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Luo Y, Tian W, Kang D, Wu L, Tang H, Wang S, Zhang C, Xie Y, Zhang Y, Xie J, Deng X, Zou H, Wu H, Lin H, Wei W. RNA modification gene WDR4 facilitates tumor progression and immunotherapy resistance in breast cancer. J Adv Res 2024:S2090-1232(24)00266-2. [PMID: 38960276 DOI: 10.1016/j.jare.2024.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 06/30/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024] Open
Abstract
INTRODUCTION Growing interest toward RNA modification in cancer has inspired the exploration of gene sets related to multiple RNA modifications. However, a comprehensive elucidation of the clinical value of various RNA modifications in breast cancer is still lacking. OBJECTIVES This study aimed to provide a strategy based on RNA modification-related genes for predicting therapy response and survival outcomes in breast cancer patients. METHODS Genes related to thirteen RNA modification patterns were integrated for establishing a nine-gene-containing signature-RMscore. Alterations of tumor immune microenvironment and therapy response featured by different RMscore levels were assessed by bulk transcriptome, single-cell transcriptome and genomics analyses. The biological function of key RMscore-related molecules was investigated by cellular experiments in vitro and in vivo, using flow cytometry, immunohistochemistry and immunofluorescence staining. RESULTS This study has raised an effective therapy strategy for breast cancer patients after a well-rounded investigation of RNA modification-related genes. With a great performance of predicting patient prognosis, high levels of the RMscore proposed in this study represented suppressive immune microenvironment and therapy resistance, including adjuvant chemotherapy and PD-L1 blockade treatment. As the key contributor of the RMscore, inhibition of WDR4 impaired breast cancer progression significantly in vitro and in vivo, as well as participated in regulating cell cycle and mTORC1 signaling pathway via m7G modification. CONCLUSION Briefly, this study has developed promising and effective tactics to achieve the prediction of survival probabilities and treatment response in breast cancer patients.
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Affiliation(s)
- Yongzhou Luo
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Wenwen Tian
- Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, No.78, Hengzhigang Road, Guangzhou 510095, China
| | - Da Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Linyu Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Sifen Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Chao Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Yi Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Yue Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hao Zou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hao Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China.
| | - Huan Lin
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Weidong Wei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China.
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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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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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4
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Yang M, Jiang J, Ren R, Gao N, He J, Zhang Y. Role of ADAR1 on Proliferation and Differentiation in Porcine Preadipocytes. Animals (Basel) 2024; 14:1201. [PMID: 38672349 PMCID: PMC11047480 DOI: 10.3390/ani14081201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/30/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Recent research has identified ADAR1 as a participant in the regulation of lipid accumulation in mice. However, there are no reports on the roles of ADAR1 in proliferation, apoptosis and differentiation of porcine preadipocytes. In this study, we investigated the role of ADAR1 in differentiation, proliferation and apoptosis of porcine preadipocytes using CCK-8, EdU staining, cell cycle detection, RT-qPCR, Western blot, a triglyceride assay and Oil Red O staining. The over-expression of ADAR1 significantly promoted proliferation but inhibited the differentiation and apoptosis of porcine preadipocytes. The inhibition of ADAR1 had the opposite effect on the proliferation, differentiation and apoptosis of porcine preadipocytes with over-expressed ADAR1. Then, the regulation mechanisms of ADAR1 on preadipocyte proliferation were identified using RNA-seq, and 197 DEGs in response to ADAR1 knockdown were identified. The MAPK signaling pathway is significantly enriched, indicating its importance in mediating fat accumulation regulated by ADAR1. The study's findings will aid in uncovering the mechanisms that regulate fat accumulation through ADAR1.
