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Cheng CL, Lin YY, Hsu CL, Li CL, Yuan CT, Lai YY, Fang WQ, Chen PJ, Yeh SH, Tien HF. Unraveling the role of hepatitis B virus DNA integration in B-cell lymphomagenesis. Br J Cancer 2024:10.1038/s41416-024-02763-y. [PMID: 39026081 DOI: 10.1038/s41416-024-02763-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Studies have shown that hepatitis B virus (HBV)-associated B-cell non-Hodgkin lymphoma (NHL) constitutes a unique subgroup with distinct clinical features. It still leaves open the question of whether the integration of HBV DNA into the B-cell genome is a causal mechanism in the development of lymphoma. METHODS Using the hybridisation capture-based next generation sequencing and RNA sequencing, we characterised the HBV integration pattern in 45 HBV-associated B-cell NHL tumour tissues. RESULTS A total of 354 HBV integration sites were identified in 13 (28.9%) samples, indicating the relatively low integration frequency in B-cell NHLs. High plasma HBV DNA loads were not associated with the existence of HBV integration. The insertion sites distributed randomly across all the lymphoma genome without any preferential hotspot neither at the chromosomal level nor at the genetic level. Intriguingly, most HBV integrations were nonclonal in B-cell NHLs, implying that they did not confer a survival advantage. Analysis of the paired diagnosis-relapse samples showed the unstable status of HBV integrations during disease progression. Furthermore, transcriptomic analysis revealed the limited biological impact of HBV integration. CONCLUSION Our study provides an unbiased HBV integration map in B-cell NHLs, revealing the insignificant role of HBV DNA integration in B-cell lymphomagenesis.
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Affiliation(s)
- Chieh-Lung Cheng
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - You-Yu Lin
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan, ROC
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Chiao-Ling Li
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Chang-Tsu Yuan
- Department of Pathology, National Taiwan University Cancer Center, Taipei, Taiwan, ROC
| | - Ya-Yun Lai
- Microbial Genomics Core Laboratory, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Wei-Quan Fang
- Division of New Drug, Center for Drug Evaluation, Taipei, Taiwan, ROC
| | - Pei-Jer Chen
- Microbial Genomics Core Laboratory, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan, ROC
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Shiou-Hwei Yeh
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC.
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC.
- Department of Laboratory Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC.
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan, ROC.
- Department of Internal Medicine, Far-Eastern Memorial Hospital, New Taipei City, Taiwan, ROC.
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2
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Tang AD, Felton C, Hrabeta-Robinson E, Volden R, Vollmers C, Brooks AN. Detecting haplotype-specific transcript variation in long reads with FLAIR2. Genome Biol 2024; 25:173. [PMID: 38956576 PMCID: PMC11218413 DOI: 10.1186/s13059-024-03301-y] [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: 06/13/2023] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme that mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung adenocarcinoma cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, the use of short-read RNA-seq has limited the community's ability to interrogate both forms of RNA variation simultaneously. RESULTS We employ long-read sequencing technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We develop a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generate nanopore data with high sequence accuracy from H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We apply our workflow to identify key inosine isoform associations to help clarify the prominence of ADAR in tumorigenesis. CONCLUSIONS Ultimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns.
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Affiliation(s)
- Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Roger Volden
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA.
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3
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Kong FS, Feng J, Yao JP, Lu Y, Guo T, Sun M, Ren CY, Jin YY, Ma Y, Chen JH. Dysregulated RNA editing of EIF2AK2 in polycystic ovary syndrome: clinical relevance and functional implications. BMC Med 2024; 22:229. [PMID: 38853264 PMCID: PMC11163819 DOI: 10.1186/s12916-024-03434-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/21/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder affecting women of reproductive ages. Our previous study has implicated a possible link between RNA editing and PCOS, yet the actual role of RNA editing, its association with clinical features, and the underlying mechanisms remain unclear. METHODS Ten RNA-Seq datasets containing 269 samples of multiple tissue types, including granulosa cells, T helper cells, placenta, oocyte, endometrial stromal cells, endometrium, and adipose tissues, were retrieved from public databases. Peripheral blood samples were collected from twelve PCOS and ten controls and subjected to RNA-Seq. Transcriptome-wide RNA-Seq data analysis was conducted to identify differential RNA editing (DRE) between PCOS and controls. The functional significance of DRE was evaluated by luciferase reporter assays and overexpression in human HEK293T cells. Dehydroepiandrosterone and lipopolysaccharide were used to stimulate human KGN granulosa cells to evaluate gene expression. RESULTS RNA editing dysregulations across multiple tissues were found to be associated with PCOS in public datasets. Peripheral blood transcriptome analysis revealed 798 DRE events associated with PCOS. Through weighted gene co-expression network analysis, our results revealed a set of hub DRE events in PCOS blood. A DRE event in the eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2:chr2:37,100,559) was associated with PCOS clinical features such as luteinizing hormone (LH) and the ratio of LH over follicle-stimulating hormone. Luciferase assays, overexpression, and knockout of RNA editing enzyme adenosine deaminase RNA specific (ADAR) showed that the ADAR-mediated editing cis-regulated EIF2AK2 expression. EIAF2AK2 showed a higher expression after dehydroepiandrosterone and lipopolysaccharide stimulation, triggering changes in the downstrean MAPK pathway. CONCLUSIONS Our study presented the first evidence of cross-tissue RNA editing dysregulation in PCOS and its clinical associations. The dysregulation of RNA editing mediated by ADAR and the disrupted target EIF2AK2 may contribute to PCOS development via the MPAK pathway, underlining such epigenetic mechanisms in the disease.
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Affiliation(s)
- Fan-Sheng Kong
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Junjie Feng
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Jin-Ping Yao
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yinghua Lu
- Department of Reproductive Medicine, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Tao Guo
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Meng Sun
- Department of Reproductive Medicine, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yaping Ma
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China.
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China.
