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Huang E, Frydman C, Xiao X. Navigating the landscape of epitranscriptomics and host immunity. Genome Res 2024; 34:515-529. [PMID: 38702197 PMCID: PMC11146601 DOI: 10.1101/gr.278412.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for genome-wide identification of RNA modifications and their immunogenic substrates. Finally, we highlight recent advances in cancer immunotherapies that aim to reduce cancer cell viability by targeting the enzymes responsible for RNA modifications. Our presentation of these dynamic research avenues sets the stage for future investigations in this field.
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Affiliation(s)
- Elaine Huang
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Clara Frydman
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA;
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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2
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Ashley CN, Broni E, Miller WA. ADAR Family Proteins: A Structural Review. Curr Issues Mol Biol 2024; 46:3919-3945. [PMID: 38785511 PMCID: PMC11120146 DOI: 10.3390/cimb46050243] [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: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
This review aims to highlight the structures of ADAR proteins that have been crucial in the discernment of their functions and are relevant to future therapeutic development. ADAR proteins can correct or diversify genetic information, underscoring their pivotal contribution to protein diversity and the sophistication of neuronal networks. ADAR proteins have numerous functions in RNA editing independent roles and through the mechanisms of A-I RNA editing that continue to be revealed. Provided is a detailed examination of the ADAR family members-ADAR1, ADAR2, and ADAR3-each characterized by distinct isoforms that offer both structural diversity and functional variability, significantly affecting RNA editing mechanisms and exhibiting tissue-specific regulatory patterns, highlighting their shared features, such as double-stranded RNA binding domains (dsRBD) and a catalytic deaminase domain (CDD). Moreover, it explores ADARs' extensive roles in immunity, RNA interference, and disease modulation, demonstrating their ambivalent nature in both the advancement and inhibition of diseases. Through this comprehensive analysis, the review seeks to underline the potential of targeting ADAR proteins in therapeutic strategies, urging continued investigation into their biological mechanisms and health implications.
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Affiliation(s)
- Carolyn N. Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
| | - Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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3
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Hong X, Wei Z, He L, Bu Q, Wu G, Chen G, He W, Deng Q, Huang S, Huang Y, Yu C, Luo X, Lin Y. High-throughput virtual screening to identify potential small molecule inhibitors of the Zα domain of the adenosine deaminases acting on RNA 1(ADAR1). Eur J Pharm Sci 2024; 193:106672. [PMID: 38103658 DOI: 10.1016/j.ejps.2023.106672] [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: 06/25/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Changes in RNA editing are closely associated with diseases such as cancer, viral infections, and autoimmune disorders. Adenosine deaminase (ADAR1), which acts on RNA 1, plays a key role in adenosine to inosine editing and is a potential therapeutic target for these various diseases. The p150 subtype of ADAR1 is the only one that contains a Zα domain that binds to both Z-DNA and Z-RNA. The Zα domain modulates immune responses and may be suitable targets for antiviral therapy and cancer immunotherapy. In this study, we attempted to utilize molecular docking to identify potential inhibitors that bind to the ADAR1 Zα domain. The virtual docking method screened the potential activity of more than 100,000 compounds on the Zα domain of ADAR1 and filtered to obtain the highest scoring results.We identified 71 compounds promising to bind to ADAR1 and confirmed that two of them, lithospermic acid and Regaloside B, interacts with the ADAR1 Zα domain by surface plasmonic resonance technique. The molecular dynamics calculation of the complex of lithospermic acid and ADAR1 also showed that the binding effect of lithospermic acid to ADAR1 was stable.This study provides a new perspective for the search of ADAR1 inhibitors, and further studies on the anti-ADAR11 activity of these compounds have broad prospects.
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Affiliation(s)
- Xiaoshan Hong
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Zhifu Wei
- Department of gynecology, The Affiliated Shunde Hospital of Jinan University, Foshan 528300, China
| | - Lulu He
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Qiaowen Bu
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Guosong Wu
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China
| | - Guanqiao Chen
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Wanshan He
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China
| | - Qiuhua Deng
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China
| | - Shiqi Huang
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China
| | - Yongmei Huang
- Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China.
| | - Cai Yu
- College of Pharmacy, Jinan University, Guangzhou 511436, China.
| | - Xiping Luo
- Department of gynecology, Guangdong Women and Children Medical Hospital, Guangzhou 511400, China.
| | - Yu Lin
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China; Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou 510006, China.