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Affiliation(s)
- Menghuan Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Ruimin Ren
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.Y.); (J.J.); (R.R.); (N.G.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
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Jiao Y, Xu Y, Liu C, Miao R, Liu C, Wang Y, Liu J. The role of ADAR1 through and beyond its editing activity in cancer. Cell Commun Signal 2024; 22:42. [PMID: 38233935 PMCID: PMC10795376 DOI: 10.1186/s12964-023-01465-x] [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: 11/06/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) editing of RNA, catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, is a prevalent RNA modification in mammals. It has been shown that A-to-I editing plays a critical role in multiple diseases, such as cardiovascular disease, neurological disorder, and particularly cancer. ADARs are the family of enzymes, including ADAR1, ADAR2, and ADAR3, that catalyze the occurrence of A-to-I editing. Notably, A-to-I editing is mainly catalyzed by ADAR1. Given the significance of A-to-I editing in disease development, it is important to unravel the complex roles of ADAR1 in cancer for the development of novel therapeutic interventions.In this review, we briefly describe the progress of research on A-to-I editing and ADARs in cancer, mainly focusing on the role of ADAR1 in cancer from both editing-dependent and independent perspectives. In addition, we also summarized the factors affecting the expression and editing activity of ADAR1 in cancer.
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Affiliation(s)
- Yue Jiao
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Yuqin Xu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China.
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Heruye S, Myslinski J, Zeng C, Zollman A, Makino S, Nanamatsu A, Mir Q, Janga SC, Doud EH, Eadon MT, Maier B, Hamada M, Tran TM, Dagher PC, Hato T. Inflammation primes the kidney for recovery by activating AZIN1 A-to-I editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566426. [PMID: 37986799 PMCID: PMC10659426 DOI: 10.1101/2023.11.09.566426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The progression of kidney disease varies among individuals, but a general methodology to quantify disease timelines is lacking. Particularly challenging is the task of determining the potential for recovery from acute kidney injury following various insults. Here, we report that quantitation of post-transcriptional adenosine-to-inosine (A-to-I) RNA editing offers a distinct genome-wide signature, enabling the delineation of disease trajectories in the kidney. A well-defined murine model of endotoxemia permitted the identification of the origin and extent of A-to-I editing, along with temporally discrete signatures of double-stranded RNA stress and Adenosine Deaminase isoform switching. We found that A-to-I editing of Antizyme Inhibitor 1 (AZIN1), a positive regulator of polyamine biosynthesis, serves as a particularly useful temporal landmark during endotoxemia. Our data indicate that AZIN1 A-to-I editing, triggered by preceding inflammation, primes the kidney and activates endogenous recovery mechanisms. By comparing genetically modified human cell lines and mice locked in either A-to-I edited or uneditable states, we uncovered that AZIN1 A-to-I editing not only enhances polyamine biosynthesis but also engages glycolysis and nicotinamide biosynthesis to drive the recovery phenotype. Our findings implicate that quantifying AZIN1 A-to-I editing could potentially identify individuals who have transitioned to an endogenous recovery phase. This phase would reflect their past inflammation and indicate their potential for future recovery.
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Affiliation(s)
- Segewkal Heruye
- Department of Medicine, Indiana University School of Medicine
| | - Jered Myslinski
- Department of Medicine, Indiana University School of Medicine
| | - Chao Zeng
- Faculty of Science and Engineering, Waseda University, Tokyo
| | - Amy Zollman
- Department of Medicine, Indiana University School of Medicine
| | - Shinichi Makino
- Department of Medicine, Indiana University School of Medicine
| | - Azuma Nanamatsu
- Department of Medicine, Indiana University School of Medicine
| | - Quoseena Mir
- Luddy School of Informatics, Computing, and Engineering, Indiana University
| | | | - Emma H Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine
| | - Michael T Eadon
- Department of Medicine, Indiana University School of Medicine
| | - Bernhard Maier
- Department of Medicine, Indiana University School of Medicine
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, Tokyo
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo
- Graduate School of Medicine, Nippon Medical School, Tokyo
| | - Tuan M Tran
- Department of Medicine, Indiana University School of Medicine
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis
| | - Pierre C Dagher
- Department of Medicine, Indiana University School of Medicine
| | - Takashi Hato