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4
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Zawisza-Álvarez M, Peñuela-Melero J, Vegas E, Reverter F, Garcia-Fernàndez J, Herrera-Úbeda C. Exploring functional conservation in silico: a new machine learning approach to RNA-editing. Brief Bioinform 2024; 25:bbae332. [PMID: 38980372 PMCID: PMC11232462 DOI: 10.1093/bib/bbae332] [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: 04/19/2024] [Revised: 06/09/2024] [Accepted: 06/25/2024] [Indexed: 07/10/2024] Open
Abstract
Around 50 years ago, molecular biology opened the path to understand changes in forms, adaptations, complexity, or the basis of human diseases through myriads of reports on gene birth, gene duplication, gene expression regulation, and splicing regulation, among other relevant mechanisms behind gene function. Here, with the advent of big data and artificial intelligence (AI), we focus on an elusive and intriguing mechanism of gene function regulation, RNA editing, in which a single nucleotide from an RNA molecule is changed, with a remarkable impact in the increase of the complexity of the transcriptome and proteome. We present a new generation approach to assess the functional conservation of the RNA-editing targeting mechanism using two AI learning algorithms, random forest (RF) and bidirectional long short-term memory (biLSTM) neural networks with an attention layer. These algorithms, combined with RNA-editing data coming from databases and variant calling from same-individual RNA and DNA-seq experiments from different species, allowed us to predict RNA-editing events using both primary sequence and secondary structure. Then, we devised a method for assessing conservation or divergence in the molecular mechanisms of editing completely in silico: the cross-testing analysis. This novel method not only helps to understand the conservation of the editing mechanism through evolution but could set the basis for achieving a better understanding of the adenosine-targeting mechanism in other fields.
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Affiliation(s)
- Michał Zawisza-Álvarez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Jesús Peñuela-Melero
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
| | - Esteban Vegas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Calle Sinesio Delgado 4, 28029 Madrid, Spain
| | - Ferran Reverter
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
| | - Jordi Garcia-Fernàndez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Carlos Herrera-Úbeda
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Digonal 643, 08028 Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
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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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6
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Yang L, Yi L, Yang J, Zhang R, Xie Z, Wang H. Temporal landscape and translational regulation of A-to-I RNA editing in mouse retina development. BMC Biol 2024; 22:106. [PMID: 38715001 PMCID: PMC11077751 DOI: 10.1186/s12915-024-01908-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The significance of A-to-I RNA editing in nervous system development is widely recognized; however, its influence on retina development remains to be thoroughly understood. RESULTS In this study, we performed RNA sequencing and ribosome profiling experiments on developing mouse retinas to characterize the temporal landscape of A-to-I editing. Our findings revealed temporal changes in A-to-I editing, with distinct editing patterns observed across different developmental stages. Further analysis showed the interplay between A-to-I editing and alternative splicing, with A-to-I editing influencing splicing efficiency and the quantity of splicing events. A-to-I editing held the potential to enhance translation diversity, but this came at the expense of reduced translational efficiency. When coupled with splicing, it could produce a coordinated effect on gene translation. CONCLUSIONS Overall, this study presents a temporally resolved atlas of A-to-I editing, connecting its changes with the impact on alternative splicing and gene translation in retina development.
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Affiliation(s)
- Ludong Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Liang Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Jiaqi Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, 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, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
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7
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Jin YY, Liang YP, Huang WH, Guo L, Cheng LL, Ran TT, Yao JP, Zhu L, Chen JH. Ocular A-to-I RNA editing signatures associated with SARS-CoV-2 infection. BMC Genomics 2024; 25:431. [PMID: 38693480 PMCID: PMC11061923 DOI: 10.1186/s12864-024-10324-z] [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: 10/12/2023] [Accepted: 04/19/2024] [Indexed: 05/03/2024] Open
Abstract
Ophthalmic manifestations have recently been observed in acute and post-acute complications of COVID-19 caused by SARS-CoV-2 infection. Our precious study has shown that host RNA editing is linked to RNA viral infection, yet ocular adenosine to inosine (A-to-I) RNA editing during SARS-CoV-2 infection remains uninvestigated in COVID-19. Herein we used an epitranscriptomic pipeline to analyze 37 samples and investigate A-to-I editing associated with SARS-CoV-2 infection, in five ocular tissue types including the conjunctiva, limbus, cornea, sclera, and retinal organoids. Our results revealed dramatically altered A-to-I RNA editing across the five ocular tissues. Notably, the transcriptome-wide average level of RNA editing was increased in the cornea but generally decreased in the other four ocular tissues. Functional enrichment analysis showed that differential RNA editing (DRE) was mainly in genes related to ubiquitin-dependent protein catabolic process, transcriptional regulation, and RNA splicing. In addition to tissue-specific RNA editing found in each tissue, common RNA editing was observed across different tissues, especially in the innate antiviral immune gene MAVS and the E3 ubiquitin-protein ligase MDM2. Analysis in retinal organoids further revealed highly dynamic RNA editing alterations over time during SARS-CoV-2 infection. Our study thus suggested the potential role played by RNA editing in ophthalmic manifestations of COVID-19, and highlighted its potential transcriptome impact, especially on innate immunity.
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Affiliation(s)
- Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China
| | - Ya-Ping Liang
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China
| | - Wen-Hao Huang
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China
| | - Liang Guo
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China
| | - Li-Li Cheng
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China
| | - Tian-Tian Ran
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China
| | - Jin-Ping Yao
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China
| | - Lin Zhu
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China.
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China.
- Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Wuxi, Jiangsu, China.
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Zhang D, Zhu L, Gao Y, Wang Y, Li P. RNA editing enzymes: structure, biological functions and applications. Cell Biosci 2024; 14:34. [PMID: 38493171 PMCID: PMC10944622 DOI: 10.1186/s13578-024-01216-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
With the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ubiquitous modification in mammalian transcriptomes and is an important co/posttranscriptional modification that plays a crucial role in various cellular processes. There are two main types of RNA editing events: adenosine to inosine (A-to-I) editing, catalyzed by ADARs on double-stranded RNA or ADATs on tRNA, and cytosine to uridine (C-to-U) editing catalyzed by APOBECs. This article provides an overview of the structure, function, and applications of RNA editing enzymes. We discuss the structural characteristics of three RNA editing enzyme families and their catalytic mechanisms in RNA editing. We also explain the biological role of RNA editing, particularly in innate immunity, cancer biogenesis, and antiviral activity. Additionally, this article describes RNA editing tools for manipulating RNA to correct disease-causing mutations, as well as the potential applications of RNA editing enzymes in the field of biotechnology and therapy.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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9
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Wang Y, Wu J, Zhao J, Xu T, Zhang M, Liu J, Wang Y, Wang Q, Song X. Global characterization of RNA editing in genetic regulation of multiple ovarian cancer subtypes. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102127. [PMID: 38352860 PMCID: PMC10863325 DOI: 10.1016/j.omtn.2024.102127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
RNA editing plays an extensive role in the initiation and progression of cancer. However, the overall profile and molecular functions of RNA editing in different ovarian cancer subtypes have not been fully characterized and elucidated. Here, we conducted a study on RNA editing in four cohorts of ovarian cancer subtypes through large-scale parallel reporting and bioinformatics analysis. Our findings revealed that RNA editing patterns exhibit subtype-specific characteristics within cancer subtypes. The expression pattern of ADAR and the number of differential editing sites varied under different conditions. CCOC and EOC exhibited significant editing deficiency, whereas HGSC and MOC displayed significant editing excess. The sites within the turquoise module of the coedited network also revealed their correlation with ovarian cancer. In addition, we identified an average of over 40,000 cis-edQTLs in the four subtypes. Finally, we explored the association between RNA editing and drug response, uncovering several potentially effective editing-drug pairs (EDP) and suggesting the conceivable utility of RNA editing sites as therapeutic targets for cancer treatment. Overall, our comprehensive study has identified and characterized RNA editing events in various subtypes of ovarian cancer, providing a new perspective for ovarian cancer research and facilitating the development of medical interventions and treatments.
