations are important in cancer initiation and progression as well as in creation of tumor diversity. Now also modifications of the transcriptome are emerging as a significant force during the transition from normal cell to malignant tumor. Editing of adenosine (A) to inosine (I) in double-stranded RNA, catalyzed by adenosine deaminases acting on RNA (ADARs), is one dynamic modification that in a combinatorial manner can give rise to a very diverse transcriptome. Since the cell interprets inosine as guanosine (G), editing can result in non-synonymous codon changes in transcripts as well as yield alternative splicing, but also affect targeting and disrupt maturation of microRNA. ADAR editing is essential for survival in mammals but its dysregulation can lead to cancer. ADAR1 is for instance overexpressed in, e.g., lung cancer, liver cancer, esophageal cancer and chronic myoelogenous leukemia, which with few exceptions promotes cancer progression. In contrast, ADAR2 is lowly expressed in e.g. glioblastoma, where the lower levels of ADAR2 editing leads to malignant phenotypes. Altogether, RNA editing by the ADAR enzymes is a powerful regulatory mechanism during tumorigenesis. Depending on the cell type, cancer progression seems to mainly be induced by ADAR1 upregulation or ADAR2 downregulation, although in a few cases ADAR1 is instead downregulated. In this review, we discuss how aberrant editing of specific substrates contributes to malignancy.
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Affiliation(s)
- Kajsa Fritzell
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 106 91, Stockholm, Sweden
| | - Li-Di Xu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 106 91, Stockholm, Sweden
| | - Jens Lagergren
- School of Computer Science and Communication, Science for Life Laboratory (SciLifeLab), Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 106 91, Stockholm, Sweden.
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118
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The role of A-to-I RNA editing in cancer development. Curr Opin Genet Dev 2017; 48:51-56. [PMID: 29127844 DOI: 10.1016/j.gde.2017.10.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/10/2017] [Accepted: 10/13/2017] [Indexed: 01/11/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is the most common type of post-transcriptional nucleotide modification in humans, which is catalyzed in ADAR enzymes. Recent genomic studies have revealed thousands of altered RNA editing events in various cancer tissues, leading to diverse functional consequences. A critical role of individual A-to-I RNA editing events in cancer has been reported. Here, we review the current state of our knowledge on key A-to-I RNA editing events in coding and non-coding regions for their roles in cancer development and discuss their potential clinical utility. A better understanding of A-to-I RNA editing and its oncogenic mechanisms may facilitate the development of novel cancer therapeutic strategies.
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119
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Abstract
One of the most prevalent forms of post-transcritpional RNA modification is the conversion of adenosine nucleosides to inosine (A-to-I), mediated by the ADAR family of enzymes. The functional requirement and regulatory landscape for the majority of A-to-I editing events are, at present, uncertain. Recent studies have identified key in vivo functions of ADAR enzymes, informing our understanding of the biological importance of A-to-I editing. Large-scale studies have revealed how editing is regulated both in cis and in trans. This review will explore these recent studies and how they broaden our understanding of the functions and regulation of ADAR-mediated RNA editing.
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Affiliation(s)
- Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia. .,Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, 3065, Australia.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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120
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Wang C, Zou J, Ma X, Wang E, Peng G. Mechanisms and implications of ADAR-mediated RNA editing in cancer. Cancer Lett 2017; 411:27-34. [PMID: 28974449 DOI: 10.1016/j.canlet.2017.09.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/11/2022]
Abstract
Adenosine deaminases acting on RNA (ADARs) are enzymes that catalyze the conversion of adenosine (A) to inosine (I) in double-stranded RNAs. Inosine exhibits similar properties as guanosine. As a result, A-to-I editing has a great impact on edited RNAs, not only affecting the base pairing properties, but also altering codons after translation. A-to-I editing are known to mediate and diversify transcripts. However, the overall biological effect of ADARs are still largely unknown. Aberrant ADAR activity and editing dysregulation are present in a variety of cancers, including hepatocellular carcinoma, chronic myelogenous leukemia, glioblastoma and melanoma. ADAR-mediated A-to-I editing can influence uncontrolled nucleotide changes, resulting in susceptibility of cells to developmental defects and potential carcinogenicity. A deeper understanding of the biological function of ADARs may provide mechanistic insights in the development of new cancer therapy. Here, we discuss recent advances in research on ADAR in detail including the structure and function of ADARs, the biochemistry of ADAR-mediated RNA editing, and the relevance of ADAR proteins in cancer.
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Affiliation(s)
- Chen Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Zou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangyi Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Edward Wang
- OncoMed Pharmaceuticals, Redwood City, CA 94063, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA.
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121
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Zhou J, Huang H, Tong S, Huo R. Overexpression of long non-coding RNA cancer susceptibility 2 inhibits cell invasion and angiogenesis in gastric cancer. Mol Med Rep 2017; 16:5235-5240. [PMID: 28849111 PMCID: PMC5647078 DOI: 10.3892/mmr.2017.7233] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/13/2017] [Indexed: 12/22/2022] Open
Abstract
Increasing evidence has indicated that long non‑coding RNAs (lncRNAs) were aberrantly expressed and acted as key regulators in various types of disease, including cancer. lncRNA cancer susceptibility 2 (CASC2) has been found to be downregulated and acts as a tumor suppressor in various type of cancer, including gastric cancer (GC). However, the precise function of lncRNA CASC2 in GC remains unclear. In the present study, the expression level of lncRNA CASC2 in GC was investigated and the molecular mechanisms by which CASC2 acted as a tumor suppressor in this disease were elucidated. It was found that the expression level of lncRNA CASC2 was decreased, which correlated with TNM stages, vessel invasion, metastasis, and overall survival of patients with GC. Furthermore, overexpression of CASC2 inhibited the invasion and angiogenesis of GC cells. Thus, the present study indicated the important roles and underlying molecular mechanisms of lncRNA CASC2 on GC, and indicated that lncRNA CASC2 may present as a potential therapeutic target for the treatment of GC.