- Department of Medicine, Indiana University School of Medicine
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis
- Department of Medical and Molecular Genetics, Indiana University School of Medicine
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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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8
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Zhong Y, Zhong X, Qiao L, Wu H, Liu C, Zhang T. Zα domain proteins mediate the immune response. Front Immunol 2023; 14:1241694. [PMID: 37771585 PMCID: PMC10523160 DOI: 10.3389/fimmu.2023.1241694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023] Open
Abstract
The Zα domain has a compact α/β architecture containing a three-helix bundle flanked on one side by a twisted antiparallel β sheet. This domain displays a specific affinity for double-stranded nucleic acids that adopt a left-handed helical conformation. Currently, only three Zα-domain proteins have been identified in eukaryotes, specifically ADAR1, ZBP1, and PKZ. ADAR1 is a double-stranded RNA (dsRNA) binding protein that catalyzes the conversion of adenosine residues to inosine, resulting in changes in RNA structure, function, and expression. In addition to its editing function, ADAR1 has been shown to play a role in antiviral defense, gene regulation, and cellular differentiation. Dysregulation of ADAR1 expression and activity has been associated with various disease states, including cancer, autoimmune disorders, and neurological disorders. As a sensing molecule, ZBP1 exhibits the ability to recognize nucleic acids with a left-handed conformation. ZBP1 harbors a RIP homotypic interaction motif (RHIM), composed of a highly charged surface region and a leucine-rich hydrophobic core, enabling the formation of homotypic interactions between proteins with similar structure. Upon activation, ZBP1 initiates a downstream signaling cascade leading to programmed cell death, a process mediated by RIPK3 via the RHIM motif. PKZ was identified in fish, and contains two Zα domains at the N-terminus. PKZ is essential for normal growth and development and may contribute to the regulation of immune system function in fish. Interestingly, some pathogenic microorganisms also encode Zα domain proteins, such as, Vaccinia virus and Cyprinid Herpesvirus. Zα domain proteins derived from pathogenic microorganisms have been demonstrated to be pivotal contributors in impeding the host immune response and promoting virus replication and spread. This review focuses on the mammalian Zα domain proteins: ADAR1 and ZBP1, and thoroughly elucidates their functions in the immune response.
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Affiliation(s)
- Yuhan Zhong
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao Zhong
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Liangjun Qiao
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Hong Wu
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Chang Liu
- Division of Liver, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Zhang
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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9
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Ge F, Cao X, Jiang Y. A-to-I RNA editing shows dramatic up-regulation in osteosarcoma and broadly regulates tumor-related genes by altering microRNA target regions. J Appl Genet 2023; 64:493-505. [PMID: 37542613 DOI: 10.1007/s13353-023-00777-5] [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: 07/11/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
A-to-I RNA editing is a prevalent type of RNA modification in animals. The dysregulation of RNA editing has led to multiple human cancers. However, the role of RNA editing has never been studied in osteosarcoma, a complex bone cancer with unknown molecular basis. We retrieved the RNA-sequencing data from 24 primary osteosarcoma patients and 3 healthy controls. We systematically profiled the RNA editomes in these samples and quantitatively identified reliable differential editing sites (DES) between osteosarcoma and normal samples. RNA editing efficiency is dramatically increased in osteosarcoma, presumably due to the significant up-regulation of editing enzymes ADAR1 and ADAR2. Up-regulated DES in osteosarcoma are enriched in 3'UTRs. Strikingly, such 3'UTR sites are further enriched in microRNA binding regions of gene EMP2 and other oncogenes, abolishing the microRNA suppression on target genes. Accordingly, the expression of these tumor-promoting genes is elevated in osteosarcoma. There might be an RNA editing-dependent pathway leading to osteosarcoma. We expanded our knowledge on the potential roles of RNA editing in oncogenesis. Based on these molecular features, our work is valuable for future prognosis and diagnosis of osteosarcoma.
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Affiliation(s)
- Fuqun Ge
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Xinyue Cao
- School of Clinical Medicine, Qilu Medical University, Zibo, 255300, Shandong, China
| | - Yankai Jiang
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China.