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4
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Murphy LA, Winters AC. Emerging and Future Targeted Therapies for Pediatric Acute Myeloid Leukemia: Targeting the Leukemia Stem Cells. Biomedicines 2023; 11:3248. [PMID: 38137469 PMCID: PMC10741170 DOI: 10.3390/biomedicines11123248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Acute myeloid leukemia (AML) is a rare subtype of acute leukemia in the pediatric and adolescent population but causes disproportionate morbidity and mortality in this age group. Standard chemotherapeutic regimens for AML have changed very little in the past 3-4 decades, but the addition of targeted agents in recent years has led to improved survival in select subsets of patients as well as a better biological understanding of the disease. Currently, one key paradigm of bench-to-bedside practice in the context of adult AML is the focus on leukemia stem cell (LSC)-targeted therapies. Here, we review current and emerging immunotherapies and other targeted agents that are in clinical use for pediatric AML through the lens of what is known (and not known) about their LSC-targeting capability. Based on a growing understanding of pediatric LSC biology, we also briefly discuss potential future agents on the horizon.
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Affiliation(s)
- Lindsey A. Murphy
- Department of Pediatrics, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Amanda C. Winters
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Jamieson CHM, Weissman IL. Stem-Cell Aging and Pathways to Precancer Evolution. N Engl J Med 2023; 389:1310-1319. [PMID: 37792614 DOI: 10.1056/nejmra2304431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Affiliation(s)
- Catriona H M Jamieson
- From the Sanford Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, University of California at San Diego, La Jolla (C.H.M.J.), and the Institute for Stem Cell Biology and Regenerative Medicine, Stanford University Medical Center, Stanford (I.L.W.) - both in California
| | - Irving L Weissman
- From the Sanford Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, University of California at San Diego, La Jolla (C.H.M.J.), and the Institute for Stem Cell Biology and Regenerative Medicine, Stanford University Medical Center, Stanford (I.L.W.) - both in California
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Liu J, Huang T, Yao J, Zhao T, Zhang Y, Zhang R. Epitranscriptomic subtyping, visualization, and denoising by global motif visualization. Nat Commun 2023; 14:5944. [PMID: 37741827 PMCID: PMC10517956 DOI: 10.1038/s41467-023-41653-4] [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: 01/01/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
Advances in sequencing technologies have empowered epitranscriptomic profiling at the single-base resolution. Putative RNA modification sites identified from a single high-throughput experiment may contain one type of modification deposited by different writers or different types of modifications, along with false positive results because of the challenge of distinguishing signals from noise. However, current tools are insufficient for subtyping, visualization, and denoising these signals. Here, we present iMVP, which is an interactive framework for epitranscriptomic analysis with a nonlinear dimension reduction technique and density-based partition. As exemplified by the analysis of mRNA m5C and ModTect variant data, we show that iMVP allows the identification of previously unknown RNA modification motifs and writers and the discovery of false positives that are undetectable by traditional methods. Using putative m6A/m6Am sites called from 8 profiling approaches, we illustrate that iMVP enables comprehensive comparison of different approaches and advances our understanding of the difference and pattern of true positives and artifacts in these methods. Finally, we demonstrate the ability of iMVP to analyze an extremely large human A-to-I editing dataset that was previously unmanageable. Our work provides a general framework for the visualization and interpretation of epitranscriptomic data.
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Affiliation(s)
- Jianheng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
| | - Tao Huang
- Department of Pathology and Pathophysiology, Shantou University Medical College, Shantou, 515041, P. R. China
| | - Jing Yao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Tianxuan Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Yusen Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
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7
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Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
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Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
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Chan WC, Trieger KA, La Clair JJ, Jamieson CHM, Burkart MD. Stereochemical Control of Splice Modulation in FD-895 Analogues. J Med Chem 2023; 66:6577-6590. [PMID: 37155693 PMCID: PMC10586521 DOI: 10.1021/acs.jmedchem.2c01893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Highly functionalized skeletons of macrolide natural products gain access to rare spatial arrangements of atoms, where changes in stereochemistry can have a profound impact on the structure and function. Spliceosome modulators present a unique consensus motif, with the majority targeting a key interface within the SF3B spliceosome complex. Our recent preparative-scale synthetic campaign of 17S-FD-895 provided unique access to stereochemical analogues of this complex macrolide. Here, we report on the preparation and systematic activity evaluation of multiple FD-895 analogues. These studies examine the effects of modifications at specific stereocenters within the molecule and highlight future directions for medicinal chemical optimization of spliceosome modulators.
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Affiliation(s)
- Warren C Chan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Kelsey A Trieger
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Catriona H M Jamieson
- The Division of Regenerative Medicine, Moores Cancer Center, and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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