1
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Omata Y, Haraguchi M, Yoshinaga S, Ogino T, Okawa M, Tsuruta A, Koyanagi S, Ohdo S. RNA editing enzyme ADAR2 regulates P-glycoprotein expression in murine breast cancer cells through the circRNA-miRNA pathway. Biochem Biophys Res Commun 2024; 726:150289. [PMID: 38917633 DOI: 10.1016/j.bbrc.2024.150289] [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: 06/16/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Among the various RNA modifications, adenosine-to-inosine RNA editing, catalyzed by adenosine deaminase acting on RNA (ADAR) family, ADAR1 and ADAR2, is the most common nucleotide conversion in mammalian cells. The pathological relevance of ADAR expression has been highlighted in recent human genetic studies. Low expression of the ADAR2 gene is correlated with a poor prognosis in breast cancer patients, but the underlying mechanism remains enigmatic. In this study, we constructed Adar2-knockdown (Adar2-KD) murine breast cancer 4T1 cells and observed their reduced susceptibility to chemotherapeutic drug doxorubicin. Downregulation of ADAR2 induced the expression of P-glycoprotein (P-gp), leading to a reduction in the intracellular accumulation of doxorubicin. The upregulation of P-gp occurred at the post-transcriptional level due to the decreased miR-195a-3p function. The search for the underlying cause of the induction of P-gp expression in Adar2-KD 4T1 cells led to the identification of circular RNA (circRNA) circHif1a as a sponge for miR-195a-3p. The enhanced expression of circHif1a inhibited miR-195a-3p function, resulting in the upregulation of P-gp expression. These results suggest that ADAR2 acts as a suppressor of circHif1a biogenesis and then allows miR-195a-3p to interfere with P-gp translation. Our findings may help to improve drug efficacy by clarifying the mechanism of chemoresistance in breast cancer.
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MESH Headings
- Animals
- Adenosine Deaminase/metabolism
- Adenosine Deaminase/genetics
- Mice
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Female
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA Editing
- Doxorubicin/pharmacology
- Cell Line, Tumor
- Gene Expression Regulation, Neoplastic
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/genetics
- Drug Resistance, Neoplasm/genetics
- Antibiotics, Antineoplastic/pharmacology
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Affiliation(s)
- Yuji Omata
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Mai Haraguchi
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Sae Yoshinaga
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Takashi Ogino
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Maseri Okawa
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akito Tsuruta
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Satoru Koyanagi
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Shigehiro Ohdo
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan.
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2
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Niu X, Liu W, Zhang Y, Liu J, Zhang J, Li B, Qiu Y, Zhao P, Wang Z, Wang Z. Cancer plasticity in therapy resistance: Mechanisms and novel strategies. Drug Resist Updat 2024; 76:101114. [PMID: 38924995 DOI: 10.1016/j.drup.2024.101114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/12/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024]
Abstract
Therapy resistance poses a significant obstacle to effective cancer treatment. Recent insights into cell plasticity as a new paradigm for understanding resistance to treatment: as cancer progresses, cancer cells experience phenotypic and molecular alterations, corporately known as cell plasticity. These alterations are caused by microenvironment factors, stochastic genetic and epigenetic changes, and/or selective pressure engendered by treatment, resulting in tumor heterogeneity and therapy resistance. Increasing evidence suggests that cancer cells display remarkable intrinsic plasticity and reversibly adapt to dynamic microenvironment conditions. Dynamic interactions between cell states and with the surrounding microenvironment form a flexible tumor ecosystem, which is able to quickly adapt to external pressure, especially treatment. Here, this review delineates the formation of cancer cell plasticity (CCP) as well as its manipulation of cancer escape from treatment. Furthermore, the intrinsic and extrinsic mechanisms driving CCP that promote the development of therapy resistance is summarized. Novel treatment strategies, e.g., inhibiting or reversing CCP is also proposed. Moreover, the review discusses the multiple lines of ongoing clinical trials globally aimed at ameliorating therapy resistance. Such advances provide directions for the development of new treatment modalities and combination therapies against CCP in the context of therapy resistance.
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Affiliation(s)
- Xing Niu
- China Medical University, Shenyang, Liaoning 110122, China; Experimental Center of BIOQGene, YuanDong International Academy Of Life Sciences, 999077, Hong Kong, China
| | - Wenjing Liu
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Yinling Zhang
- Department of Oncology Radiotherapy 1, Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao, Shandong 266042, China
| | - Jing Liu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jianjun Zhang
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Bo Li
- Department of Orthopedics, Beijing Luhe Hospital, Capital Medical University, Beijing 101149, China
| | - Yue Qiu
- Department of Digestive Diseases 1, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Peng Zhao
- Department of Medical Imaging, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Zhongmiao Wang
- Department of Digestive Diseases 1, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
| | - Zhe Wang
- Department of Digestive Diseases 1, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
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3
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Bernal YA, Durán E, Solar I, Sagredo EA, Armisén R. ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer. Int J Mol Sci 2024; 25:7424. [PMID: 39000531 PMCID: PMC11242177 DOI: 10.3390/ijms25137424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Epitranscriptomics is a field that delves into post-transcriptional changes. Among these modifications, the conversion of adenosine to inosine, traduced as guanosine (A>I(G)), is one of the known RNA-editing mechanisms, catalyzed by ADARs. This type of RNA editing is the most common type of editing in mammals and contributes to biological diversity. Disruption in the A>I(G) RNA-editing balance has been linked to diseases, including several types of cancer. Drug resistance in patients with cancer represents a significant public health concern, contributing to increased mortality rates resulting from therapy non-responsiveness and disease progression, representing the greatest challenge for researchers in this field. The A>I(G) RNA editing is involved in several mechanisms over the immunotherapy and genotoxic drug response and drug resistance. This review investigates the relationship between ADAR1 and specific A>I(G) RNA-edited sites, focusing particularly on breast cancer, and the impact of these sites on DNA damage repair and the immune response over anti-cancer therapy. We address the underlying mechanisms, bioinformatics, and in vitro strategies for the identification and validation of A>I(G) RNA-edited sites. We gathered databases related to A>I(G) RNA editing and cancer and discussed the potential clinical and research implications of understanding A>I(G) RNA-editing patterns. Understanding the intricate role of ADAR1-mediated A>I(G) RNA editing in breast cancer holds significant promise for the development of personalized treatment approaches tailored to individual patients' A>I(G) RNA-editing profiles.
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Affiliation(s)
- Yanara A Bernal
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo Durán
- Subdepartamento de Genómica y Genética Molecular, Sección Genética Humana, Instituto de Salud Pública de Chile, Avenida Marathon 1000, Ñuñoa, Santiago 7780050, Chile
| | - Isidora Solar
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo A Sagredo
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-171 77 Stockholm, Sweden
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
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4
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Zhu T, Li Q, Zhang Z, Shi J, Li Y, Zhang F, Li L, Song X, Shen J, Jia R. ARID1A loss promotes RNA editing of CDK13 in an ADAR1-dependent manner. BMC Biol 2024; 22:132. [PMID: 38835016 PMCID: PMC11151582 DOI: 10.1186/s12915-024-01927-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/22/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is thought to play a significant role both in tumor suppression and tumor initiation, which is highly dependent upon context. Previous studies have suggested that ARID1A deficiency may contribute to cancer development. The specific mechanisms of whether ARID1A loss affects tumorigenesis by RNA editing remain unclear. RESULTS Our findings indicate that the deficiency of ARID1A leads to an increase in RNA editing levels and alterations in RNA editing categories mediated by adenosine deaminases acting on RNA 1 (ADAR1). ADAR1 edits the CDK13 gene at two previously unidentified sites, namely Q113R and K117R. Given the crucial role of CDK13 as a cyclin-dependent kinase, we further observed that ADAR1 deficiency results in changes in the cell cycle. Importantly, the sensitivity of ARID1A-deficient tumor cells to SR-4835, a CDK12/CDK13 inhibitor, suggests a promising therapeutic approach for individuals with ARID1A-mutant tumors. Knockdown of ADAR1 restored the sensitivity of ARID1A deficient cells to SR-4835 treatment. CONCLUSIONS ARID1A deficiency promotes RNA editing of CDK13 by regulating ADAR1.
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Affiliation(s)
- Tianyu Zhu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Zhe Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Jiahao Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Yongyun Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Feng Zhang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Xin Song
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China.
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China.
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5
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Miliotis C, Ma Y, Katopodi XL, Karagkouni D, Kanata E, Mattioli K, Kalavros N, Pita-Juárez YH, Batalini F, Ramnarine VR, Nanda S, Slack FJ, Vlachos IS. Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci. Nat Commun 2024; 15:4319. [PMID: 38773080 PMCID: PMC11109163 DOI: 10.1038/s41467-024-48436-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/01/2024] [Indexed: 05/23/2024] Open
Abstract
The landscape of non-coding mutations in cancer progression and immune evasion is largely unexplored. Here, we identify transcrptome-wide somatic and germline 3' untranslated region (3'-UTR) variants from 375 gastric cancer patients from The Cancer Genome Atlas. By performing gene expression quantitative trait loci (eQTL) and immune landscape QTL (ilQTL) analysis, we discover 3'-UTR variants with cis effects on expression and immune landscape phenotypes, such as immune cell infiltration and T cell receptor diversity. Using a massively parallel reporter assay, we distinguish between causal and correlative effects of 3'-UTR eQTLs in immune-related genes. Our approach identifies numerous 3'-UTR eQTLs and ilQTLs, providing a unique resource for the identification of immunotherapeutic targets and biomarkers. A prioritized ilQTL variant signature predicts response to immunotherapy better than standard-of-care PD-L1 expression in independent patient cohorts, showcasing the untapped potential of non-coding mutations in cancer.
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Affiliation(s)
- Christos Miliotis
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Program in Virology, Harvard University Graduate School of Arts and Sciences, Boston, MA, USA
| | - Yuling Ma
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xanthi-Lida Katopodi
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Dimitra Karagkouni
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Eleni Kanata
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kaia Mattioli
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nikolas Kalavros
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Yered H Pita-Juárez
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felipe Batalini
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Division of Oncology, Department of Medicine, Mayo Clinic, Phoenix, AZ, USA
| | - Varune R Ramnarine
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shivani Nanda
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Ioannis S Vlachos
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cancer Center & Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Spatial Technologies Unit, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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6
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Lu Q, Zhou W, Fan L, Ding T, Wang W, Zhang X. Tumor neoantigens derived from RNA editing events show significant clinical relevance in melanoma patients treated with immunotherapy. Anticancer Drugs 2024; 35:305-314. [PMID: 38170793 DOI: 10.1097/cad.0000000000001565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
This study aimed to investigate the clinical significance of RNA editing (RE) and RNA editing derived (RED-) neoantigens in melanoma patients treated with immunotherapy. Vardict and VEP were used to identify the somatic mutations. RE events were identified by Reditools2 and filtered by the custom pipeline. miRTar2GO was implemented to predict the RE whether located in miRNA targets within the 3' UTR region. NetMHCpan and NetCTLpan were used to identify and characterize RED-neoantigens. In total, 7116 RE events were identified, most of which were A-to-I events. Using our custom pipeline, 631 RED-neoantigens were identified that show a significantly greater peptide-MHC affinity, and facilitate epitope processing and presentation than wild-type peptides. The OS of the patients with high RED-neoantigens burden was significantly longer ( P = 0.035), and a significantly higher RED-neoantigens burden was observed in responders ( P = 0.048). The area under the curve of the RED-neoantigen was 0.831 of OS. Then, we validated the reliability of RED-neoantigens in predicting the prognosis in an independent cohort and found that patients with high RED-neoantigens exhibited a longer OS ( P = 0.008). To our knowledge, this is the first study to systematically assess the clinical relevance of RED-neoantigens in melanoma patients treated with immunotherapy.