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Affiliation(s)
- Yulan Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Jing Wu
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Tianyi Xu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Meng Zhang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Yixuan Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Quan Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
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10
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Qian CJ, He YS, Guo T, Tao J, Wei ZY, Zhang JL, Bao C, Chen JH. ADAR-mediated RNA editing regulates PVR immune checkpoint in colorectal cancer. Biochem Biophys Res Commun 2024; 695:149373. [PMID: 38176170 DOI: 10.1016/j.bbrc.2023.149373] [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: 11/20/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
Recent studies have revealed that tumor immunotherapy resistance is influenced by ADAR-mediated RNA editing, but its targets remain unelucidated. Our current study identified the poliovirus receptor (PVR) oncogene, which encodes an immune checkpoint in colorectal cancer (CRC), as a potential target for RNA editing. We performed transcriptome sequencing analysis and experimental validation in two Chinese CRC cohorts. PVR and ADAR expressions significantly increased in CRC tumors and showed positive correlations in both cohorts, coupled with upregulated PVR RNA editing in CRC tumors. Manipulation of ADAR expression by over-expression or knockdown substantially changed PVR expression and RNA editing in HTC116 CRC cells. Luciferase reporter and actinomycin D assays further revealed that RNA editing in PVR 3'-UTR could upregulate PVR RNA expression, probably by increasing the RNA stability. By increasing PVR expression, ADAR-mediate RNA editing might contribute to tumor- and immune-related gene functions and pathways in CRC. Moreover, a signature combining PVR RNA editing and expression showed promising predictive performance in CRC diagnosis in both Chinese CRC cohorts. Our findings thus highlight the importance of ADAR-mediated RNA editing in PVR up-regulation in CRC tumors and provide new insight into the application of PVR RNA editing as a novel diagnostic biomarker for CRC.
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Affiliation(s)
- Cheng-Jia Qian
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China
| | - Yu-Shan He
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Guo
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ji Tao
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhi-Yuan Wei
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jia-Li Zhang
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Chuanqing Bao
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangnan University, No. 1000 Hefeng Road, Wuxi, China.
| | - Jian-Huan Chen
- Department of General Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China; Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, 1800 Lihu Avenue, Wuxi, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Science, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
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11
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Xu J, He J, Yang J, Wang F, Huo Y, Guo Y, Si Y, Gao Y, Wang F, Cheng H, Cheng T, Yu J, Wang X, Ma Y. REDH: A database of RNA editome in hematopoietic differentiation and malignancy. Chin Med J (Engl) 2024; 137:283-293. [PMID: 37386732 PMCID: PMC10836905 DOI: 10.1097/cm9.0000000000002782] [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: 04/23/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND The conversion of adenosine (A) to inosine (I) through deamination is the prevailing form of RNA editing, impacting numerous nuclear and cytoplasmic transcripts across various eukaryotic species. Millions of high-confidence RNA editing sites have been identified and integrated into various RNA databases, providing a convenient platform for the rapid identification of key drivers of cancer and potential therapeutic targets. However, the available database for integration of RNA editing in hematopoietic cells and hematopoietic malignancies is still lacking. METHODS We downloaded RNA sequencing (RNA-seq) data of 29 leukemia patients and 19 healthy donors from National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, and RNA-seq data of 12 mouse hematopoietic cell populations obtained from our previous research were also used. We performed sequence alignment, identified RNA editing sites, and obtained characteristic editing sites related to normal hematopoietic development and abnormal editing sites associated with hematologic diseases. RESULTS We established a new database, "REDH", represents RNA editome in hematopoietic differentiation and malignancy. REDH is a curated database of associations between RNA editome and hematopoiesis. REDH integrates 30,796 editing sites from 12 murine adult hematopoietic cell populations and systematically characterizes more than 400,000 edited events in malignant hematopoietic samples from 48 cohorts (human). Through the Differentiation, Disease, Enrichment, and knowledge modules, each A-to-I editing site is systematically integrated, including its distribution throughout the genome, its clinical information (human sample), and functional editing sites under physiological and pathological conditions. Furthermore, REDH compares the similarities and differences of editing sites between different hematologic malignancies and healthy control. CONCLUSIONS REDH is accessible at http://www.redhdatabase.com/ . This user-friendly database would aid in understanding the mechanisms of RNA editing in hematopoietic differentiation and malignancies. It provides a set of data related to the maintenance of hematopoietic homeostasis and identifying potential therapeutic targets in malignancies.
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Affiliation(s)
- Jiayue Xu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiahuan He
- Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiabin Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Fengjiao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yue Huo
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yuehong Guo
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yanmin Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yufeng Gao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Fang Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610052, China
| | - Xiaoshuang Wang
- Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
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12
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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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13
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Xuan J, Chen L, Chen Z, Pang J, Huang J, Lin J, Zheng L, Li B, Qu L, Yang J. RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications. Nucleic Acids Res 2024; 52:D273-D284. [PMID: 37956310 PMCID: PMC10767931 DOI: 10.1093/nar/gkad1070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the 'RNA Modifications' module reveals the map of 73 RNA modifications of 62 species. the 'Genes' module allows to retrieve RNA modification profiles and clusters by gene and transcript. The 'Mechanisms' module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The 'Co-localization' module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The 'RMP' module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The 'Interactome' integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The 'Motif' illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The 'Tools' introduces a novel web-based 'modGeneTool' for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.