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10
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Cai M, Liu X, Luo A, Yang X, Yan Y, Liu S, Wang X, Luo Z, Wu X, Huang K, Yang L, Jiang H, Xu L, Liu X. ADAR1 polymorphisms contribute to increased susceptibility in pediatric acute lymphoblastic leukemia. Ann Hematol 2023; 102:2483-2492. [PMID: 37217676 DOI: 10.1007/s00277-023-05285-4] [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: 01/31/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Adenosine deaminase acting on RNA1 (ADAR1), catalyzing post-transcriptional adenosine-to-inosine RNA editing, promotes cancer progression and therapeutic resistance. However, very little is known about the association of ADAR1 variants with acute lymphoblastic leukemia (ALL). Here we first explored the potential association of three polymorphisms (rs9616, rs2229857, and rs1127313) of ADAR1 with susceptibility in Chinese children ALL, then functionally characterized ADAR1 in ALL. Our results demonstrated that rs9616 T and rs2229857 T were associated with increased expression of ADAR1 mRNA and higher risk to ALL. Of note, a stronger risk effect of rs2229857 T genotypes was found among relapse children. Furthermore, ADAR1 knockdown specifically inhibited proliferation and promoted apoptosis in ALL cells. These findings give insights into a mechanism by which the risk variant at rs9616 and rs2229857 modulate ADAR1 expression and confers a predisposition and relapse risk to ALL, and representing a potential novel biomarker for pediatric ALL.
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Affiliation(s)
- Mansi Cai
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xiaoping Liu
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Ailing Luo
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xu Yang
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Yaping Yan
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Shanshan Liu
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xueliang Wang
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
| | - Ziyan Luo
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
| | - Xuedong Wu
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ke Huang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lihua Yang
- Pediatric Hematology Department, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hua Jiang
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China
| | - Ling Xu
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China.
| | - Xiaodan Liu
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China.
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, 9 Jinsui Road, Zhujiang Newtown, Tianhe District, Guangzhou, 510623, Guangdong, China.
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11
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Yang S, Zhu G, He R, Fang D, Feng J. Advances in transcriptomics and proteomics in differentiated thyroid cancer: An updated perspective (Review). Oncol Lett 2023; 26:396. [PMID: 37600346 PMCID: PMC10433702 DOI: 10.3892/ol.2023.13982] [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: 02/14/2023] [Accepted: 05/25/2023] [Indexed: 08/22/2023] Open
Abstract
Thyroid cancer (TC) is a broad classification of neoplasms that includes differentiated thyroid cancer (DTC) as a common histological subtype. DTC is characterized by an increased mortality rate in advanced stages, which contributes to the overall high mortality rate of DTC. This progression is mainly attributed to alterations in molecular driver genes, resulting in changes in phenotypes such as invasion, metastasis and dedifferentiation. Clinical management of DTC is challenging due to insufficient diagnostic and therapeutic options. The advent of-omics technology has presented a promising avenue for the diagnosis and treatment of DTC. Identifying molecular markers that can predict the early progression of DTC to a late adverse outcome is essential for precise diagnosis and treatment. The present review aimed to enhance our understanding of DTC by integrating big data with biological systems through-omics technology, specifically transcriptomics and proteomics, which can shed light on the molecular mechanisms underlying carcinogenesis.
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Affiliation(s)
- Shici Yang
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Gaohong Zhu
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Rui He
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Dong Fang
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Jiaojiao Feng
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
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12
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Tang Q, Li L, Wang Y, Wu P, Hou X, Ouyang J, Fan C, Li Z, Wang F, Guo C, Zhou M, Liao Q, Wang H, Xiang B, Jiang W, Li G, Zeng Z, Xiong W. RNA modifications in cancer. Br J Cancer 2023; 129:204-221. [PMID: 37095185 PMCID: PMC10338518 DOI: 10.1038/s41416-023-02275-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Currently, more than 170 modifications have been identified on RNA. Among these RNA modifications, various methylations account for two-thirds of total cases and exist on almost all RNAs. Roles of RNA modifications in cancer are garnering increasing interest. The research on m6A RNA methylation in cancer is in full swing at present. However, there are still many other popular RNA modifications involved in the regulation of gene expression post-transcriptionally besides m6A RNA methylation. In this review, we focus on several important RNA modifications including m1A, m5C, m7G, 2'-O-Me, Ψ and A-to-I editing in cancer, which will provide a new perspective on tumourigenesis by peeking into the complex regulatory network of epigenetic RNA modifications, transcript processing, and protein translation.