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Affiliation(s)
- Qicheng Lu
- Department of Gastrointestinal Surgery, Changzhou First People's Hospital, Changzhou, Jiangsu
| | - Wenhao Zhou
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, Guangdong
| | - Ligang Fan
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou
| | - Tian Ding
- Department of Clinical Medicine, Medical School, Nantong University
| | - Wei Wang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, Guangdong
| | - Xiaodong Zhang
- Department of Medical Oncology, Tumor Hospital Affiliated To Nantong University, Nantong, Jiangsu, China
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7
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Zhang X, Wu L, Jia L, Hu X, Yao Y, Liu H, Ma J, Wang W, Li L, Chen K, Liu B. The implication of integrative multiple RNA modification-based subtypes in gastric cancer immunotherapy and prognosis. iScience 2024; 27:108897. [PMID: 38318382 PMCID: PMC10839690 DOI: 10.1016/j.isci.2024.108897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/28/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Previous studies have focused on the impact of individual RNA modifications on tumor development. This study comprehensively investigated the effects of multiple RNA modifications, including m6A, alternative polyadenylation, pseudouridine, adenosine-to-inosine editing, and uridylation, on gastric cancer (GC). By analyzing 1,946 GC samples from eleven independent cohorts, we identified distinct clusters of RNA modification genes with varying survival rates and immunological characteristics. We assessed the chromatin activity of these RNA modification clusters through regulon enrichment analysis. A prognostic model was developed using Stepwise Regression and Random Survival Forest algorithms and validated in ten independent datasets. Notably, the low-risk group showed a more favorable prognosis and positive response to immune checkpoint blockade therapy. Single-cell RNA sequencing confirmed the abundant expression of signature genes in B cells and plasma cells. Overall, our findings shed light on the potential significance of multiple RNA modifications in GC prognosis, stemness development, and chemotherapy resistance.
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Affiliation(s)
- Xiangnan Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Liuxing Wu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Liqing Jia
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Xin Hu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Yanxin Yao
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Huahuan Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Junfu Ma
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
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8
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Frezza V, Chellini L, Del Verme A, Paronetto MP. RNA Editing in Cancer Progression. Cancers (Basel) 2023; 15:5277. [PMID: 37958449 PMCID: PMC10648226 DOI: 10.3390/cancers15215277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Coding and noncoding RNA molecules play their roles in ensuring cell function and tissue homeostasis in an ordered and systematic fashion. RNA chemical modifications can occur both at bases and ribose sugar, and, similarly to DNA and histone modifications, can be written, erased, and recognized by the corresponding enzymes, thus modulating RNA activities and fine-tuning gene expression programs. RNA editing is one of the most prevalent and abundant forms of post-transcriptional RNA modification in normal physiological processes. By altering the sequences of mRNAs, it makes them different from the corresponding genomic template. Hence, edited mRNAs can produce protein isoforms that are functionally different from the corresponding genome-encoded variants. Abnormalities in regulatory enzymes and changes in RNA-modification patterns are closely associated with the occurrence and development of various human diseases, including cancer. To date, the roles played by RNA modifications in cancer are gathering increasing interest. In this review, we focus on the role of RNA editing in cancer transformation and provide a new perspective on its impact on tumorigenesis, by regulating cell proliferation, differentiation, invasion, migration, stemness, metabolism, and drug resistance.
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Affiliation(s)
- Valentina Frezza
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Arianna Del Verme
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
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9
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Pfeiffer LS, Stafforst T. Precision RNA base editing with engineered and endogenous effectors. Nat Biotechnol 2023; 41:1526-1542. [PMID: 37735261 DOI: 10.1038/s41587-023-01927-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
RNA base editing refers to the rewriting of genetic information within an intact RNA molecule and serves various functions, such as evasion of the endogenous immune system and regulation of protein function. To achieve this, certain enzymes have been discovered in human cells that catalyze the conversion of one nucleobase into another. This natural process could be exploited to manipulate and recode any base in a target transcript. In contrast to DNA base editing, analogous changes introduced in RNA are not permanent or inheritable but rather allow reversible and doseable effects that appeal to various therapeutic applications. The current practice of RNA base editing involves the deamination of adenosines and cytidines, which are converted to inosines and uridines, respectively. In this Review, we summarize current site-directed RNA base-editing strategies and highlight recent achievements to improve editing efficiency, precision, codon-targeting scope and in vivo delivery into disease-relevant tissues. Besides engineered editing effectors, we focus on strategies to harness endogenous adenosine deaminases acting on RNA (ADAR) enzymes and discuss limitations and future perspectives to apply the tools in basic research and as a therapeutic modality. We expect the field to realize the first RNA base-editing drug soon, likely on a well-defined genetic disease. However, the long-term challenge will be to carve out the sweet spot of the technology where its unique ability is exploited to modulate signaling cues, metabolism or other clinically relevant processes in a safe and doseable manner.
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Affiliation(s)
- Laura S Pfeiffer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center, Faculty of Medicine, University of Tübingen, Tübingen, Germany.
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10
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Wang C, Hou X, Guan Q, Zhou H, Zhou L, Liu L, Liu J, Li F, Li W, Liu H. RNA modification in cardiovascular disease: implications for therapeutic interventions. Signal Transduct Target Ther 2023; 8:412. [PMID: 37884527 PMCID: PMC10603151 DOI: 10.1038/s41392-023-01638-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/15/2023] [Accepted: 09/03/2023] [Indexed: 10/28/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death in the world, with a high incidence and a youth-oriented tendency. RNA modification is ubiquitous and indispensable in cell, maintaining cell homeostasis and function by dynamically regulating gene expression. Accumulating evidence has revealed the role of aberrant gene expression in CVD caused by dysregulated RNA modification. In this review, we focus on nine common RNA modifications: N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, adenosine-to-inosine (A-to-I) RNA editing, and modifications of U34 on tRNA wobble. We summarize the key regulators of RNA modification and their effects on gene expression, such as RNA splicing, maturation, transport, stability, and translation. Then, based on the classification of CVD, the mechanisms by which the disease occurs and progresses through RNA modifications are discussed. Potential therapeutic strategies, such as gene therapy, are reviewed based on these mechanisms. Herein, some of the CVD (such as stroke and peripheral vascular disease) are not included due to the limited availability of literature. Finally, the prospective applications and challenges of RNA modification in CVD are discussed for the purpose of facilitating clinical translation. Moreover, we look forward to more studies exploring the mechanisms and roles of RNA modification in CVD in the future, as there are substantial uncultivated areas to be explored.
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Affiliation(s)
- Cong Wang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xuyang Hou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qing Guan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Huiling Zhou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Li Zhou
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, The Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lijun Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jijia Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Feng Li
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wei Li
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Haidan Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
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11
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Zeng Z, Fu M, Hu Y, Wei Y, Wei X, Luo M. Regulation and signaling pathways in cancer stem cells: implications for targeted therapy for cancer. Mol Cancer 2023; 22:172. [PMID: 37853437 PMCID: PMC10583419 DOI: 10.1186/s12943-023-01877-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
Cancer stem cells (CSCs), initially identified in leukemia in 1994, constitute a distinct subset of tumor cells characterized by surface markers such as CD133, CD44, and ALDH. Their behavior is regulated through a complex interplay of networks, including transcriptional, post-transcriptional, epigenetic, tumor microenvironment (TME), and epithelial-mesenchymal transition (EMT) factors. Numerous signaling pathways were found to be involved in the regulatory network of CSCs. The maintenance of CSC characteristics plays a pivotal role in driving CSC-associated tumor metastasis and conferring resistance to therapy. Consequently, CSCs have emerged as promising targets in cancer treatment. To date, researchers have developed several anticancer agents tailored to specifically target CSCs, with some of these treatment strategies currently undergoing preclinical or clinical trials. In this review, we outline the origin and biological characteristics of CSCs, explore the regulatory networks governing CSCs, discuss the signaling pathways implicated in these networks, and investigate the influential factors contributing to therapy resistance in CSCs. Finally, we offer insights into preclinical and clinical agents designed to eliminate CSCs.
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Affiliation(s)
- Zhen Zeng
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Minyang Fu
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuan Hu
- Department of Pediatric Nephrology Nursing, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Min Luo
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China.
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12
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Zhang Q, Yang M, Zhang P, Wu B, Wei X, Li S. Deciphering gastric inflammation-induced tumorigenesis through multi-omics data and AI methods. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0129. [PMID: 37589244 PMCID: PMC11033716 DOI: 10.20892/j.issn.2095-3941.2023.0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/26/2023] [Indexed: 08/18/2023] Open
Abstract
Gastric cancer (GC), the fifth most common cancer globally, remains the leading cause of cancer deaths worldwide. Inflammation-induced tumorigenesis is the predominant process in GC development; therefore, systematic research in this area should improve understanding of the biological mechanisms that initiate GC development and promote cancer hallmarks. Here, we summarize biological knowledge regarding gastric inflammation-induced tumorigenesis, and characterize the multi-omics data and systems biology methods for investigating GC development. Of note, we highlight pioneering studies in multi-omics data and state-of-the-art network-based algorithms used for dissecting the features of gastric inflammation-induced tumorigenesis, and we propose translational applications in early GC warning biomarkers and precise treatment strategies. This review offers integrative insights for GC research, with the goal of paving the way to novel paradigms for GC precision oncology and prevention.
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Affiliation(s)
- Qian Zhang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Mingran Yang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Peng Zhang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Bowen Wu
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaosen Wei
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shao Li
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
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13
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Liu F, Liu J, Shi X, Hu X, Wei L, Huo B, Chang L, Han Y, Liu G, Yang L. Identification of INHBA as a potential biomarker for gastric cancer through a comprehensive analysis. Sci Rep 2023; 13:12494. [PMID: 37528145 PMCID: PMC10394090 DOI: 10.1038/s41598-023-39784-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
Inhibin subunit beta A (INHBA) is a member of the transforming growth factor-beta (TGF-β) superfamily that plays a fundamental role in various cancers. However, a systematic analysis of the exact role of INHBA in patients with gastric cancer (GC) has not yet been conducted. We evaluated the expression levels of INHBA and the correlation between INHBA and GC prognosis in GC. The relationship between INHBA expression, immune infiltration levels, and type markers of immune cells in GC was also explored. In addition, we studied INHBA mutations, promoter methylation, and functional enrichment analysis. Besides, high expression levels of INHBA in GC were significantly related to unfavorable prognosis. INHBA was negatively correlated with B cell infiltration, but positively correlated with macrophage and most anticancer immunity steps. INHBA expression was positively correlated with the type markers of CD8+ T cells, neutrophils, macrophages, and dendritic cells. INHBA has a weak significant methylation level change between tumor and normal tissues and mainly enriched in cancer-related signaling pathways. The present study implies that INHBA may serve as a potential biomarker for predicting the prognosis of patients with GC. INHBA is a promising predictor of immunotherapy response, with higher levels of INHBA indicating greater sensitivity.