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Affiliation(s)
- Jiajia Xuan
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lifan Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhirong Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Pang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junhong Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jinran Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai 201203, China
| | - Lingling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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14
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Li M, Zhou T, Han M, Wang H, Bao P, Tao Y, Chen X, Wu G, Liu T, Wang X, Lu Q, Zhu Y, Lu ZJ. cfOmics: a cell-free multi-Omics database for diseases. Nucleic Acids Res 2024; 52:D607-D621. [PMID: 37757861 PMCID: PMC10767897 DOI: 10.1093/nar/gkad777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Liquid biopsy has emerged as a promising non-invasive approach for detecting, monitoring diseases, and predicting their recurrence. However, the effective utilization of liquid biopsy data to identify reliable biomarkers for various cancers and other diseases requires further exploration. Here, we present cfOmics, a web-accessible database (https://cfomics.ncRNAlab.org/) that integrates comprehensive multi-omics liquid biopsy data, including cfDNA, cfRNA based on next-generation sequencing, and proteome, metabolome based on mass-spectrometry data. As the first multi-omics database in the field, cfOmics encompasses a total of 17 distinct data types and 13 specimen variations across 69 disease conditions, with a collection of 11345 samples. Moreover, cfOmics includes reported potential biomarkers for reference. To facilitate effective analysis and visualization of multi-omics data, cfOmics offers powerful functionalities to its users. These functionalities include browsing, profile visualization, the Integrative Genomic Viewer, and correlation analysis, all centered around genes, microbes, or end-motifs. The primary objective of cfOmics is to assist researchers in the field of liquid biopsy by providing comprehensive multi-omics data. This enables them to explore cell-free data and extract profound insights that can significantly impact disease diagnosis, treatment monitoring, and management.
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Affiliation(s)
- Mingyang Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100084, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Tianxiu Zhou
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Mingfei Han
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 38 Life Science Park, Changping District, Beijing 102206, China
| | - Hongke Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaoqing Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 38 Life Science Park, Changping District, Beijing 102206, China
| | - Guansheng Wu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tianyou Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaojuan Wang
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
- Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, No. 168, Litang Road, Changping District, Beijing 102218, China
| | - Qian Lu
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
- Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, No. 168, Litang Road, Changping District, Beijing 102218, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 38 Life Science Park, Changping District, Beijing 102206, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
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15
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Fonzino A, Manzari C, Spadavecchia P, Munagala U, Torrini S, Conticello S, Pesole G, Picardi E. Unraveling C-to-U RNA editing events from direct RNA sequencing. RNA Biol 2024; 21:1-14. [PMID: 38090878 PMCID: PMC10732634 DOI: 10.1080/15476286.2023.2290843] [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] [Accepted: 10/29/2023] [Indexed: 12/18/2023] Open
Abstract
In mammals, RNA editing events involve the conversion of adenosine (A) in inosine (I) by ADAR enzymes or the hydrolytic deamination of cytosine (C) in uracil (U) by the APOBEC family of enzymes, mostly APOBEC1. RNA editing has a plethora of biological functions, and its deregulation has been associated with various human disorders. While the large-scale detection of A-to-I is quite straightforward using the Illumina RNAseq technology, the identification of C-to-U events is a non-trivial task. This difficulty arises from the rarity of such events in eukaryotic genomes and the challenge of distinguishing them from background noise. Direct RNA sequencing by Oxford Nanopore Technology (ONT) permits the direct detection of Us on sequenced RNA reads. Surprisingly, using ONT reads from wild-type (WT) and APOBEC1-knock-out (KO) murine cell lines as well as in vitro synthesized RNA without any modification, we identified a systematic error affecting the accuracy of the Cs call, thereby leading to incorrect identifications of C-to-U events. To overcome this issue in direct RNA reads, here we introduce a novel machine learning strategy based on the isolation Forest (iForest) algorithm in which C-to-U editing events are considered as sequencing anomalies. Using in vitro synthesized and human ONT reads, our model optimizes the signal-to-noise ratio improving the detection of C-to-U editing sites with high accuracy, over 90% in all samples tested. Our results suggest that iForest, known for its rapid implementation and minimal memory requirements, is a promising tool to denoise ONT reads and reliably identify RNA modifications.
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Affiliation(s)
- Adriano Fonzino
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | - Paola Spadavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
| | | | | | - Silvestro Conticello
- Core Research Laboratory, ISPRO, Florence, Italy
- National Research Council, Institute of Clinical Physiology, Pisa, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
- Consorzio Interuniversitario Biotecnologie, Trieste, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
- National Institute of Biostructures and Biosystems (INBB), Roma, Italy
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16
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Weng S, Yang X, Yu N, Wang PC, Xiong S, Ruan H. Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications. Int J Mol Sci 2023; 25:351. [PMID: 38203521 PMCID: PMC10779106 DOI: 10.3390/ijms25010351] [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: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
ADAR (Adenosine Deaminases Acting on RNA) proteins are a group of enzymes that play a vital role in RNA editing by converting adenosine to inosine in RNAs. This process is a frequent post-transcriptional event observed in metazoan transcripts. Recent studies indicate widespread dysregulation of ADAR-mediated RNA editing across many immune-related diseases, such as human cancer. We comprehensively review ADARs' function as pattern recognizers and their capability to contribute to mediating immune-related pathways. We also highlight the potential role of site-specific RNA editing in maintaining homeostasis and its relationship to various diseases, such as human cancers. More importantly, we summarize the latest cutting-edge computational approaches and data resources for predicting and analyzing RNA editing sites. Lastly, we cover the recent advancement in site-directed ADAR editing tool development. This review presents an up-to-date overview of ADAR-mediated RNA editing, how site-specific RNA editing could potentially impact disease pathology, and how they could be harnessed for therapeutic applications.
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Affiliation(s)
- Shenghui Weng
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Xinyi Yang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Nannan Yu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Peng-Cheng Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Hang Ruan
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou 215123, China
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17
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Di Martino J, Arcieri M, Madeddu F, Pieroni M, Carotenuto G, Bottoni P, Botta L, Castrignanò T, Gabellone S, Saladino R. Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity. Int J Mol Sci 2023; 25:234. [PMID: 38203410 PMCID: PMC10778928 DOI: 10.3390/ijms25010234] [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: 10/30/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of DNA photo-adducts, including cyclobutane pyrimidine dimers (CPDs) and Dewar valence derivatives (DVs). While CPDs usually occur at higher frequency than DVs, recent studies have shown that the latter display superior selectivity and significant stability in interaction with the human DNA/topoisomerase 1 complex (TOP1). With the aim to deeply investigate the mechanism of interaction of DVs with TOP1, we report here four all-atom molecular dynamic simulations spanning one microsecond. These simulations are focused on the stability and conformational changes of two DNA/TOP1-DV complexes in solution, the data being compared with the biomimetic thymine dimer counterparts. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, and hydrophobic interactions, as well as pinpointing the non-covalent interactions within the complexes, enabled the identification of specific TOP1 residues involved in the interactions over time and suggested a potential TOP1 inhibition mechanism in action.