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Affiliation(s)
- Qiling Tang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Lvyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Pan Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Xiangchan Hou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Jiawei Ouyang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Chunmei Fan
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Zheng Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Hui Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Weihong Jiang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China.
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13
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Yu H, Bai K, Cheng Y, Lv J, Song Q, Yang H, Lu Q, Yang X. Clinical significance, tumor immune landscape and immunotherapy responses of ADAR in pan-cancer and its association with proliferation and metastasis of bladder cancer. Aging (Albany NY) 2023; 15:6302-6330. [PMID: 37414093 PMCID: PMC10373965 DOI: 10.18632/aging.204853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND ADAR is an enzyme involved in adenosine-inosine RNA editing. However, the role of ADAR in tumorigenesis, progression, and immunotherapy has not been fully elucidated. METHODS The TCGA, GTEx and GEO databases were extensively utilized to explore the expression level of ADAR across cancers. Combined with the clinical information of patients, the risk profile of ADAR in various cancers was delineated. We identified pathways enriched in ADAR and their related genes and explored the association between ADAR expression and the cancer immune microenvironment score and response to immunotherapy. Finally, we specifically explored the potential value of ADAR in the treatment of the bladder cancer immune response and verified the critical role of ADAR in the development and progression of bladder cancer through experiments. RESULTS ADAR is highly expressed in most cancers at both the RNA and protein level. ADAR is associated with the aggressiveness of some cancers, especially bladder cancer. In addition, ADAR is associated with immune-related genes, especially immune checkpoint genes, in the tumor immune microenvironment. Moreover, ADAR expression is positively correlated with tumor mutation burden and microsatellite instability in a variety of cancers, indicating that ADAR could be used as a biomarker of immunotherapy. Finally, we demonstrated that ADAR is a key pathogenic factor in bladder cancer. ADAR promoted proliferation and metastasis of bladder cancer cells. CONCLUSION ADAR regulates the tumor immune microenvironment and can be used as a biomarker of the tumor immunotherapy response, providing a novel strategy for the treatment of tumors, especially bladder cancer.
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Affiliation(s)
- Hao Yu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
- Institute of Urology and Andrology, Nanjing Medical University, Nanjing 210029, PR China
| | - Kexin Bai
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
- Institute of Urology and Andrology, Nanjing Medical University, Nanjing 210029, PR China
| | - Yidong Cheng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Jiancheng Lv
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
- Institute of Urology and Andrology, Nanjing Medical University, Nanjing 210029, PR China
| | - Qiang Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
- Institute of Urology and Andrology, Nanjing Medical University, Nanjing 210029, PR China
| | - Qiang Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Xiao Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
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14
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Yuan J, Xu L, Bao HJ, Wang JL, Zhao Y, Chen S. Biological roles of A-to-I editing: implications in innate immunity, cell death, and cancer immunotherapy. J Exp Clin Cancer Res 2023; 42:149. [PMID: 37328893 DOI: 10.1186/s13046-023-02727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing, a key RNA modification widely found in eukaryotes, is catalyzed by adenosine deaminases acting on RNA (ADARs). Such RNA editing destabilizes endogenous dsRNAs, which are subsequently recognized by the sensors of innate immune and other proteins as autologous dsRNAs. This prevents the activation of innate immunity and type I interferon-mediated responses, thereby reducing the downstream cell death induced by the activation of the innate immune sensing system. ADARs-mediated editing can also occur in mRNAs and non-coding RNAs (ncRNAs) in different species. In mRNAs, A-to-I editing may lead to missense mutations and the selective splicing of coding regions. Meanwhile, in ncRNAs, A-to-I editing may affect targeting and disrupt ncRNAs maturation, leading to anomalous cell proliferation, invasion, and responses to immunotherapy. This review highlights the biological functions of A-to-I editing, its role in regulating innate immunity and cell death, and its potential molecular significance in tumorigenesis and cancer targeted therapy and immunotherapy.