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Affiliation(s)
- Fang Liu
- Department of Thoracic Surgery, Hebei Medical University Fourth Affiliated Hospital, Shijiazhuang, 050001, Hebei, People's Republic of China
| | - Jiayi Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, 050017, People's Republic of China
| | - Xinrui Shi
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, 050017, People's Republic of China
| | - Xiaojie Hu
- Department of General Surgery, Hebei Provincial People's Hospital, Shijiazhuang, 050055, Hebei, People's Republic of China
| | - Lai Wei
- Department of Thoracic Surgery, Hebei Medical University Fourth Affiliated Hospital, Shijiazhuang, 050001, Hebei, People's Republic of China
| | - Bingjie Huo
- Department of Chinese Medicine, Hebei Medical University Fourth Affiliated Hospital, Shijiazhuang, 050001, Hebei, People's Republic of China
| | - Liang Chang
- Department of Pathology, Hebei Medical University Fourth Affiliated Hospital, Shijiazhuang, 050001, Hebei, People's Republic of China
| | - Yaqing Han
- Department of Thoracic Surgery, Hebei Medical University Fourth Affiliated Hospital, Shijiazhuang, 050001, Hebei, People's Republic of China
| | - Guangjie Liu
- Department of Thoracic Surgery, Hebei Medical University Fourth Affiliated Hospital, Shijiazhuang, 050001, Hebei, People's Republic of China.
| | - Lei Yang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, 050017, People's Republic of China.
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14
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Wang B, Tian P, Sun Q, Zhang H, Han L, Zhu B. A novel, effective machine learning-based RNA editing profile for predicting the prognosis of lower-grade gliomas. Heliyon 2023; 9:e18075. [PMID: 37483735 PMCID: PMC10362151 DOI: 10.1016/j.heliyon.2023.e18075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023] Open
Abstract
Patients with low-grade glioma (LGG) may survive for long time periods, but their tumors often progress to higher-grade lesions. Currently, no cure for LGG is available. A-to-I RNA editing accounts for nearly 90% of all RNA editing events in humans and plays a role in tumorigenesis in various cancers. However, little is known regarding its prognostic role in LGG. On the basis of The Cancer Genome Atlas (TCGA) data, we used LASSO and univariate Cox regression to construct an RNA editing site signature. The results derived from the TCGA dataset were further validated with Gene Expression Omnibus (GEO) and Chinese Glioma Genome Atlas (CGGA) datasets. Five machine learning algorithms (Decision Trees C5.0, XGboost, GBDT, Lightgbm, and Catboost) were used to confirm the prognosis associated with the RNA editing site signature. Finally, we explored immune function, immunotherapy, and potential therapeutic agents in the high- and low-risk groups by using multiple biological prediction websites. A total of 22,739 RNA editing sites were identified, and a signature model consisting of four RNA editing sites (PRKCSH|chr19:11561032, DSEL|chr18:65174489, UGGT1|chr2:128952084, and SOD2|chr6:160101723) was established. Cox regression analysis indicated that the RNA editing signature was an independent prognostic factor, according to the ROC curve (AUC = 0.823), and the nomogram model had good predictive power (C-index = 0.824). In addition, the predictive ability of the RNA editing signature was confirmed with the machine learning model. The sensitivity of PCI-34051 and Elephantin was significantly higher in the high-risk group than the low-risk group, thus potentially providing a marker to predict the effects of lung cancer drug treatment. RNA editing may serve as a novel survival prediction tool, thus offering hope for developing editing-based therapeutic strategies to combat LGG progression. In addition, this tool may help optimize survival risk assessment and individualized care for patients with low-grade gliomas.
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Affiliation(s)
- Boshen Wang
- Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210000, Jiangsu, China
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Peijie Tian
- Department of Pathology, Weifang Medical University, China
| | - Qianyu Sun
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Hengdong Zhang
- Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210000, Jiangsu, China
| | - Lei Han
- Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210000, Jiangsu, China
| | - Baoli Zhu
- Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210000, Jiangsu, China
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
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15
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Li Z, Zhang X, Weng W, Zhang G, Ren Q, Tian Y. Cross-talk of RNA modification "writers" describes tumor stemness and microenvironment and guides personalized immunotherapy for gastric cancer. Aging (Albany NY) 2023; 15:5445-5481. [PMID: 37319315 PMCID: PMC10333070 DOI: 10.18632/aging.204802] [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: 03/24/2023] [Accepted: 05/27/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND RNA modifications, TME, and cancer stemness play significant roles in tumor development and immunotherapy. The study investigated cross-talk and RNA modification roles in the TME, cancer stemness, and immunotherapy of gastric cancer (GC). METHODS We applied an unsupervised clustering method to distinguish RNA modification patterns in GC. GSVA and ssGSEA algorithms were applied. The WM_Score model was constructed for evaluating the RNA modification-related subtypes. Also, we conducted an association analysis between the WM_Score and biological and clinical features in GC and explored the WM_Score model's predictive value in immunotherapy. RESULTS We identified four RNA modification patterns with diverse survival and TME features. One pattern consistent with the immune-inflamed tumor phenotype showed a better prognosis. Patients in WM_Score high group were related to adverse clinical outcomes, immune suppression, stromal activation, and enhanced cancer stemness, while WM_Score low group showed opposite results. The WM_Score was correlated with genetic, epigenetic alterations, and post-transcriptional modifications in GC. Low WM_Score was related to enhanced efficacy of anti-PD-1/L1 immunotherapy. CONCLUSIONS We revealed the cross-talk of four RNA modification types and their functions in GC, providing a scoring system for GC prognosis and personalized immunotherapy predictions.
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Affiliation(s)
- Zhuoqi Li
- Radiotherapy Department, Shandong Second Provincial General Hospital, Shandong University, Jinan, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Peking University, Beijing, China
| | - Xuehong Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Peking University, Beijing, China
| | - Wenjie Weng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Peking University, Beijing, China
| | - Ge Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Peking University, Beijing, China
| | - Qianwen Ren
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Peking University, Beijing, China
| | - Yuan Tian
- Radiotherapy Department, Shandong Second Provincial General Hospital, Shandong University, Jinan, China
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
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16
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Wu S, Fan Z, Kim P, Huang L, Zhou X. The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:619-631. [PMID: 36708807 PMCID: PMC10787018 DOI: 10.1016/j.gpb.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 11/04/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, constituting nearly 90% of all RNA editing events in humans, has been reported to contribute to the tumorigenesis in diverse cancers. However, the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient. To fill this gap, we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas. For individual candidate among ∼ 1,500,000 quantified RNA editing events, we performed diverse types of downstream functional annotations. Finally, we identified 24,236 potentially functional A-to-I RNA editing events, including the cases in APOL1, IGFBP3, GRIA2, BLCAP, and miR-589-3p. These events might play crucial roles in the scenarios of tumorigenesis, due to their tumor-related editing frequencies or probable effects on altered expression profiles, protein functions, splicing patterns, and microRNA regulations of tumor genes. Our functional A-to-I RNA editing events (https://ccsm.uth.edu/CAeditome/) will help better understand the cancer pathology from the A-to-I RNA editing aspect.
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Affiliation(s)
- Sijia Wu
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Zhiwei Fan
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610040, China; Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi'an 710071, China.
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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17
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Mendez Ruiz S, Chalk AM, Goradia A, Heraud-Farlow J, Walkley C. Over-expression of ADAR1 in mice does not initiate or accelerate cancer formation in vivo. NAR Cancer 2023; 5:zcad023. [PMID: 37275274 PMCID: PMC10233902 DOI: 10.1093/narcan/zcad023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 06/07/2023] Open
Abstract
Adenosine to inosine editing (A-to-I) in regions of double stranded RNA (dsRNA) is mediated by adenosine deaminase acting on RNA 1 (ADAR1) or ADAR2. ADAR1 and A-to-I editing levels are increased in many human cancers. Inhibition of ADAR1 has emerged as a high priority oncology target, however, whether ADAR1 overexpression enables cancer initiation or progression has not been directly tested. We established a series of in vivo models to allow overexpression of full-length ADAR1, or its individual isoforms, to test if increased ADAR1 expression was oncogenic. Widespread over-expression of ADAR1 or the p110 or p150 isoforms individually as sole lesions was well tolerated and did not result in cancer initiation. Therefore, ADAR1 overexpression alone is not sufficient to initiate cancer. We demonstrate that endogenous ADAR1 and A-to-I editing increased upon immortalization in murine cells, consistent with the observations from human cancers. We tested if ADAR1 over-expression could co-operate with cancer initiated by loss of tumour suppressors using a model of osteosarcoma. We did not see a disease potentiating or modifying effect of overexpressing ADAR1 or its isoforms in the models assessed. We conclude that increased ADAR1 expression and A-to-I editing in cancers is most likely a consequence of tumor formation.
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Affiliation(s)
- Shannon Mendez Ruiz
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Alistair M Chalk
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Ankita Goradia
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | | | - Carl R Walkley
- To whom correspondence should be addressed. Tel: +61 3 9231 2480;
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18
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Wong TL, Loh JJ, Lu S, Yan HHN, Siu HC, Xi R, Chan D, Kam MJF, Zhou L, Tong M, Copland JA, Chen L, Yun JP, Leung SY, Ma S. ADAR1-mediated RNA editing of SCD1 drives drug resistance and self-renewal in gastric cancer. Nat Commun 2023; 14:2861. [PMID: 37208334 PMCID: PMC10199093 DOI: 10.1038/s41467-023-38581-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 05/05/2023] [Indexed: 05/21/2023] Open
Abstract
Targetable drivers governing 5-fluorouracil and cisplatin (5FU + CDDP) resistance remain elusive due to the paucity of physiologically and therapeutically relevant models. Here, we establish 5FU + CDDP resistant intestinal subtype GC patient-derived organoid lines. JAK/STAT signaling and its downstream, adenosine deaminases acting on RNA 1 (ADAR1), are shown to be concomitantly upregulated in the resistant lines. ADAR1 confers chemoresistance and self-renewal in an RNA editing-dependent manner. WES coupled with RNA-seq identify enrichment of hyper-edited lipid metabolism genes in the resistant lines. Mechanistically, ADAR1-mediated A-to-I editing on 3'UTR of stearoyl-CoA desaturase (SCD1) increases binding of KH domain-containing, RNA-binding, signal transduction-associated 1 (KHDRBS1), thereby augmenting SCD1 mRNA stability. Consequently, SCD1 facilitates lipid droplet formation to alleviate chemotherapy-induced ER stress and enhances self-renewal through increasing β-catenin expression. Pharmacological inhibition of SCD1 abrogates chemoresistance and tumor-initiating cell frequency. Clinically, high proteomic level of ADAR1 and SCD1, or high SCD1 editing/ADAR1 mRNA signature score predicts a worse prognosis. Together, we unveil a potential target to circumvent chemoresistance.
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Affiliation(s)
- Tin-Lok Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jia-Jian Loh
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shixun Lu
- Department of Pathology, Sun Yat-Sen University Cancer Centre, Guangzhou, Guangdong, China
| | - Helen H N Yan
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Hoi Cheong Siu
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Ren Xi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Dessy Chan
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Max J F Kam
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lei Zhou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Man Tong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jing-Ping Yun
- Department of Pathology, Sun Yat-Sen University Cancer Centre, Guangzhou, Guangdong, China
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
- The Jockey Club Centre for Clinical Innovation and Discovery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Stephanie Ma
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China.