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Affiliation(s)
- Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Manuel Arcieri
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Francesco Madeddu
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Michele Pieroni
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Giovanni Carotenuto
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Paolo Bottoni
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Lorenzo Botta
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Sofia Gabellone
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
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Ren L, Duan X, Dong L, Zhang R, Yang J, Gao Y, Peng R, Hou W, Liu Y, Li J, Yu Y, Zhang N, Shang J, Liang F, Wang D, Chen H, Sun L, Hao L, Scherer A, Nordlund J, Xiao W, Xu J, Tong W, Hu X, Jia P, Ye K, Li J, Jin L, Hong H, Wang J, Fan S, Fang X, Zheng Y, Shi L. Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance. Genome Biol 2023; 24:270. [PMID: 38012772 PMCID: PMC10680274 DOI: 10.1186/s13059-023-03109-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome. RESULTS We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data. CONCLUSIONS The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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Affiliation(s)
- Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaoke Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | | | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China
| | - Yuechen Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, Hubei, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Fan Liang
- Nextomics Biosciences Institute, Wuhan, Hubei, China
| | - Depeng Wang
- Nextomics Biosciences Institute, Wuhan, Hubei, China
| | - Hui Chen
- OrigiMed Co., Ltd, Shanghai, China
| | - Lele Sun
- Sequanta Technologies Co., Ltd, Shanghai, China
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Jessica Nordlund
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Xin Hu
- Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peng Jia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Jing Wang
- National Institute of Metrology, Beijing, China.
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.
| | - Xiang Fang
- National Institute of Metrology, Beijing, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Shanghai Cancer Center, Fudan University, Shanghai, China
- International Human Phenome Institutes, Shanghai, China
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19
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Wales-McGrath B, Mercer H, Piontkivska H. Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections. BMC Genomics 2023; 24:685. [PMID: 37968596 PMCID: PMC10652522 DOI: 10.1186/s12864-023-09778-4] [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: 06/18/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND RNA editing is a process that increases transcriptome diversity, often through Adenosine Deaminases Acting on RNA (ADARs) that catalyze the deamination of adenosine to inosine. ADAR editing plays an important role in regulating brain function and immune activation, and is dynamically regulated during brain development. Additionally, the ADAR1 p150 isoform is induced by interferons in viral infection and plays a role in antiviral immune response. However, the question of how virus-induced ADAR expression affects host transcriptome editing remains largely unanswered. This question is particularly relevant in the context of congenital infections, given the dynamic regulation of ADAR editing during brain development, the importance of this editing for brain function, and subsequent neurological symptoms of such infections, including microcephaly, sensory issues, and other neurodevelopmental abnormalities. Here, we begin to address this question, examining ADAR expression in publicly available datasets of congenital infections of human cytomegalovirus (HCMV) microarray expression data, as well as mouse cytomegalovirus (MCMV) and mouse/ human induced pluripotent neuroprogenitor stem cell (hiNPC) Zika virus (ZIKV) RNA-seq data. RESULTS We found that in all three datasets, ADAR1 was overexpressed in infected samples compared to uninfected samples. In the RNA-seq datasets, editing rates were also analyzed. In all mouse infections cases, the number of editing sites was significantly increased in infected samples, albeit this was not the case for hiNPC ZIKV samples. Mouse ZIKV samples showed altered editing of well-established protein-recoding sites such as Gria3, Grik5, and Nova1, as well as editing sites that may impact miRNA binding. CONCLUSIONS Our findings provide evidence for changes in ADAR expression and subsequent dysregulation of ADAR editing of host transcriptomes in congenital infections. These changes in editing patterns of key neural genes have potential significance in the development of neurological symptoms, thus contributing to neurodevelopmental abnormalities. Further experiments should be performed to explore the full range of editing changes that occur in different congenital infections, and to confirm the specific functional consequences of these editing changes.
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Affiliation(s)
- Benjamin Wales-McGrath
- University of Pennsylvania, Perelman School of Medicine, Department of Genetics, Philadelphia, PA, USA
- Children's Hospital of Philadelphia, Division of Cancer Pathobiology, Philadelphia, PA, USA
| | - Heather Mercer
- Department of Biological and Environmental Sciences, University of Mount Union, Alliance, OH, USA
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, USA.
- School of Biomedical Sciences, Kent State University, Kent, OH, USA.
- Brain Health Research Institute, Kent State University, Kent, OH, USA.
- Healthy Communities Research Institute, Kent State University, Kent, OH, USA.
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20
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Yamamoto R, Liu Z, Choudhury M, Xiao X. dsRID: in silico identification of dsRNA regions using long-read RNA-seq data. Bioinformatics 2023; 39:btad649. [PMID: 37871161 PMCID: PMC10628436 DOI: 10.1093/bioinformatics/btad649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/02/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023] Open
Abstract
MOTIVATION Double-stranded RNAs (dsRNAs) are potent triggers of innate immune responses upon recognition by cytosolic dsRNA sensor proteins. Identification of endogenous dsRNAs helps to better understand the dsRNAome and its relevance to innate immunity related to human diseases. RESULTS Here, we report dsRID (double-stranded RNA identifier), a machine-learning-based method to predict dsRNA regions in silico, leveraging the power of long-read RNA-sequencing (RNA-seq) and molecular traits of dsRNAs. Using models trained with PacBio long-read RNA-seq data derived from Alzheimer's disease (AD) brain, we show that our approach is highly accurate in predicting dsRNA regions in multiple datasets. Applied to an AD cohort sequenced by the ENCODE consortium, we characterize the global dsRNA profile with potentially distinct expression patterns between AD and controls. Together, we show that dsRID provides an effective approach to capture global dsRNA profiles using long-read RNA-seq data. AVAILABILITY AND IMPLEMENTATION Software implementation of dsRID, and genomic coordinates of regions predicted by dsRID in all samples are available at the GitHub repository: https://github.com/gxiaolab/dsRID.