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Affiliation(s)
- Jing Yuan
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Li Xu
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Hai-Juan Bao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Jie-Lin Wang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China.
| | - Shuo Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China.
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15
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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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16
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Bai Y, Liu Z, Li Y, Zhao H, Lai C, Zhao S, Chen K, Luo C, Yang X, Wang F. Structural Mass Spectrometry Probes the Inhibitor-Induced Allosteric Activation of CDK12/CDK13-Cyclin K Dissociation. J Am Chem Soc 2023; 145:11477-11481. [PMID: 37207290 DOI: 10.1021/jacs.3c01697] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rational design and development of effective inhibitors for cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) are largely dependent on the understanding of the dynamic inhibition conformations but are difficult to be achieved by conventional characterization tools. Herein, we integrate the structural mass spectrometry (MS) methods of lysine reactivity profiling (LRP) and native MS (nMS) to systematically interrogate both the dynamic molecular interactions and overall protein assembly of CDK12/CDK13-cyclin K (CycK) complexes under the modulation of small molecule inhibitors. The essential structure insights, including inhibitor binding pocket, binding strength, interfacial molecular details, and dynamic conformation changes, can be derived from the complementary results of LRP and nMS. We find the inhibitor SR-4835 binding can greatly destabilize the CDK12/CDK13-CycK interactions in an unusual allosteric activation way, thereby providing a novel alternative for the kinase activity inhibition. Our results underscore the great potential of LRP combination with nMS for the evaluation and rational design of effective kinase inhibitors at the molecular level.
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Affiliation(s)
- Yu Bai
- School of Pharmacy, China Medical University, Shenyang 110122, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanqing Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kaixian Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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17
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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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18
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Wu C, Xie T, Guo Y, Wang D, Qiu M, Han R, Qing G, Liang K, Liu H. CDK13 phosphorylates the translation machinery and promotes tumorigenic protein synthesis. Oncogene 2023; 42:1321-1330. [PMID: 36882522 DOI: 10.1038/s41388-023-02653-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/09/2023]
Abstract
Cyclin-dependent kinase 13 (CDK13) has been suggested to phosphorylate RNA polymerase II and is involved in transcriptional activation. However, whether CDK13 catalyzes other protein substrates and how CDK13 contributes to tumorigenesis remain largely unclear. We here identify key translation machinery components, 4E-BP1 and eIF4B, as novel CDK13 substrates. CDK13 directly phosphorylates 4E-BP1 at Thr46 and eIF4B at Ser422; genetically or pharmacologically inhibiting CDK13 disrupts mRNA translation. Polysome profiling analysis shows that MYC oncoprotein synthesis strictly depends on CDK13-regulated translation in colorectal cancer (CRC), and CDK13 is required for CRC cell proliferation. As mTORC1 is implicated in 4E-BP1 and eIF4B phosphorylation, inactivation of CDK13 in combination with the mTORC1 inhibitor rapamycin further dephosphorylates 4E-BP1 and eIF4B and blocks protein synthesis. As a result, dual inhibition of CDK13 and mTORC1 induces more profound tumor cell death. These findings clarify the pro-tumorigenic role of CDK13 by direct phosphorylation of translation initiation factors and enhancing protein synthesis. Therefore, therapeutic targeting of CDK13 alone or in combination with rapamycin may pave a new way for cancer treatment.
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Affiliation(s)
- Chao Wu
- Department of Hematology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, 430071, Wuhan, China.,Frontier Science Center of Immunology and Metabolism, Wuhan University, 430071, Wuhan, China
| | - Ting Xie
- Department of Hematology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, 430071, Wuhan, China.,Frontier Science Center of Immunology and Metabolism, Wuhan University, 430071, Wuhan, China
| | - Ying Guo
- Frontier Science Center of Immunology and Metabolism, Wuhan University, 430071, Wuhan, China
| | - Donghai Wang
- Frontier Science Center of Immunology and Metabolism, Wuhan University, 430071, Wuhan, China
| | - Min Qiu
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, China
| | - Ruyi Han
- Frontier Science Center of Immunology and Metabolism, Wuhan University, 430071, Wuhan, China
| | - Guoliang Qing
- Frontier Science Center of Immunology and Metabolism, Wuhan University, 430071, Wuhan, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, China
| | - Hudan Liu
- Department of Hematology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, 430071, Wuhan, China. .,Frontier Science Center of Immunology and Metabolism, Wuhan University, 430071, Wuhan, China.