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19
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Wei ZY, Wang ZX, Li JH, Wen YS, Gao D, Xia SY, Li YN, Pan XB, Liu YS, Jin YY, Chen JH. Host A-to-I RNA editing signatures in intracellular bacterial and single-strand RNA viral infections. Front Immunol 2023; 14:1121096. [PMID: 37081881 PMCID: PMC10112020 DOI: 10.3389/fimmu.2023.1121096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
BackgroundMicrobial infection is accompanied by remodeling of the host transcriptome. Involvement of A-to-I RNA editing has been reported during viral infection but remains to be elucidated during intracellular bacterial infections.ResultsHerein we analyzed A-to-I RNA editing during intracellular bacterial infections based on 18 RNA-Seq datasets of 210 mouse samples involving 7 tissue types and 8 intracellular bacterial pathogens (IBPs), and identified a consensus signature of RNA editing for IBP infections, mainly involving neutrophil-mediated innate immunity and lipid metabolism. Further comparison of host RNA editing patterns revealed remarkable similarities between pneumonia caused by IBPs and single-strand RNA (ssRNA) viruses, such as altered editing enzyme expression, editing site numbers, and levels. In addition, functional enrichment analysis of genes with RNA editing highlighted that the Rab GTPase family played a common and vital role in the host immune response to IBP and ssRNA viral infections, which was indicated by the consistent up-regulated RNA editing of Ras-related protein Rab27a. Nevertheless, dramatic differences between IBP and viral infections were also observed, and clearly distinguished the two types of intracellular infections.ConclusionOur study showed transcriptome-wide host A-to-I RNA editing alteration during IBP and ssRNA viral infections. By identifying and comparing consensus signatures of host A-to-I RNA editing, our analysis implicates the importance of host A-to-I RNA editing during these infections and provides new insights into the diagnosis and treatment of infectious diseases.
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Affiliation(s)
- Zhi-Yuan Wei
- 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
| | - Zhi-Xin Wang
- 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
| | - Jia-Huan Li
- 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
| | - Yan-Shuo Wen
- 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
| | - Di Gao
- 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
| | - Shou-Yue Xia
- 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
| | - Yu-Ning Li
- 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
| | - Xu-Bin Pan
- 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
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Wuxi Children’s Hospital, Wuxi, Jiangsu, China
| | - Yun-Yun Jin
- 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
- *Correspondence: Jian-Huan Chen, ; Yun-Yun Jin,
| | - 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
- *Correspondence: Jian-Huan Chen, ; Yun-Yun Jin,
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20
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Nakamura K, Shigeyasu K, Okamoto K, Matsuoka H, Masuyama H. ADAR1 has an oncogenic function and can be a prognostic factor in cervical cancer. Sci Rep 2023; 13:4720. [PMID: 36959226 PMCID: PMC10036526 DOI: 10.1038/s41598-023-30452-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/23/2023] [Indexed: 03/25/2023] Open
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1), a recently described epigenetic modifier, is believed to play a critical oncogenic role in human cancers. However, its functional role and clinical significance in cervical cancer (CC) remain unclear. ADAR1 knockdown was performed to investigate its oncogenic functions in SiHa (HPV16), HeLa (HPV18), and Yumoto (non-HPV) CC cell lines. Cytoplasmic and nuclear ADAR1 expression were examined to clarify their correlation with clinicopathological parameters and prognosis in patients with CC. This resulted in increased apoptosis and necroptosis in HPV16 -type SiHa, HPV18-type HeLa, and non-HPV-type Yumoto CC cell lines. Progression-free survival (PFS) rates of patients exhibiting high cytoplasmic and nuclear ADAR1 expression were poorer than those in the other groups (P = 0.016). Multivariate analysis indicated that the combination of higher cytoplasmic and nuclear ADAR1 expression was an independent predictor of prognosis in patients with CC (P = 0.017). ADAR1 could be a potential therapeutic target for HPV-positive or HPV-negative CC. The combination of cytoplasmic and nuclear ADAR1 comprises a better prognostic factor for CC.
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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
| | - Kazuhiro Okamoto
- 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
| | - Hirofumi Matsuoka
- 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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21
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Shi S, Chen S, Wang M, Guo B, He Y, Chen H. Clinical relevance of RNA editing profiles in lung adenocarcinoma. Front Genet 2023; 14:1084869. [PMID: 36999050 PMCID: PMC10043753 DOI: 10.3389/fgene.2023.1084869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Background: Lung adenocarcinoma (LUAD) is the most frequently occurring lung cancer worldwide, with increasing death rates. It belongs to the non-small cell lung cancer (NSCLC) type and has a strong association with previous smoking history. Growing evidence has demonstrated the significance of adenosine-to-inosine RNA editing (ATIRE) dysregulation in cancer. The aim of the present study was to evaluate ATIRE events that might be clinically useful or tumorigenic.Methods: To explore survival-related ATIRE events in LUAD, its ATIRE profiles, gene expression data, and corresponding patients’ clinical information were downloaded from the Cancer Genome Atlas (TCGA) and the synapse database. We evaluated 10441 ATIRE in 440 LUAD patients from the TCGA database. ATIRE profiles were merged with TCGA survival data. We selected prognostic ATIRE sites, using a univariate Cox analysis (p < 0.001). Cox proportional hazards regression and lasso regression analysis were used to determine survival-related ATIRE sites, create risk ratings for those sites, and build a prognostic model and a nomogram for assessing overall survival (OS). Six ATIRE sites were used in the prognostic model construction and patients were randomly divided into a validation cohort (n = 176) and a training cohort (n = 264). The “Pheatmap” program was used to create risk curves that included risk score, survival time, and expression of ATIRE sites. We also determined the clinical prediction model’s discrimination. The decision curve analysis and the 1-, 2-, and 3-year corrective curves were simultaneously used to evaluate the nomogram. We also evaluated the relationship between the amount of ATIRE sites and host gene expression and the impact of ATIRE expression on transcriptome expression.Results: The pyroglutamyl-peptidase I (PGPEP1) chr19:18476416A > I, ankyrin repeat domain 36B pseudogene 1 (ANKRD36BP1) (dist = 3,795), T-box transcription factor (TBX19) (dist = 29815) chr1:168220463A > I, Syntrophin Beta 2 (SNTB2) chr16:69338598A > I, hook microtubule-tethering protein 3 (HOOK3) chr8:42883441A > I, NADH dehydrogenase flavoprotein 3 (NDUFV3) chr21:44329452A > I, and FK506-binding protein 11 (FKBP11) chr12:49316769A > I were used in the prognostic model construction. High levels of risk score were significantly associated with worse OS and progression-free survival. Tumour stage and risk score were related to OS in LUAD patients. The predictors were among the prognostic nomogram model’s risk score, age, gender, and tumor stage. The calibration plot and C-index (0.718) demonstrated the significant accuracy of nomogram’s predictions. ATIRE level was markedly elevated in tumor tissues and was highly variable between patients.Conclusion: Events involving ATIRE in LUAD were highly functional and clinically relevant. The RNA editing-based model provides a solid framework for further investigation of the functions of RNA editing in non-coding areas and may be used as a unique method for predicting LUAD survival.
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Affiliation(s)
- Si Shi
- The Respiratory Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Shibin Chen
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Menghang Wang
- The Respiratory Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bingchen Guo
- Department of Cardiology, The first Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yaowu He
- The Respiratory Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hong Chen
- The Respiratory Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- *Correspondence: Hong Chen,
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22
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Wang SY, Zhang LJ, Chen GJ, Ni QQ, Huang Y, Zhang D, Han FY, He WF, He LL, Ding YQ, Jiao HL, Ye YP. COPA A-to-I RNA editing hijacks endoplasmic reticulum stress to promote metastasis in colorectal cancer. Cancer Lett 2023; 553:215995. [PMID: 36336148 DOI: 10.1016/j.canlet.2022.215995] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
RNA editing is among the most common RNA level modifications for generating amino acid changes. We identified a COPA A-to-I RNA editing event in CRC metastasis. Our results showed that the COPA A-to-I RNA editing rate was significantly increased in metastatic CRC tissues and was closely associated with aggressive tumors in the T and N stages. The COPA I164V protein damaged the Golgi-ER reverse transport function, induced ER stress, promoted the translocation of the transcription factors ATF6, XBP1 and ATF4 into the nucleus, and activated the expression of MALAT1, MET, ZEB1, and lead to CRC cell invasion and metastasis. Moreover, the COPA A-to-I RNA editing rate was positively correlated with the immune infiltration score. Collectively, the COPA I164V protein hijacked ER stress to promote the metastasis of CRC, and the COPA A-to-I RNA editing rate may be a potential predictor for patient response to immune checkpoint inhibitor (ICIs) treatment.
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Affiliation(s)
- Shu-Yang Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Ling-Jie Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Guo-Jun Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Qi-Qi Ni
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Yuan Huang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Dan Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Fang-Yi Han
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Wen-Feng He
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Li-Ling He
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China
| | - Yan-Qing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China.
| | - Hong-Li Jiao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China.
| | - Ya-Ping Ye
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, China.
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23
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Wang Y, Liu Y, Zhao Z, Wu X, Lin J, Li Y, Yan W, Wu Y, Shi Y, Wu X, Xue Y, He J, Liu S, Zhang X, Xu H, Tang Y, Yin S. The involvement of ADAR1 in chronic unpredictable stress-induced cognitive impairment by targeting DARPP-32 with miR-874-3p in BALB/c mice. Front Cell Dev Biol 2023; 11:919297. [PMID: 37123418 PMCID: PMC10132208 DOI: 10.3389/fcell.2023.919297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/07/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction: Chronic stress exposure is the main environmental factor leading to cognitive impairment, but the detailed molecular mechanism is still unclear. Adenosine Deaminase acting on double-stranded RNA1(ADAR1) is involved in the occurrence of chronic stress-induced cognitive impairment. In addition, dopamine and Adenosine 3'5'-monophosphate-regulated phospho-protein (DARPP-32) gene variation affects cognitive function. Therefore, we hypothesized that ADAR1 plays a key role in chronic stress-induced cognitive impairment by acting on DARPP-32. Methods: In this study, postnatal 21-day-old male BALB/c mice were exposed to chronic unpredictable stressors. After that, the mice were treated with ADAR1 inducer/inhibitor. The cognitive ability and cerebral DARPP-32 protein expression of BALB/c mice were evaluated. In order to explore the link between ADAR1 and DARPP-32, the effects of ADAR1 high/low expression on DARPP-32 protein expression in vitro were detected. Results: ADAR1 inducer alleviates cognitive impairment and recovers decreased DARPP-32 protein expression of the hippocampus and prefrontal cortex in BALB/c mice with chronic unpredictable stress exposure. In vivo and in vitro studies confirm the results predicted by bio-informatics; that is, ADAR1 affects DARPP-32 expression via miR-874-3p. Discussion: The results in this study demonstrate that ADAR1 affects the expression of DARPP-32 via miR-874-3p, which is involved in the molecular mechanism of pathogenesis in chronic unpredictable stress-induced cognitive impairment. The new findings of this study provide a new therapeutic strategy for the prevention and treatment of stress cognitive impairment from epigenetics.