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Affiliation(s)
- Ryo Yamamoto
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095-1570, United States
| | - Zhiheng Liu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095-7246, United States
| | - Mudra Choudhury
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095-7246, United States
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095-1570, United States
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095-7246, United States
- Molecular Biology Institute, University of California, Los Angeles, CA 90095-1570, United States
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21
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Jin Z, Sheng J, Hu Y, Zhang Y, Wang X, Huang Y. Shining a spotlight on m6A and the vital role of RNA modification in endometrial cancer: a review. Front Genet 2023; 14:1247309. [PMID: 37886684 PMCID: PMC10598767 DOI: 10.3389/fgene.2023.1247309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
RNA modifications are mostly dynamically reversible post-transcriptional modifications, of which m6A is the most prevalent in eukaryotic mRNAs. A growing number of studies indicate that RNA modification can finely tune gene expression and modulate RNA metabolic homeostasis, which in turn affects the self-renewal, proliferation, apoptosis, migration, and invasion of tumor cells. Endometrial carcinoma (EC) is the most common gynecologic tumor in developed countries. Although it can be diagnosed early in the onset and have a preferable prognosis, some cases might develop and become metastatic or recurrent, with a worse prognosis. Fortunately, immunotherapy and targeted therapy are promising methods of treating endometrial cancer patients. Gene modifications may also contribute to these treatments, as is especially the case with recent developments of new targeted therapeutic genes and diagnostic biomarkers for EC, even though current findings on the relationship between RNA modification and EC are still very limited, especially m6A. For example, what is the elaborate mechanism by which RNA modification affects EC progression? Taking m6A modification as an example, what is the conversion mode of methylation and demethylation for RNAs, and how to achieve selective recognition of specific RNA? Understanding how they cope with various stimuli as part of in vivo and in vitro biological development, disease or tumor occurrence and development, and other processes is valuable and RNA modifications provide a distinctive insight into genetic information. The roles of these processes in coping with various stimuli, biological development, disease, or tumor development in vivo and in vitro are self-evident and may become a new direction for cancer in the future. In this review, we summarize the category, characteristics, and therapeutic precis of RNA modification, m6A in particular, with the purpose of seeking the systematic regulation axis related to RNA modification to provide a better solution for the treatment of EC.
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Affiliation(s)
- Zujian Jin
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Jingjing Sheng
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yingying Hu
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Zhang
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Xiaoxia Wang
- Reproductive Medicine Center, School of Medicine, The Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China
| | - Yiping Huang
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
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22
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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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23
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Kong FS, Lu Z, Zhou Y, Lu Y, Ren CY, Jia R, Zeng B, Huang P, Wang J, Ma Y, Chen JH. Transcriptome analysis identification of A-to-I RNA editing in granulosa cells associated with PCOS. Front Endocrinol (Lausanne) 2023; 14:1170957. [PMID: 37547318 PMCID: PMC10401594 DOI: 10.3389/fendo.2023.1170957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/06/2023] [Indexed: 08/08/2023] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is a complex, multifactor disorder in women of reproductive age worldwide. Although RNA editing may contribute to a variety of diseases, its role in PCOS remains unclear. Methods A discovery RNA-Seq dataset was obtained from the NCBI Gene Expression Omnibus database of granulosa cells from women with PCOS and women without PCOS (controls). A validation RNA-Seq dataset downloaded from the European Nucleotide Archive Databank was used to validate differential editing. Transcriptome-wide investigation was conducted to analyze adenosine-to-inosine (A-to-I) RNA editing in PCOS and control samples. Results A total of 17,395 high-confidence A-to-I RNA editing sites were identified in 3,644 genes in all GC samples. As for differential RNA editing, there were 545 differential RNA editing (DRE) sites in 259 genes with Nucleoporin 43 (NUP43), Retinoblastoma Binding Protein 4 (RBBP4), and leckstrin homology-like domain family A member 1 (PHLDA) showing the most significant three 3'-untranslated region (3'UTR) editing. Furthermore, we identified 20 DRE sites that demonstrated a significant correlation between editing levels and gene expression levels. Notably, MIR193b-365a Host Gene (MIR193BHG) and Hook Microtubule Tethering Protein 3 (HOOK3) exhibited significant differential expression between PCOS and controls. Functional enrichment analysis showed that these 259 differentially edited genes were mainly related to apoptosis and necroptosis pathways. RNA binding protein (RBP) analysis revealed that RNA Binding Motif Protein 45 (RBM45) was predicted as the most frequent RBP binding with RNA editing sites. Additionally, we observed a correlation between editing levels of differential editing sites and the expression level of the RNA editing enzyme Adenosine Deaminase RNA Specific B1 (ADARB1). Moreover, the existence of 55 common differentially edited genes and nine differential editing sites were confirmed in the validation dataset. Conclusion Our current study highlighted the potential role of RNA editing in the pathophysiology of PCOS as an epigenetic process. These findings could provide valuable insights into the development of more targeted and effective treatment options for PCOS.
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Affiliation(s)
- Fan-Sheng Kong
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Zijing Lu
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yuan Zhou
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yinghua Lu
- Department of Reproductive Medicine, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Ruofan Jia
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Beilei Zeng
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Panwang Huang
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Jihong Wang
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yaping Ma
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
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24
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Liu Z, Quinones-Valdez G, Fu T, Huang E, Choudhury M, Reese F, Mortazavi A, Xiao X. L-GIREMI uncovers RNA editing sites in long-read RNA-seq. Genome Biol 2023; 24:171. [PMID: 37474948 PMCID: PMC10360234 DOI: 10.1186/s13059-023-03012-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: 03/22/2022] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in single molecules and double-stranded RNA structures. L-GIREMI provides a valuable means to study nucleotide variants in long-read RNA-seq.
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Affiliation(s)
- Zhiheng Liu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Ting Fu
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Elaine Huang
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, CA, USA.