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Affiliation(s)
- Jianfeng Zhou
- Department of Clinical Medicine, Xiaogang Hospital, Ningbo, Zhejiang 315800, P.R. China
| | - Haiyan Huang
- Department of Clinical Medicine, Xiaogang Hospital, Ningbo, Zhejiang 315800, P.R. China
| | - Shijie Tong
- Department of Clinical Medicine, Xiaogang Hospital, Ningbo, Zhejiang 315800, P.R. China
| | - Rong Huo
- Department of Clinical Medicine, Xiaogang Hospital, Ningbo, Zhejiang 315800, P.R. China
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122
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Abstract
Gastric cancer is a deadly malignancy afflicting close to a million people worldwide. Patient survival is poor and largely due to late diagnosis and suboptimal therapies. Disease heterogeneity is a substantial obstacle, underscoring the need for precision treatment strategies. Studies have identified different subgroups of gastric cancer displaying not just genetic, but also distinct epigenetic hallmarks. Accumulating evidence suggests that epigenetic abnormalities in gastric cancer are not mere bystander events, but rather promote carcinogenesis through active mechanisms. Epigenetic aberrations, induced by pathogens such as Helicobacter pylori, are an early component of gastric carcinogenesis, probably preceding genetic abnormalities. This Review summarizes our current understanding of the gastric cancer epigenome, highlighting key advances in recent years in both tumours and pre-malignant lesions, made possible through targeted and genome-wide technologies. We focus on studies related to DNA methylation and histone modifications, linking these findings to potential therapeutic opportunities. Lessons learned from the gastric cancer epigenome might also prove relevant for other gastrointestinal cancers.
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Baysal BE, Sharma S, Hashemikhabir S, Janga SC. RNA Editing in Pathogenesis of Cancer. Cancer Res 2017; 77:3733-3739. [DOI: 10.1158/0008-5472.can-17-0520] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/27/2017] [Accepted: 05/22/2017] [Indexed: 11/16/2022]
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COL1A2 is a Novel Biomarker to Improve Clinical Prediction in Human Gastric Cancer: Integrating Bioinformatics and Meta-Analysis. Pathol Oncol Res 2017; 24:129-134. [DOI: 10.1007/s12253-017-0223-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/03/2017] [Indexed: 01/10/2023]
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ADAR1 and MicroRNA; A Hidden Crosstalk in Cancer. Int J Mol Sci 2017; 18:ijms18040799. [PMID: 28398248 PMCID: PMC5412383 DOI: 10.3390/ijms18040799] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 11/17/2022] Open
Abstract
The evolution of cancer cells is believed to be dependent on genetic or epigenetic alterations. However, this concept has recently been challenged by another mode of nucleotide alteration, RNA editing, which is frequently up-regulated in cancer. RNA editing is a biochemical process in which either Adenosine or Cytosine is deaminated by a group of RNA editing enzymes including ADAR (Adenosine deaminase; RNA specific) or APOBEC3B (Apolipoprotein B mRNA Editing Enzyme Catalytic Subunit 3B). The result of RNA editing is usually adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) transition, which can affect protein coding, RNA stability, splicing and microRNA-target interactions. The functional impact of these alterations is largely unclear and is a subject of extensive research. In the present review, we will specifically focus on the influence of ADARs on carcinogenesis via the regulation of microRNA processing and functioning. This follows a brief review of the current knowledge of properties of ADAR enzyme, RNA editing, and microRNA processing.
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Functions of the RNA Editing Enzyme ADAR1 and Their Relevance to Human Diseases. Genes (Basel) 2016; 7:genes7120129. [PMID: 27999332 PMCID: PMC5192505 DOI: 10.3390/genes7120129] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 12/17/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA (dsRNA). Among the three types of mammalian ADARs, ADAR1 has long been recognized as an essential enzyme for normal development. The interferon-inducible ADAR1p150 is involved in immune responses to both exogenous and endogenous triggers, whereas the functions of the constitutively expressed ADAR1p110 are variable. Recent findings that ADAR1 is involved in the recognition of self versus non-self dsRNA provide potential explanations for its links to hematopoiesis, type I interferonopathies, and viral infections. Editing in both coding and noncoding sequences results in diseases ranging from cancers to neurological abnormalities. Furthermore, editing of noncoding sequences, like microRNAs, can regulate protein expression, while editing of Alu sequences can affect translational efficiency and editing of proximal sequences. Novel identifications of long noncoding RNA and retrotransposons as editing targets further expand the effects of A-to-I editing. Besides editing, ADAR1 also interacts with other dsRNA-binding proteins in editing-independent manners. Elucidating the disease-specific patterns of editing and/or ADAR1 expression may be useful in making diagnoses and prognoses. In this review, we relate the mechanisms of ADAR1′s actions to its pathological implications, and suggest possible mechanisms for the unexplained associations between ADAR1 and human diseases.
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Blanc V, Davidson NO. RNA Editing: Another Level of Somatic Mutagenic Activity in Gastric Cancer. Gastroenterology 2016; 151:584-7. [PMID: 27590792 DOI: 10.1053/j.gastro.2016.08.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Valerie Blanc
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri.
| | - Nicholas O Davidson
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri
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