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Affiliation(s)
- Yanfang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yingxin Liu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ziwei Zhao
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xinyu Wu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jiabin Lin
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yufei Li
- National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, China
| | - Wei Yan
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yi Wu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yanfei Shi
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xindi Wu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ying Xue
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jiaqian He
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Shuqi Liu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xiaonan Zhang
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hong Xu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yiyuan Tang
- College of Health Solutions, Phoenix, AZ, United States
| | - Shengming Yin
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
- *Correspondence: Shengming Yin,
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24
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Gao C, Zhou G, Shi J, Shi P, Jin L, Li Y, Wang X, Liao S, Yan H, Wu J, Lu Y, Zhai Y, Zhang J, Zhang H, Zhang H, Yang C, Cao P, Cheng S, Zhou G. The A-to-I editing of KPC1 promotes intrahepatic cholangiocarcinoma by attenuating proteasomal processing of NF-κB1 p105 to p50. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:338. [PMID: 36476255 PMCID: PMC9730630 DOI: 10.1186/s13046-022-02549-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Aberrant RNA editing of adenosine-to-inosine (A-to-I) has been linked to multiple human cancers, but its role in intrahepatic cholangiocarcinoma (iCCA) remains unknown. We conducted an exome-wide investigation to search for dysregulated RNA editing that drive iCCA pathogenesis. METHODS An integrative whole-exome and transcriptome sequencing analysis was performed to elucidate the RNA editing landscape in iCCAs. Putative RNA editing sites were validated by Sanger sequencing. In vitro and in vivo experiments were used to assess the effects of an exemplary target gene Kip1 ubiquitination-promoting complex 1 (KPC1) and its editing on iCCA cells growth and metastasis. Crosstalk between KPC1 RNA editing and NF-κB signaling was analyzed by molecular methods. RESULTS Through integrative omics analyses, we revealed an adenosine deaminases acting on RNA 1A (ADAR1)-mediated over-editing pattern in iCCAs. ADAR1 is frequently amplified and overexpressed in iCCAs and plays oncogenic roles. Notably, we identified a novel ADAR1-mediated A-to-I editing of KPC1 transcript, which results in substitution of methionine with valine at residue 8 (p.M8V). KPC1 p.M8V editing confers loss-of-function phenotypes through blunting the tumor-suppressive role of wild-type KPC1. Mechanistically, KPC1 p.M8V weakens the affinity of KPC1 to its substrate NF-κB1 p105, thereby reducing the ubiquitinating and proteasomal processing of p105 to p50, which in turn enhances the activity of oncogenic NF-κB signaling. CONCLUSIONS Our findings established that amplification-driven ADAR1 overexpression results in overediting of KPC1 p.M8V in iCCAs, leading to progression via activation of the NF-κB signaling pathway, and suggested ADAR1-KPC1-NF-κB axis as a potential therapeutic target for iCCA.
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Affiliation(s)
- Chengming Gao
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Guangming Zhou
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Jie Shi
- grid.414375.00000 0004 7588 8796Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, 225 Changhai Road, Shanghai, 200433 China
| | - Peipei Shi
- grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China
| | - Liang Jin
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Yuanfeng Li
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Xiaowen Wang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Song Liao
- grid.488137.10000 0001 2267 2324Medical School of Chinese PLA, Beijing, China
| | - Han Yan
- grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China
| | - Junjie Wu
- grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei City, China
| | - Yiming Lu
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Yun Zhai
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Jinxu Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Haitao Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Hongxing Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Chenning Yang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Pengbo Cao
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Shuqun Cheng
- grid.414375.00000 0004 7588 8796Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, 225 Changhai Road, Shanghai, 200433 China
| | - Gangqiao Zhou
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China ,grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei City, China ,grid.89957.3a0000 0000 9255 8984Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China
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C-to-U RNA Editing: A Site Directed RNA Editing Tool for Restoration of Genetic Code. Genes (Basel) 2022; 13:genes13091636. [PMID: 36140804 PMCID: PMC9498875 DOI: 10.3390/genes13091636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
The restoration of genetic code by editing mutated genes is a potential method for the treatment of genetic diseases/disorders. Genetic disorders are caused by the point mutations of thymine (T) to cytidine (C) or guanosine (G) to adenine (A), for which gene editing (editing of mutated genes) is a promising therapeutic technique. In C-to-Uridine (U) RNA editing, it converts the base C-to-U in RNA molecules and leads to nonsynonymous changes when occurring in coding regions; however, for G-to-A mutations, A-to-I editing occurs. Editing of C-to-U is not as physiologically common as that of A-to-I editing. Although hundreds to thousands of coding sites have been found to be C-to-U edited or editable in humans, the biological significance of this phenomenon remains elusive. In this review, we have tried to provide detailed information on physiological and artificial approaches for C-to-U RNA editing.
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Chen J, Li L, Liu TY, Fu HF, Lai YH, Lei X, Xu JF, Yu JS, Xia YJ, Zhang TH, Yang DJ, He YL. CPEB3 suppresses gastric cancer progression by inhibiting ADAR1-mediated RNA editing via localizing ADAR1 mRNA to P bodies. Oncogene 2022; 41:4591-4605. [PMID: 36068334 DOI: 10.1038/s41388-022-02454-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022]
Abstract
Deciphering the crosstalk between RNA-binding proteins and corresponding RNAs will provide a better understanding of gastric cancer (GC) progression. The comprehensive bioinformatics study identified cytoplasmic polyadenylation element-binding protein 3 (CPEB3) might play a vital role in GC progression. Then we found CPEB3 was downregulated in GC and correlated with prognosis. In addition, CPEB3 suppressed GC cell proliferation, invasion and migration in vitro, as well as tumor growth and metastasis in vivo. Mechanistic study demonstrated CPEB3 interacted with 3'-UTR of ADAR1 mRNA through binding to CPEC nucleotide element, and then inhibited its translation by localizing it to processing bodies (P bodies), eventually leading to the suppression of ADAR1-mediated RNA editing. Microscale thermophoresis assay further revealed that the direct interaction between CPEB3 and GW182, the P-body's major component, was through the 440-698AA region of CPEB3 binding to the 403-860AA region of GW182. Finally, AAV9-CPEB3 was developed and administrated in mouse models to assess its potential value in gene therapy. We found AAV9-CPEB3 inhibited GC growth and metastasis. Besides, AAV9-CPEB3 induced hydropic degeneration in mouse liver, but did not cause kidney damage. These findings concluded that CPEB3 suppresses GC progression by inhibiting ADAR1-mediated RNA editing via localizing ADAR1 mRNA to P bodies.
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Affiliation(s)
- Jian Chen
- Center for Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lu Li
- Department of Clinical Microbiology Laboratory, Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, China
| | - Tian-Yu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hua-Feng Fu
- Center for Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuan-Hui Lai
- Department of Thyroid and Breast Surgery, The Eastern Division of the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiong Lei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jun-Fa Xu
- Department of Clinical Immunology, Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, China
| | - Ji-Shang Yu
- Center for Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu-Jian Xia
- Center for Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tian-Hao Zhang
- Center for Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dong-Jie Yang
- Center for Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Yu-Long He
- Center for Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China. .,Digestive Medicine Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China.
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Fu T, Chan TW, Bahn JH, Kim TH, Rowat AC, Xiao X. Multifaceted role of RNA editing in promoting loss-of-function of PODXL in cancer. iScience 2022; 25:104836. [PMID: 35992085 PMCID: PMC9382340 DOI: 10.1016/j.isci.2022.104836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
PODXL, a protein that is dysregulated in multiple cancers, plays an important role in promoting cancer metastasis. In this study, we report that RNA editing promotes the inclusion of a PODXL alternative exon. The resulting edited PODXL long isoform is more prone to protease digestion and has the strongest effects on reducing cell migration and cisplatin chemoresistance among the three PODXL isoforms (short, unedited long, and edited long isoforms). Importantly, the editing level of the PODXL recoding site and the inclusion level of the PODXL alternative exon are strongly associated with overall patient survival in Kidney Renal Clear Cell Carcinoma (KIRC). Supported by significant enrichment of exonic RNA editing sites in alternatively spliced exons, we hypothesize that exonic RNA editing sites may enhance proteomic diversity through alternative splicing, in addition to amino acid changes, a previously under-appreciated aspect of RNA editing function.
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Affiliation(s)
- Ting Fu
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tracey W. Chan
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tae-Hyung Kim
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amy C. Rowat
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Kokot KE, Kneuer JM, John D, Rebs S, Möbius-Winkler MN, Erbe S, Müller M, Andritschke M, Gaul S, Sheikh BN, Haas J, Thiele H, Müller OJ, Hille S, Leuschner F, Dimmeler S, Streckfuss-Bömeke K, Meder B, Laufs U, Boeckel JN. Reduction of A-to-I RNA editing in the failing human heart regulates formation of circular RNAs. Basic Res Cardiol 2022; 117:32. [PMID: 35737129 PMCID: PMC9226085 DOI: 10.1007/s00395-022-00940-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 01/31/2023]
Abstract
Alterations of RNA editing that affect the secondary structure of RNAs can cause human diseases. We therefore studied RNA editing in failing human hearts. Transcriptome sequencing showed that adenosine-to-inosine (A-to-I) RNA editing was responsible for 80% of the editing events in the myocardium. Failing human hearts were characterized by reduced RNA editing. This was primarily attributable to Alu elements in introns of protein-coding genes. In the failing left ventricle, 166 circRNAs were upregulated and 7 circRNAs were downregulated compared to non-failing controls. Most of the upregulated circRNAs were associated with reduced RNA editing in the host gene. ADAR2, which binds to RNA regions that are edited from A-to-I, was decreased in failing human hearts. In vitro, reduction of ADAR2 increased circRNA levels suggesting a causal effect of reduced ADAR2 levels on increased circRNAs in the failing human heart. To gain mechanistic insight, one of the identified upregulated circRNAs with a high reduction of editing in heart failure, AKAP13, was further characterized. ADAR2 reduced the formation of double-stranded structures in AKAP13 pre-mRNA, thereby reducing the stability of Alu elements and the circularization of the resulting circRNA. Overexpression of circAKAP13 impaired the sarcomere regularity of human induced pluripotent stem cell-derived cardiomyocytes. These data show that ADAR2 mediates A-to-I RNA editing in the human heart. A-to-I RNA editing represses the formation of dsRNA structures of Alu elements favoring canonical linear mRNA splicing and inhibiting the formation of circRNAs. The findings are relevant to diseases with reduced RNA editing and increased circRNA levels and provide insights into the human-specific regulation of circRNA formation.
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Affiliation(s)
- Karoline E Kokot
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Jasmin M Kneuer
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - David John
- Institute for Cardiovascular Regeneration, Goethe-University Hospital, Theodor Stern Kai 7, Frankfurt, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Sabine Rebs
- Institute of Pharmacology and Toxicology, Versbacher-Str. 9, Würzburg, Germany
- Heartcenter - Clinic for Cardiology and Pneumology, University Medicine Goettingen, Robert-Koch-Str. 40, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | | | - Stephan Erbe
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Marion Müller
- Department of General and Interventional Cardiology/Angiology, Ruhr University of Bochum, Heart-and Diabetes Center North Rhine-Westphalia, Bad Oeynhausen, Germany
| | - Michael Andritschke
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Susanne Gaul
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Bilal N Sheikh
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Jan Haas
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Holger Thiele
- Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute, Leipzig, Germany
| | - Oliver J Müller
- Department of Internal Medicine III, University of Kiel, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Susanne Hille
- Department of Internal Medicine III, University of Kiel, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Florian Leuschner
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe-University Hospital, Theodor Stern Kai 7, Frankfurt, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Katrin Streckfuss-Bömeke
- Institute of Pharmacology and Toxicology, Versbacher-Str. 9, Würzburg, Germany
- Heartcenter - Clinic for Cardiology and Pneumology, University Medicine Goettingen, Robert-Koch-Str. 40, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Ulrich Laufs
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Jes-Niels Boeckel
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany.