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19
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A Comprehensive and Systematic Analysis Revealed the Role of ADAR1 in Pan-Cancer Prognosis and Immune Implications. DISEASE MARKERS 2023; 2023:7620181. [PMID: 36865502 PMCID: PMC9974249 DOI: 10.1155/2023/7620181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/09/2022] [Accepted: 11/25/2022] [Indexed: 02/23/2023]
Abstract
Adenosine deaminase RNA specific 1 (ADAR1) has been identified as an enzyme that deaminates adenosine within the dsRNA region to produce inosine, whose amplification reinforced the exhaustion of the immune system. Although there were currently cellular and animal assays supporting the relationship between ADAR1 and specific cancers, there was no correlation analysis that has been performed at the pan-cancer level. Therefore, we first analyzed the expression of ADAR1 in 33 cancers based on the TCGA (The Cancer Genome Atlas) database. ADAR1 was highly expressed in most cancers, and there was a closely association between ADAR1 expression and prognosis of patients. Furthermore, pathway enrichment analysis revealed that ADAR1 was involved in multiple antigens presenting and processing inflammatory and interferon pathways. Moreover, ADAR1 expression was positively correlated with CD8+ T cell infiltration levels in renal papillary cell carcinoma, prostate cancer, and endometrial cancer and negatively correlated with Treg cell infiltration. In addition, we further found that ADAR1 expression was closely associated with various immune checkpoints and chemokines. Meanwhile, we observed that ADAR1 may be involved in the regulation of pan-cancer stemness. In conclusion, we provided a comprehensive understanding of the oncogenic role of ADAR1 in pan-cancer, and ADAR1 might serve as a new potential target for antitumor therapy.
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20
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Unifying Different Cancer Theories in a Unique Tumour Model: Chronic Inflammation and Deaminases as Meeting Points. Int J Mol Sci 2022; 23:ijms23158720. [PMID: 35955853 PMCID: PMC9368936 DOI: 10.3390/ijms23158720] [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: 07/05/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
The increase in cancer incidences shows that there is a need to better understand tumour heterogeneity to achieve efficient treatments. Interestingly, there are several common features among almost all types of cancers, with chronic inflammation induction and deaminase dysfunctions singled out. Deaminases are a family of enzymes with nucleotide-editing capacity, which are classified into two main groups: DNA-based and RNA-based. Remarkably, a close relationship between inflammation and the dysregulation of these molecules has been widely documented, which may explain the characteristic intratumor heterogeneity, both at DNA and transcriptional levels. Indeed, heterogeneity in cancer makes it difficult to establish a unique tumour progression model. Currently, there are three main cancer models—stochastic, hierarchic, and dynamic—although there is no consensus on which one better resembles cancer biology because they are usually overly simplified. Here, to accurately explain tumour progression, we propose interactions among chronic inflammation, deaminases dysregulation, intratumor genetic heterogeneity, cancer phenotypic plasticity, and even the previously proposed appearance of cancer stem-like cell populations in the edges of advanced solid tumour masses (instead of being the cells of origin of primary malignancies). The new tumour development model proposed in this study does not contradict previously accepted models and it may open up a window to interesting therapeutic approaches.