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
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25
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Wang F, Cao H, Xia Q, Liu Z, Wang M, Gao F, Xu D, Deng B, Diao Y, Kapranov P. Lessons from discovery of true ADAR RNA editing sites in a human cell line. BMC Biol 2023; 21:160. [PMID: 37468903 PMCID: PMC10357658 DOI: 10.1186/s12915-023-01651-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Conversion or editing of adenosine (A) into inosine (I) catalyzed by specialized cellular enzymes represents one of the most common post-transcriptional RNA modifications with emerging connection to disease. A-to-I conversions can happen at specific sites and lead to increase in proteome diversity and changes in RNA stability, splicing, and regulation. Such sites can be detected as adenine-to-guanine sequence changes by next-generation RNA sequencing which resulted in millions reported sites from multiple genome-wide surveys. Nonetheless, the lack of extensive independent validation in such endeavors, which is critical considering the relatively high error rate of next-generation sequencing, leads to lingering questions about the validity of the current compendiums of the editing sites and conclusions based on them. RESULTS Strikingly, we found that the current analytical methods suffer from very high false positive rates and that a significant fraction of sites in the public databases cannot be validated. In this work, we present potential solutions to these problems and provide a comprehensive and extensively validated list of A-to-I editing sites in a human cancer cell line. Our findings demonstrate that most of true A-to-I editing sites in a human cancer cell line are located in the non-coding transcripts, the so-called RNA 'dark matter'. On the other hand, many ADAR editing events occurring in exons of human protein-coding mRNAs, including those that can recode the transcriptome, represent false positives and need to be interpreted with caution. Nonetheless, yet undiscovered authentic ADAR sites that increase the diversity of human proteome exist and warrant further identification. CONCLUSIONS Accurate identification of human ADAR sites remains a challenging problem, particularly for the sites in exons of protein-coding mRNAs. As a result, genome-wide surveys of ADAR editome must still be accompanied by extensive Sanger validation efforts. However, given the vast number of unknown human ADAR sites, there is a need for further developments of the analytical techniques, potentially those that are based on deep learning solutions, in order to provide a quick and reliable identification of the editome in any sample.
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Affiliation(s)
- Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
| | - Qiu Xia
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ziheng Liu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ming Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Bolin Deng
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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26
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Pan XB, He YS, Lu Z, Pan HR, Wei ZY, Jin YY, Wang J, Chen JH. Epitranscriptomic investigation of myopia-associated RNA editing in the retina. Front Neurosci 2023; 17:1220114. [PMID: 37449273 PMCID: PMC10336353 DOI: 10.3389/fnins.2023.1220114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 05/31/2023] [Indexed: 07/18/2023] Open
Abstract
Myopia is one of the most common causes of vision loss globally and is significantly affected by epigenetics. Adenosine-to-inosine (A-to-I RNA) editing is an epigenetic process involved in neurological disorders, yet its role in myopia remains undetermined. We performed a transcriptome-wide analysis of A-to-I RNA editing in the retina of form-deprivation myopia mice. Our study identified 91 A-to-I RNA editing sites in 84 genes associated with myopia. Notably, at least 27 (32.1%) of these genes with myopia-associated RNA editing showed existing evidence to be associated with myopia or related ocular phenotypes in humans or animal models, such as very low-density lipoprotein receptor (Vldlr) in retinal neovascularization and hypoxia-induced factor 1 alpha (Hif1a). Moreover, functional enrichment showed that RNA editing enriched in FDM was primarily involved in response to fungicides, a potentially druggable process for myopia prevention, and epigenetic regulation. In contrast, RNA editing enriched in controls was mostly involved in post-embryonic eye morphogenesis. Our results demonstrate altered A-to-I RNA editing associated with myopia in an experimental mouse model and warrant further study on its role in myopia development.
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Affiliation(s)
- Xu-Bin Pan
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yu-Shan He
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Zijing Lu
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Hao-Ran Pan
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Zhi-Yuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Jihong Wang
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
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27
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Pecori R, Ren W, Pirmoradian M, Wang X, Liu D, Berglund M, Li W, Tasakis RN, Di Giorgio S, Ye X, Li X, Arnold A, Wüst S, Schneider M, Selvasaravanan KD, Fuell Y, Stafforst T, Amini RM, Sonnevi K, Enblad G, Sander B, Wahlin BE, Wu K, Zhang H, Helm D, Binder M, Papavasiliou FN, Pan-Hammarström Q. ADAR1-mediated RNA editing promotes B cell lymphomagenesis. iScience 2023; 26:106864. [PMID: 37255666 PMCID: PMC10225930 DOI: 10.1016/j.isci.2023.106864] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is one of the most common types of aggressive lymphoid malignancies. Here, we explore the contribution of RNA editing to DLBCL pathogenesis. We observed that DNA mutations and RNA editing events are often mutually exclusive, suggesting that tumors can modulate pathway outcomes by altering sequences at either the genomic or the transcriptomic level. RNA editing targets transcripts within known disease-driving pathways such as apoptosis, p53 and NF-κB signaling, as well as the RIG-I-like pathway. In this context, we show that ADAR1-mediated editing within MAVS transcript positively correlates with MAVS protein expression levels, associating with increased interferon/NF-κB signaling and T cell exhaustion. Finally, using targeted RNA base editing tools to restore editing within MAVS 3'UTR in ADAR1-deficient cells, we demonstrate that editing is likely to be causal to an increase in downstream signaling in the absence of activation by canonical nucleic acid receptor sensing.
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Affiliation(s)
- Riccardo Pecori
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz Institute for Translational Oncology (HI-TRON), Mainz, Germany
| | - Weicheng Ren
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Mohammad Pirmoradian
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Dongbing Liu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Mattias Berglund
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Wei Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Rafail Nikolaos Tasakis
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Graduate Program in Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Salvatore Di Giorgio
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Xiaobo Li
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Annette Arnold
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Wüst
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility (W120), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Yvonne Fuell
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Rose-Marie Amini
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kristina Sonnevi
- Hematology Unit, Department of Medicine, Huddinge, Karolinska Institutet and Medical Unit Hematology, Karolinska University Hospital, Solna, StockholmSweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Björn Engelbrekt Wahlin
- Hematology Unit, Department of Medicine, Huddinge, Karolinska Institutet and Medical Unit Hematology, Karolinska University Hospital, Solna, StockholmSweden
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Dominic Helm
- Proteomics Core Facility (W120), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - F. Nina Papavasiliou
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Graduate Program in Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- BGI-Shenzhen, Shenzhen, China
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28
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Cook DE, Venkat A, Yelizarov D, Pouliot Y, Chang PC, Carroll A, De La Vega FM. A deep-learning-based RNA-seq germline variant caller. BIOINFORMATICS ADVANCES 2023; 3:vbad062. [PMID: 37416509 PMCID: PMC10320079 DOI: 10.1093/bioadv/vbad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/31/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Summary RNA sequencing (RNA-seq) can be applied to diverse tasks including quantifying gene expression, discovering quantitative trait loci and identifying gene fusion events. Although RNA-seq can detect germline variants, the complexities of variable transcript abundance, target capture and amplification introduce challenging sources of error. Here, we extend DeepVariant, a deep-learning-based variant caller, to learn and account for the unique challenges presented by RNA-seq data. Our DeepVariant RNA-seq model produces highly accurate variant calls from RNA-sequencing data, and outperforms existing approaches such as Platypus and GATK. We examine factors that influence accuracy, how our model addresses RNA editing events and how additional thresholding can be used to facilitate our models' use in a production pipeline. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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29
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Tang AD, Hrabeta-Robinson E, Volden R, Vollmers C, Brooks AN. Detecting haplotype-specific transcript variation in long reads with FLAIR2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544396. [PMID: 37398362 PMCID: PMC10312636 DOI: 10.1101/2023.06.09.544396] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background RNA-Seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme which mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung ADC cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, short read RNA-Seq has limited the community's ability to interrogate both forms of RNA variation simultaneously. Results We employed long-read technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We have developed a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generated nanopore data with high sequence accuracy of H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We applied our workflow to identify key inosine-isoform associations to help clarify the prominence of ADAR in tumorigenesis. Conclusions Ultimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns.