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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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Interplay between A-to-I Editing and Splicing of RNA: A Potential Point of Application for Cancer Therapy. Int J Mol Sci 2022; 23:ijms23095240. [PMID: 35563631 PMCID: PMC9105294 DOI: 10.3390/ijms23095240] [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: 03/24/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Adenosine-to-inosine RNA editing is a system of post-transcriptional modification widely distributed in metazoans which is catalyzed by ADAR enzymes and occurs mostly in double-stranded RNA (dsRNA) before splicing. This type of RNA editing changes the genetic code, as inosine generally pairs with cytosine in contrast to adenosine, and this expectably modulates RNA splicing. We review the interconnections between RNA editing and splicing in the context of human cancer. The editing of transcripts may have various effects on splicing, and resultant alternatively spliced isoforms may be either tumor-suppressive or oncogenic. Dysregulated RNA splicing in cancer often causes the release of excess amounts of dsRNA into cytosol, where specific dsRNA sensors provoke antiviral-like responses, including type I interferon signaling. These responses may arrest cell division, causing apoptosis and, externally, stimulate antitumor immunity. Thus, small-molecule spliceosome inhibitors have been shown to facilitate the antiviral-like signaling and are considered to be potential cancer therapies. In turn, a cytoplasmic isoform of ADAR can deaminate dsRNA in cytosol, thereby decreasing its levels and diminishing antitumor innate immunity. We propose that complete or partial inhibition of ADAR may enhance the proapoptotic and cytotoxic effects of splicing inhibitors and that it may be considered a promising addition to cancer therapies targeting RNA splicing.
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31
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A-to-I RNA editing of BLCAP promotes cell proliferation by losing the inhibitory of Rb1 in colorectal cancer. Exp Cell Res 2022; 417:113209. [DOI: 10.1016/j.yexcr.2022.113209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/03/2022] [Accepted: 05/14/2022] [Indexed: 11/23/2022]
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Zhang S, Kuang G, Huang Y, Huang X, Wang W, Wang G. Cross talk between RNA modification writers and tumor development as a basis for guiding personalized therapy of gastric cancer. Hum Genomics 2022; 16:14. [PMID: 35449086 PMCID: PMC9027049 DOI: 10.1186/s40246-022-00386-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/28/2022] [Indexed: 12/29/2022] Open
Abstract
Background Gastric cancer (GC) shows high metastasis and low survival. RNA modification writers play critical roles in tumor development. This study examined the clinical significance of RNA modification writers in GC prognosis based on four types of adenosine modifications (m1A, m6A, APA and A-to-I). Results Writers demonstrated high mutation and expression in GC patients. Different expressions of 26 RNA modification writers were differentially associated with GC prognosis. High-WM score group appeared worse overall survival, higher immune infiltration and activation of EMT pathways than low-WM score group. WM score was correlated with both miRNAs-targeted signaling pathways and patients’ sensitivity to chemotherapeutic drugs and efficacy of immunotherapy. Conclusions This study further revealed the close association between adenosine-related RNA modifications and progression of GC. A cross talk between EMT and RNA modification was identified to be one of the mechanisms underlying GC development. Our WM scoring system could serve as a clinical indicator for predicting GC prognosis. Importantly, the WM score could guide personalized treatments such as chemotherapy and immunotherapy for GC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00386-z.
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Affiliation(s)
- Shi Zhang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China
| | - Guanghao Kuang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China
| | - Yao Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China
| | - Xinxin Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China
| | - Weiyu Wang
- Department of Oncology, HaploX Biotechnology, Co., Ltd., Shenzhen, 518057, China
| | - Guoqiang Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, 250 Changgang East Road, Haizhu District, Guangzhou, 510260, Guangdong, China.
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Baker AR, Slack FJ. ADAR1 and its implications in cancer development and treatment. Trends Genet 2022; 38:821-830. [PMID: 35459560 PMCID: PMC9283316 DOI: 10.1016/j.tig.2022.03.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
The family of adenosine deaminases acting on RNA (ADARs) regulates global gene expression output by catalyzing adenosine-to-inosine (A-to-I) editing of double-stranded RNA (dsRNA) and through interacting with RNA and other proteins. ADARs play important roles in development and disease, including an increasing connection to cancer progression. ADAR1 has demonstrated a largely pro-oncogenic role in a growing list of cancer types, and its function in cancer has been attributed to diverse mechanisms. Here, we review existing literature on ADAR1 biology and function, its roles in human disease including cancer, and summarize known cancer-associated phenotypes and mechanisms. Lastly, we discuss implications and outstanding questions in the field, including strategies for targeting ADAR1 in cancer.
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Affiliation(s)
- Allison R Baker
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
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Shen H, An O, Ren X, Song Y, Tang SJ, Ke XY, Han J, Tay DJT, Ng VHE, Molias FB, Pitcheshwar P, Leong KW, Tan KK, Yang H, Chen L. ADARs act as potent regulators of circular transcriptome in cancer. Nat Commun 2022; 13:1508. [PMID: 35314703 PMCID: PMC8938519 DOI: 10.1038/s41467-022-29138-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 02/15/2022] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs) are produced by head-to-tail back-splicing which is mainly facilitated by base-pairing of reverse complementary matches (RCMs) in circRNA flanking introns. Adenosine deaminases acting on RNA (ADARs) are known to bind double-stranded RNAs for adenosine to inosine (A-to-I) RNA editing. Here we characterize ADARs as potent regulators of circular transcriptome by identifying over a thousand of circRNAs regulated by ADARs in a bidirectional manner through and beyond their editing function. We find that editing can stabilize or destabilize secondary structures formed between RCMs via correcting A:C mismatches to I(G)-C pairs or creating I(G).U wobble pairs, respectively. We provide experimental evidence that editing also favors the binding of RNA-binding proteins such as PTBP1 to regulate back-splicing. These ADARs-regulated circRNAs which are ubiquitously expressed in multiple types of cancers, demonstrate high functional relevance to cancer. Our findings support a hitherto unappreciated bidirectional regulation of circular transcriptome by ADARs and highlight the complexity of cross-talk in RNA processing and its contributions to tumorigenesis. RNA editing and circRNAs are involved in tumorigenesis. Here the authors report that ADARs regulate the circular transcriptome in a bidirectional manner through and beyond their editing function in multiple cancer cells.
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35
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Zhu H, Huang L, Liu S, Dai Z, Songyang Z, Weng Z, Xiong Y. REIA: A database for cancer A-to-I RNA editing with interactive analysis. Int J Biol Sci 2022; 18:2472-2483. [PMID: 35414795 PMCID: PMC8990463 DOI: 10.7150/ijbs.69458] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/28/2022] [Indexed: 11/05/2022] Open
Abstract
Epitranscriptomic changes caused by adenosine-to-inosine (A-to-I) RNA editing contribute to the pathogenesis of human cancers; however, only a small fraction of the millions editing sites detected so far has clear functionality. To facilitate more in-depth studies on the editing, this paper offers REIA (http://bioinfo-sysu.com/reia), an interactive web server that analyses and visualizes the association between human cancers and A-to-I RNA editing sites (RESs). As a comprehensive database, REIA curates not only 8,447,588 RESs from 9,895 patients across 34 cancers, where 33 are from TCGA and 1 from GEO, but also 13 different types of multi-omic data for the cancers. As an interactive server, REIA provides various options for the user to specify the interested sites, to browse their annotation/editing level/profile in cancer, and to compare the difference in multi-omic features between editing and non-editing groups. From the editing profiles, REIA further detects 658 peptides that are supported by mass spectrum data but not yet covered in any prior works.
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Affiliation(s)
- Huimin Zhu
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Songbin Liu
- School of Automation, Guangdong University of Technology, Guangzhou, 510006, China
| | - Zhiming Dai
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhihui Weng
- Faculty of Health Sciences, University of Macau, Macau, 999078, China
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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36
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Zhang Y, Yang X, Cui Y, Zhang X. Suppression of RNA editing by miR-17 inhibits the stemness of melanoma stem cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:439-455. [PMID: 35036056 PMCID: PMC8728536 DOI: 10.1016/j.omtn.2021.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022]
Abstract
More and more evidence suggests that microRNA (miRNA) and RNA editing play key roles in the development and progression of tumor. However, the influence of miRNA-mediated RNA editing on tumor stem cells remains unclear. In this study, the results demonstrated that miR-17, which was downregulated in melanoma stem cells, acted as a tumor inhibitor by suppressing the stemness of melanoma stem cells and promoting cell differentiation. MiR-17 targeted ADAR2 (adenosine deaminase acting on RNA 2), a gene encoding an editing enzyme required for the maintenance of melanoma stem cell stemness. In melanoma stem cells, ADAR2 was responsible for DOCK2 mRNA editing, which was able to increase the stability of DOCK2 mRNA. The in vitro and in vivo data demonstrated that DOCK2 mRNA editing upregulated the expressions of stemness and anti-apoptotic genes by activating Rac1 and then phosphorylating Akt and NF-κB, thus leading to oncogenesis of melanoma stem cells. Our findings contribute new perspectives to miRNA-regulated RNA editing in tumor progression.
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Affiliation(s)
- Yu Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Xiaoyuan Yang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Yalei Cui
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People’s Republic of China
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37
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Sáenz JB, Vargas N, Cho CJ, Mills JC. Regulation of the double-stranded RNA response through ADAR1 licenses metaplastic reprogramming in gastric epithelium. JCI Insight 2022; 7:153511. [PMID: 35132959 PMCID: PMC8855806 DOI: 10.1172/jci.insight.153511] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/15/2021] [Indexed: 01/17/2023] Open
Abstract
Cells recognize both foreign and host-derived double-stranded RNA (dsRNA) via a signaling pathway that is usually studied in the context of viral infection. It has become increasingly clear that the sensing and handling of endogenous dsRNA is also critical for cellular differentiation and development. The adenosine RNA deaminase, ADAR1, has been implicated as a central regulator of the dsRNA response, but how regulation of the dsRNA response might mediate cell fate during injury and whether such signaling is cell intrinsic remain unclear. Here, we show that the ADAR1-mediated response to dsRNA was dramatically induced in 2 distinct injury models of gastric metaplasia. Mouse organoid and in vivo genetic models showed that ADAR1 coordinated a cell-intrinsic, epithelium-autonomous, and interferon signaling–independent dsRNA response. In addition, dsRNA accumulated within a differentiated epithelial population (chief cells) in mouse and human stomachs as these cells reprogrammed to a proliferative, reparative (metaplastic) state. Finally, chief cells required ADAR1 to reenter the cell cycle during metaplasia. Thus, cell-intrinsic ADAR1 signaling is critical for the induction of metaplasia. Because metaplasia increases cancer risk, these findings support roles for ADAR1 and the response to dsRNA in oncogenesis.
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Affiliation(s)
- José B Sáenz
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Nancy Vargas
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Charles J Cho
- Section of Gastroenterology and Hepatology, Department of Medicine
| | - Jason C Mills
- Section of Gastroenterology and Hepatology, Department of Medicine.,Department of Pathology and Immunology; and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
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38
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Jiang L, Hao Y, Shao C, Wu Q, Prager BC, Gimple RC, Sulli G, Kim LJ, Zhang G, Qiu Z, Zhu Z, Fu XD, Rich JN. ADAR1-mediated RNA editing links ganglioside catabolism to glioblastoma stem cell maintenance. J Clin Invest 2022; 132:143397. [PMID: 35133980 PMCID: PMC8920333 DOI: 10.1172/jci143397] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
Glioblastoma (GBM) is the most common and lethal primary malignant brain tumor, containing GBM stem cells (GSCs) that contribute to therapeutic resistance and relapse. Exposing potential GSC vulnerabilities may provide therapeutic strategies against GBM. Here, we interrogated the role of Adenosine-to-Inosine (A-to-I) RNA editing mediated by ADAR1 (adenosine deaminase acting on RNA 1) in GSCs and found that both ADAR1 and global RNA editomes were elevated in GSCs compared to normal neural stem cells (NSCs). ADAR1 inactivation or blocking the upstream JAK/STAT pathway through TYK2 inhibition impaired GSC self-renewal and stemness. Downstream of ADAR1, RNA editing of the 3'UTR of GM2A, a key ganglioside catabolism activator, proved to be critical, as interfering with ganglioside catabolism showed similar functional impact on GSCs as ADAR1 disruption. These findings reveal RNA editing links ganglioside catabolism to GSC self-renewal and stemness, exposing a potential vulnerability of GBM for therapeutic intervention.