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21
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Liu J, Wang F, Zhang Y, Liu J, Zhao B. ADAR1-Mediated RNA Editing and Its Role in Cancer. Front Cell Dev Biol 2022; 10:956649. [PMID: 35898396 PMCID: PMC9309331 DOI: 10.3389/fcell.2022.956649] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
It is well known that the stability of RNA, the interaction between RNA and protein, and the correct translation of protein are significant forces that drive the transition from normal cell to malignant tumor. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that catalyzes the deamination of adenosine to inosine (A-to-I), which is one dynamic modification that in a combinatorial manner can give rise to a very diverse transcriptome. ADAR1-mediated RNA editing is essential for survival in mammals and its dysregulation results in aberrant editing of its substrates that may affect the phenotypic changes in cancer. This overediting phenomenon occurs in many cancers, such as liver, lung, breast, and esophageal cancers, and promotes tumor progression in most cases. In addition to its editing role, ADAR1 can also play an editing-independent role, although current research on this mechanism is relatively shallowly explored in tumors. In this review, we summarize the nature of ADAR1, mechanisms of ADAR1 editing-dependent and editing-independent and implications for tumorigenesis and prognosis, and pay special attention to effects of ADAR1 on cancers by regulating non-coding RNA formation and function.
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Affiliation(s)
- Jizhe Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Yindan Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Jingfeng Liu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
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22
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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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23
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Lin SH, Chen SCC. RNA Editing in Glioma as a Sexually Dimorphic Prognostic Factor That Affects mRNA Abundance in Fatty Acid Metabolism and Inflammation Pathways. Cells 2022; 11:cells11071231. [PMID: 35406793 PMCID: PMC8997934 DOI: 10.3390/cells11071231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/16/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
RNA editing alters the nucleotide sequence and has been associated with cancer progression. However, little is known about its prognostic and regulatory roles in glioma, one of the most common types of primary brain tumors. We characterized and analyzed RNA editomes of glioblastoma and isocitrate dehydrogenase mutated (IDH-MUT) gliomas from The Cancer Genome Atlas and the Chinese Glioma Genome Atlas (CGGA). We showed that editing change during glioma progression was another layer of molecular alterations and that editing profiles predicted the prognosis of glioblastoma and IDH-MUT gliomas in a sex-dependent manner. Hyper-editing was associated with poor survival in females but better survival in males. Moreover, noncoding editing events impacted mRNA abundance of the host genes. Genes associated with inflammatory response (e.g., EIF2AK2, a key mediator of innate immunity) and fatty acid oxidation (e.g., acyl-CoA oxidase 1, the rate-limiting enzyme in fatty acid β-oxidation) were editing-regulated and associated with glioma progression. The above findings were further validated in CGGA samples. Establishment of the prognostic and regulatory roles of RNA editing in glioma holds promise for developing editing-based therapeutic strategies against glioma progression. Furthermore, sexual dimorphism at the epitranscriptional level highlights the importance of developing sex-specific treatments for glioma.
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24
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Di Cristofano A. The Year in Basic Thyroid Cancer Research. Thyroid 2022; 32:3-8. [PMID: 34806425 PMCID: PMC8792493 DOI: 10.1089/thy.2021.0561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Background: Every year, the American Thyroid Association (ATA) Annual Meeting opening session features presentations covering the most recent advances in the three major areas of thyroidology: basic, clinical, and surgical. As the ATA did not have an annual meeting in 2020, because of the COVID19 pandemic, the 2021 meeting opened with a special "Two Years in Thyroidology" session. Methods: A PubMed electronic search was conducted to identify original basic science research studies on thyroid cancer published between October 2019 and September 2021. Methodologically rigorous studies that were deemed most likely to influence the field of basic science research in thyroid cancer were grouped into three thematic units: Genetics and Genomics, Molecular Biology and Signaling, and Preclinical and Translational Science. Four publications for each category were chosen for discussion. Results: Selected studies covered topics ranging from the genetics of thyroid cancer predisposition to the genomics of anaplastic thyroid cancer evolution, from novel molecular pathways involved in thyroid cancer pathogenesis to potentially game-changing imaging and therapeutic innovations. Conclusions: The past two years, in the face of unique COVID19 pandemic-associated hurdles, have witnessed a large number of important developments in basic and translational thyroid cancer research. These studies not only have shed novel light on a number of long-standing scientific questions but have also highlighted the major challenges and open questions that still remain to be addressed in the coming years.
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Affiliation(s)
- Antonio Di Cristofano
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA
- Address correspondence to: Antonio Di Cristofano, PhD, Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Room 302, Bronx, NY 10461, USA
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