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Affiliation(s)
- Li Jiang
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States of America
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States of America
| | - Qiulian Wu
- Hillman Cancer Center, Cancer Institute, University of Pittsburgh, Pittsburgh, United States of America
| | - Briana C Prager
- Stem Cell Biology, Cleveland Clinic, Cleveland, United States of America
| | - Ryan C Gimple
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Gabriele Sulli
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Leo Jk Kim
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Guoxin Zhang
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Zhixin Qiu
- Hillman Cancer Center, Cancer Institute, University of Pittsburgh, Pittsburgh, United States of America
| | - Zhe Zhu
- Department of Medicine, University of California, San Diego, San Diego, United States of America
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States of America
| | - Jeremy N Rich
- Hillman Cancer Center, Cancer Institute, University of Pittsburgh, Pittsburgh, United States of America
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Abstract
Gastric cancer (GC) is a leading contributor to global cancer incidence and mortality. Pioneering genomic studies, focusing largely on primary GCs, revealed driver alterations in genes such as ERBB2, FGFR2, TP53 and ARID1A as well as multiple molecular subtypes. However, clinical efforts targeting these alterations have produced variable results, hampered by complex co-alteration patterns in molecular profiles and intra-patient genomic heterogeneity. In this Review, we highlight foundational and translational advances in dissecting the genomic cartography of GC, including non-coding variants, epigenomic aberrations and transcriptomic alterations, and describe how these alterations interplay with environmental influences, germline factors and the tumour microenvironment. Mapping of these alterations over the GC life cycle in normal gastric tissues, metaplasia, primary carcinoma and distant metastasis will improve our understanding of biological mechanisms driving GC development and promoting cancer hallmarks. On the translational front, integrative genomic approaches are identifying diverse mechanisms of GC therapy resistance and emerging preclinical targets, enabled by technologies such as single-cell sequencing and liquid biopsies. Validating these insights will require specifically designed GC cohorts, converging multi-modal genomic data with longitudinal data on therapeutic challenges and patient outcomes. Genomic findings from these studies will facilitate 'next-generation' clinical initiatives in GC precision oncology and prevention.
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Affiliation(s)
- Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore, Singapore
| | - Patrick Tan
- Singapore Gastric Cancer Consortium, Singapore, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School Singapore, Singapore, Singapore.
- Genome Institute of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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40
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Yang H, Rui F, Li R, Yin S, Xue Q, Hu X, Xu Y, Wu C, Shi J, Li J. ADAR1 Inhibits HBV DNA Replication via Regulating miR-122-5p in Palmitic Acid Treated HepG2.2.15 Cells. Diabetes Metab Syndr Obes 2022; 15:4035-4047. [PMID: 36582505 PMCID: PMC9793725 DOI: 10.2147/dmso.s373385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND AIMS Changes in living standards and diet structure, non-alcoholic fatty liver disease (NAFLD) is prevalent globally, including in Asia, where chronic hepatitis B (CHB) is endemic. As such, cooccurrence of NAFLD with CHB is common in Asia. However, the pathogenesis underlying the onset of fatty liver in CHB prognosis has not been fully elucidated. Therefore, we aimed to investigate the effects and mechanisms of lipotoxicity on hepatitis B virus (HBV) DNA replication. METHODS The expression of adenosine deaminase acting on RNA-1 (ADAR1) and miR-122 was evaluated in liver tissues from patients with CHB concurrent NAFLD. Palmitic acid-treated HepG2.2.15 cells were used as the cell model. The effect of lipotoxicity on HBV DNA replication was evaluated in vitro by transfecting the ADAR1 overexpression or knockdown lentiviral vector into HepG2.2.15 cells, respectively. qRT-PCR, western blotting and immunofluorescence were performed to determine ADAR1 expression. RESULTS The expression of ADAR1 in the liver tissues of CHB patients with concurrent NAFLD was significantly down-regulated compared with that in CHB patients. Enforced expression of ADAR1 inhibited the HBV DNA replication, whereas ADAR1 knockdown resulted in increased HBV DNA expression in palmitic acid - treated HepG2.2.15 cells. Additionally, ADAR1 inhibited the HBV DNA replication by upregulating miR-122, which is most abundant in the liver and mainly inhibits HBV DNA replication. CONCLUSIONS ADAR1 may act as a suppressor of HBV replication in palmitic acid -treated HepG2.2.15 cells by increasing miR-122 levels. Thus, ADAR1 may serve as a potential biomarker and therapeutic target for CHB with concurrent NAFLD.
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Affiliation(s)
- Hongli Yang
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji’nan, People’s Republic of China
| | - Fajuan Rui
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing, People’s Republic of China
| | - Rui Li
- Department of Gastroenterology, Binzhou Medical University Hospital, Binzhou, People’s Republic of China
| | - Shengxia Yin
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People’s Republic of China
| | - Qi Xue
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji’nan, People’s Republic of China
| | - Xinyu Hu
- Department of Gastroenterology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Ji’nan, People’s Republic of China
| | - Yayun Xu
- Department of Gastroenterology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Ji’nan, People’s Republic of China
| | - Chao Wu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People’s Republic of China
| | - Junping Shi
- Department of Infectious Disease, The Affiliated Hospital of Hangzhou Normal University, Wenzhou Road, Hangzhou, People’s Republic of China
- Junping Shi, Department of Infectious Disease, The Affiliated Hospital of Hangzhou Normal University, Wenzhou Road, Hangzhou, Zhejiang, People’s Republic of China, Email
| | - Jie Li
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing, People’s Republic of China
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People’s Republic of China
- Correspondence: Jie Li, Department of Infectious Diseases, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People’s Republic of China, Email
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Amweg A, Tusup M, Cheng P, Picardi E, Dummer R, Levesque MP, French LE, Guenova E, Läuchli S, Kundig T, Mellett M, Pascolo S. The A to I editing landscape in melanoma and its relation to clinical outcome. RNA Biol 2022; 19:996-1006. [PMID: 35993275 PMCID: PMC9415457 DOI: 10.1080/15476286.2022.2110390] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
RNA editing refers to non-transient RNA modifications that occur after transcription and prior to translation by the ribosomes. RNA editing is more widespread in cancer cells than in non-transformed cells and is associated with tumorigenesis of various cancer tissues. However, RNA editing can also generate neo-antigens that expose tumour cells to host immunosurveillance. Global RNA editing in melanoma and its relevance to clinical outcome currently remain poorly characterized. The present study compared RNA editing as well as gene expression in tumour cell lines from melanoma patients of short or long metastasis-free survival, patients relapsing or not after immuno- and targeted therapy and tumours harbouring BRAF or NRAS mutations. Overall, our results showed that NTRK gene expression can be a marker of resistance to BRAF and MEK inhibition and gives some insights of candidate genes as potential biomarkers. In addition, this study revealed an increase in Adenosine-to-Inosine editing in Alu regions and in non-repetitive regions, including the hyperediting of the MOK and DZIP3 genes in relapsed tumour samples during targeted therapy and of the ZBTB11 gene in NRAS mutated melanoma cells. Therefore, RNA editing could be a promising tool for identifying predictive markers, tumour neoantigens and targetable pathways that could help in preventing relapses during immuno- or targeted therapies.
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Affiliation(s)
- Austeja Amweg
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Marina Tusup
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Phil Cheng
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Lars E French
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany.,Dr. Philip Frost, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Emmanuella Guenova
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland.,Department of Dermatology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Severin Läuchli
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mark Mellett
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
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42
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Larsen K, Heide-Jørgensen MP. Conservation of A-to-I RNA editing in bowhead whale and pig. PLoS One 2021; 16:e0260081. [PMID: 34882682 PMCID: PMC8659423 DOI: 10.1371/journal.pone.0260081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/02/2021] [Indexed: 01/18/2023] Open
Abstract
RNA editing is a post-transcriptional process in which nucleotide changes are introduced into an RNA sequence, many of which can contribute to proteomic sequence variation. The most common type of RNA editing, contributing to nearly 99% of all editing events in RNA, is A-to-I (adenosine-to-inosine) editing mediated by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. A-to-I editing at 'recoding' sites results in non-synonymous substitutions in protein-coding sequences. Here, we present studies of the conservation of A-to-I editing in selected mRNAs between pigs, bowhead whales, humans and two shark species. All examined mRNAs-NEIL1, COG3, GRIA2, FLNA, FLNB, IGFBP7, AZIN1, BLCAP, GLI1, SON, HTR2C and ADAR2 -showed conservation of A-to-I editing of recoding sites. In addition, novel editing sites were identified in NEIL1 and GLI1 in bowhead whales. The A-to-I editing site of human NEIL1 in position 242 was conserved in the bowhead and porcine homologues. A novel editing site was discovered in Tyr244. Differential editing was detected at the two adenosines in the NEIL1 242 codon in both pig and bowhead NEIL1 mRNAs in various tissues and organs. No conservation of editing of KCNB1 and EEF1A mRNAs was seen in bowhead whales. In silico analyses revealed conservation of five adenosines in ADAR2, some of which are subject to A-to-I editing in bowheads and pigs, and conservation of a regulatory sequence in GRIA2 mRNA that is responsible for recognition of the ADAR editing enzyme.
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Affiliation(s)
- Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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43
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Zhang X, Yan W, Xue Y, Xu H, Li J, Zhao Z, Sun Y, Wang Y, He J, Huang Y, Yu D, Xiao Z, Yin S. Roles of miR-432 and circ_0000418 in mediating the anti-depressant action of ADAR1. Neurobiol Stress 2021; 15:100396. [PMID: 34568523 PMCID: PMC8449188 DOI: 10.1016/j.ynstr.2021.100396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/07/2021] [Accepted: 09/11/2021] [Indexed: 12/27/2022] Open
Abstract
Adenosine deaminase acting on RNA1 (ADAR1) is a newly discovered epigenetic molecule marker that is sensitive to environmental stressors. A recent study has demonstrated that ADAR1 affects BDNF expression via miR-432 and is involved in antidepressant action. However, the detailed molecular mechanism is still unclear. We have uncovered a new molecular mechanism showing the involvement of miR-432 and circ_0000418 in mediating the antidepressant action of ADAR1. We demonstrate that the ADAR1 inducer (IFN-γ) alleviates the depressive-like behaviors of BALB/c mice treated with chronic unpredictable stress (CUS) exposure. Moreover, both in vivo and in vitro studies show that ADAR1 differently impacts miR-432 and circ_0000418 expressions. Furthermore, the in vitro results demonstrate that circ_0000418 oppositely affects BDNF expression. Together, our results indicate that ADAR1 affects CUS-induced depressive-like behavior and BDNF expression by acting on miR-432 and circ_0000418. Elucidation of this new molecular mechanism will not only provide insights into further understanding the important role of ADAR1 in stress-induced depressive-like behavior but also suggest a potential therapeutic strategy for developing novel anti-depressive drugs. MiR-432 and circ_0000418 mediates the antidepressant action of ADAR1. MiR-432 and circ_0000418 interactively affect BDNF expression. LIN28B is involved in the interaction among ADAR1, miR-432, and circ_0000418. HNRNPC is involved in the regulatory role of circ_0000418 on BDNF.
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Affiliation(s)
- Xiaonan Zhang
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China.,National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, Liaoning, China
| | - Wei Yan
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China.,National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, Liaoning, China
| | - Ying Xue
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China.,National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, Liaoning, China
| | - Hong Xu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China
| | - Jinying Li
- The 2nd Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
| | - Ziwei Zhao
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China.,National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, Liaoning, China
| | - Ye Sun
- The 2nd Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
| | - Yanfang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China.,National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, Liaoning, China
| | - Jiaqian He
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China
| | - Yuyue Huang
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China
| | - Deqin Yu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China.,National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, Liaoning, China
| | - Zhaoyang Xiao
- The 2nd Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
| | - Shengming Yin
- College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China.,National and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases, Dalian, Liaoning, China
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Tan KT, Ding LW, Wu CS, Tenen DG, Yang H. Repurposing RNA sequencing for discovery of RNA modifications in clinical cohorts. SCIENCE ADVANCES 2021; 7:eabd2605. [PMID: 34348892 PMCID: PMC8336963 DOI: 10.1126/sciadv.abd2605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/14/2021] [Indexed: 05/07/2023]
Abstract
The study of RNA modifications in large clinical cohorts can reveal relationships between the epitranscriptome and human diseases, although this is especially challenging. We developed ModTect (https://github.com/ktan8/ModTect), a statistical framework to identify RNA modifications de novo by standard RNA-sequencing with deletion and mis-incorporation signals. We show that ModTect can identify both known (N 1-methyladenosine) and previously unknown types of mRNA modifications (N 2,N 2-dimethylguanosine) at nucleotide-resolution. Applying ModTect to 11,371 patient samples and 934 cell lines across 33 cancer types, we show that the epitranscriptome was dysregulated in patients across multiple cancer types and was additionally associated with cancer progression and survival outcomes. Some types of RNA modification were also more disrupted than others in patients with cancer. Moreover, RNA modifications contribute to multiple types of RNA-DNA sequence differences, which unexpectedly escape detection by Sanger sequencing. ModTect can thus be used to discover associations between RNA modifications and clinical outcomes in patient cohorts.
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Affiliation(s)
- Kar-Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Biological and Biomedical Sciences Program, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Department of Computer Science, School of Computing, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chan-Shuo Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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45
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Wu M, Jin M, Cao X, Qian K, Zhao L. RNA editing enzyme adenosine deaminases acting on RNA 1 deficiency increases the sensitivity of non-small cell lung cancer cells to anlotinib by regulating CX3CR1-fractalkine expression. Drug Dev Res 2021; 83:328-338. [PMID: 34319598 DOI: 10.1002/ddr.21861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/12/2021] [Accepted: 07/16/2021] [Indexed: 02/02/2023]
Abstract
Adenosine deaminases acting on RNA 1 (ADAR1) has been identified to play key roles in non-small cell lung cancer (NSCLC) progression, and can modulate the sensitivity of cancer cells to anticancer drugs. The current study aimed to investigate the effect of ADAR1 on the sensitivity of NSCLC cells to anlotinib. We established anlotinib-resistant NSCLC (NSCLC/AR) cells, including NCI-H1975/AR and A549/AR cells. Results showed that ADAR1 was significantly upregulated in NSCLC/AR cells. Genetic-knockdown of ADAR1 increased the sensitivity of NSCLC/AR cells to anlotinib by inducing cell proliferation suppression, cell cycle arrest, and apoptosis. Furthermore, knockdown of ADAR1 decreased the level of C-X3-C motif chemokine ligand 1 (CX3CL1) in NCI-H1975/AR and A549/AR cells after anlotinib treatment. Introduction of exogenous CX3CL1 significantly reversed the positive effect of ADAR1 deficiency on NSCLC/AR cell sensitivity, exhibited by the increase of cell viability and decrease of apoptosis. Further in-vivo study demonstrated that knockdown of ADAR1 inhibited NCI-H1975/AR cell tumorigenesis by reducing CX3CL1 expression. Collectively, ADAR1 deficiency increased the sensitivity of NSCLC/AR cells to anlotinib by downregulating CX3CL1, which might provide a potential strategy for NSCLC/AR therapy.
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Affiliation(s)
- Min Wu
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mengmeng Jin
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaohui Cao
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Kun Qian
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lei Zhao
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
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46
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Berdasco M, Esteller M. Towards a druggable epitranscriptome: Compounds that target RNA modifications in cancer. Br J Pharmacol 2021; 179:2868-2889. [PMID: 34185879 DOI: 10.1111/bph.15604] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/27/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022] Open
Abstract
Epitranscriptomics is an exciting emerging area that studies biochemical modifications of RNA. The field has been opened up by the technical efforts of the last decade to characterize and quantify RNA modifications, and this has led to a map of post-transcriptional RNA marks in normal cell fate and development. However, the scientific interest has been fuelled by the discovery of aberrant epitranscriptomes associated with human diseases, mainly cancer. The challenge is now to see whether epitrancriptomics offers mechanisms that can be effectively targeted by low MW compounds and are thus druggable. In this review, we will describe the principal RNA modifications (with a focus on mRNA), summarize the latest scientific evidence of their dysregulation in cancer and provide an overview of the state-of-the-art drug discovery to target the epitranscriptome. Finally, we will discuss the principal challenges in the field of chemical biology and drug development to increase the potential of targeted-RNA for clinical benefit.
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Affiliation(s)
- María Berdasco
- Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC), Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
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Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M. Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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Wang C, Huang M, Chen C, Li Y, Qin N, Ma Z, Fan J, Gong L, Zeng H, Yang L, Xu X, Zhou J, Dai J, Jin G, Hu Z, Ma H, Tan F, Shen H. Identification of A-to-I RNA editing profiles and their clinical relevance in lung adenocarcinoma. SCIENCE CHINA-LIFE SCIENCES 2021; 65:19-32. [PMID: 34050895 DOI: 10.1007/s11427-020-1928-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/03/2021] [Indexed: 12/24/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a widespread posttranscriptional modification that has been shown to play an important role in tumorigenesis. Here, we evaluated a total of 19,316 RNA editing sites in the tissues of 80 lung adenocarcinoma (LUAD) patients from our Nanjing Lung Cancer Cohort (NJLCC) and 486 LUAD patients from the TCGA database. The global RNA editing level was significantly increased in tumor tissues and was highly heterogeneous across patients. The high RNA editing level in tumors was attributed to both RNA (ADAR1 expression) and DNA alterations (mutation load). Consensus clustering on RNA editing sites revealed a new molecular subtype (EC3) that was associated with the poorest prognosis of LUAD patients. Importantly, the new classification was independent of classic molecular subtypes based on gene expression or DNA methylation. We further proposed a simplified model including eight RNA editing sites to accurately distinguish the EC3 subtype in our patients. The model was further validated in the TCGA dataset and had an area under the curve (AUC) of the receiver operating characteristic curve of 0.93 (95%CI: 0.91-0.95). In addition, we found that LUAD cell lines with the EC3 subtype were sensitive to four chemotherapy drugs. These findings highlighted the importance of RNA editing events in the tumorigenesis of LUAD and provided insight into the application of RNA editing in the molecular subtyping and clinical treatment of cancer.
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Affiliation(s)
- Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Mingtao Huang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Congcong Chen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yuancheng Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Na Qin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zijian Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Jingyi Fan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Linnan Gong
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hui Zeng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Liu Yang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Xianfeng Xu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Jun Zhou
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personized Medicine, Nanjing Medical University, Nanjing, 211166, China.
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Tai Tay DJ, Song Y, Peng B, Toh TB, Hooi L, Kaixin Toh DF, Hong H, Tang SJ, Han J, Gan WL, Man Chan TH, Krishna MS, Patil KM, Maraswami M, Loh TP, Dan YY, Zhou L, Bonney GK, Kah-Hoe Chow P, Chen G, Kai-Hua Chow E, Le MT, Chen L. Targeting RNA Editing of Antizyme Inhibitor 1: a Potential Oligonucleotide-Based Antisense Therapy for Cancer. Mol Ther 2021; 29:3258-3273. [PMID: 33974998 PMCID: PMC8571177 DOI: 10.1016/j.ymthe.2021.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/29/2021] [Accepted: 05/05/2021] [Indexed: 11/26/2022] Open
Abstract
Dysregulated adenosine-to-inosine (A-to-I) RNA editing is implicated in various cancers. However, no available RNA editing inhibitors have so far been developed to inhibit cancer-associated RNA editing events. Here, we decipher the RNA secondary structure of antizyme inhibitor 1 (AZIN1), one of the best-studied A-to-I editing targets in cancer, by locating its editing site complementary sequence (ECS) at the 3′ end of exon 12. Chemically modified antisense oligonucleotides (ASOs) that target the editing region of AZIN1 caused a substantial exon 11 skipping, whereas ECS-targeting ASOs effectively abolished AZIN1 editing without affecting splicing and translation. We demonstrate that complete 2′-O-methyl (2′-O-Me) sugar ring modification in combination with partial phosphorothioate (PS) backbone modification may be an optimal chemistry for editing inhibition. ASO3.2, which targets the ECS, specifically inhibits cancer cell viability in vitro and tumor incidence and growth in xenograft models. Our results demonstrate that this AZIN1-targeting, ASO-based therapeutics may be applicable to a wide range of tumor types.
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Affiliation(s)
- Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Boya Peng
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore 117600; Department of Biomedical Sciences, School of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong
| | - Tan Boon Toh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599; The N.1 Institute for Health (N.1), 28 Medical Dr, Singapore 117456
| | - Lissa Hooi
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 21 Nanyang Link, Singapore 637371
| | - HuiQi Hong
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore 117593
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Wei Liang Gan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 21 Nanyang Link, Singapore 637371
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 21 Nanyang Link, Singapore 637371
| | - Manikantha Maraswami
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 21 Nanyang Link, Singapore 637371
| | - Teck Peng Loh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 21 Nanyang Link, Singapore 637371
| | - Yock Young Dan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599; Division of Gastroenterology and Hepatology, National University Health System, Singapore 119228
| | - Lei Zhou
- Division of Gastroenterology and Hepatology, National University Health System, Singapore 119228
| | - Glenn Kunnath Bonney
- Division of Hepatobiliary and Liver Transplantation Surgery, National University Health System, Singapore 119228
| | - Pierce Kah-Hoe Chow
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610; Department of Hepato-Pancreato-Biliary and Transplant Surgery, Singapore General Hospital, Singapore 169608; Duke-NUS Medical School, Singapore 169857
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 21 Nanyang Link, Singapore 637371
| | - Edward Kai-Hua Chow
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore 117600; The N.1 Institute for Health (N.1), 28 Medical Dr, Singapore 117456
| | - Minh Tn Le
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore 117600; Department of Biomedical Sciences, School of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore 117594.
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50
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Srinivasan S, Torres AG, Ribas de Pouplana L. Inosine in Biology and Disease. Genes (Basel) 2021; 12:600. [PMID: 33921764 PMCID: PMC8072771 DOI: 10.3390/genes12040600] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.
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Affiliation(s)
- Sundaramoorthy Srinivasan
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Catalonia, Spain
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