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Affiliation(s)
- Alison D. Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | | | - Roger Volden
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | | | - Angela N. Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz
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30
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Yamamoto R, Liu Z, Choudhury M, Xiao X. dsRID: Editing-free in silico identification of dsRNA region using long-read RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543466. [PMID: 37333092 PMCID: PMC10274638 DOI: 10.1101/2023.06.02.543466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Double-stranded RNAs (dsRNAs) are potent triggers of innate immune responses upon recognition by cytosolic dsRNA sensor proteins. Identification of endogenous dsRNAs helps to better understand the dsRNAome and its relevance to innate immunity related to human diseases. Here, we report dsRID (double-stranded RNA identifier), a machine learning-based method to predict dsRNA regions in silico, leveraging the power of long-read RNA-sequencing (RNA-seq) and molecular traits of dsRNAs. Using models trained with PacBio long-read RNA-seq data derived from Alzheimer's disease (AD) brain, we show that our approach is highly accurate in predicting dsRNA regions in multiple datasets. Applied to an AD cohort sequenced by the ENCODE consortium, we characterize the global dsRNA profile with potentially distinct expression patterns between AD and controls. Together, we show that dsRID provides an effective approach to capture global dsRNA profiles using long-read RNA-seq data.
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Affiliation(s)
- Ryo Yamamoto
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California, USA
| | - Zhiheng Liu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, California, USA
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31
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Wu S, Fan Z, Kim P, Huang L, Zhou X. The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:619-631. [PMID: 36708807 PMCID: PMC10787018 DOI: 10.1016/j.gpb.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 11/04/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, constituting nearly 90% of all RNA editing events in humans, has been reported to contribute to the tumorigenesis in diverse cancers. However, the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient. To fill this gap, we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas. For individual candidate among ∼ 1,500,000 quantified RNA editing events, we performed diverse types of downstream functional annotations. Finally, we identified 24,236 potentially functional A-to-I RNA editing events, including the cases in APOL1, IGFBP3, GRIA2, BLCAP, and miR-589-3p. These events might play crucial roles in the scenarios of tumorigenesis, due to their tumor-related editing frequencies or probable effects on altered expression profiles, protein functions, splicing patterns, and microRNA regulations of tumor genes. Our functional A-to-I RNA editing events (https://ccsm.uth.edu/CAeditome/) will help better understand the cancer pathology from the A-to-I RNA editing aspect.
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Affiliation(s)
- Sijia Wu
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Zhiwei Fan
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610040, China; Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi'an 710071, China.
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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32
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Chen R, Li F, Guo X, Bi Y, Li C, Pan S, Coin LJM, Song J. ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Brief Bioinform 2023; 24:bbad170. [PMID: 37150785 PMCID: PMC10565902 DOI: 10.1093/bib/bbad170] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/09/2023] Open
Abstract
A-to-I editing is the most prevalent RNA editing event, which refers to the change of adenosine (A) bases to inosine (I) bases in double-stranded RNAs. Several studies have revealed that A-to-I editing can regulate cellular processes and is associated with various human diseases. Therefore, accurate identification of A-to-I editing sites is crucial for understanding RNA-level (i.e. transcriptional) modifications and their potential roles in molecular functions. To date, various computational approaches for A-to-I editing site identification have been developed; however, their performance is still unsatisfactory and needs further improvement. In this study, we developed a novel stacked-ensemble learning model, ATTIC (A-To-I ediTing predICtor), to accurately identify A-to-I editing sites across three species, including Homo sapiens, Mus musculus and Drosophila melanogaster. We first comprehensively evaluated 37 RNA sequence-derived features combined with 14 popular machine learning algorithms. Then, we selected the optimal base models to build a series of stacked ensemble models. The final ATTIC framework was developed based on the optimal models improved by the feature selection strategy for specific species. Extensive cross-validation and independent tests illustrate that ATTIC outperforms state-of-the-art tools for predicting A-to-I editing sites. We also developed a web server for ATTIC, which is publicly available at http://web.unimelb-bioinfortools.cloud.edu.au/ATTIC/. We anticipate that ATTIC can be utilized as a useful tool to accelerate the identification of A-to-I RNA editing events and help characterize their roles in post-transcriptional regulation.
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Affiliation(s)
- Ruyi Chen
- College of Information Engineering, Northwest A&F University, Shaanxi 712100, China
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3000, Australia
| | - Fuyi Li
- College of Information Engineering, Northwest A&F University, Shaanxi 712100, China
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3000, Australia
| | - Xudong Guo
- College of Information Engineering, Northwest A&F University, Shaanxi 712100, China
| | - Yue Bi
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Shirui Pan
- School of Information and Communication Technology, Griffith University, QLD 4222, Australia
| | - Lachlan J M Coin
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3000, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, VIC 3800, Australia
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33
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Wu S, Xue Q, Qin X, Wu X, Kim P, Chyr J, Zhou X, Huang L. The Potential Regulation of A-to-I RNA Editing on Genes in Parkinson's Disease. Genes (Basel) 2023; 14:genes14040919. [PMID: 37107677 PMCID: PMC10137963 DOI: 10.3390/genes14040919] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Parkinson's disease (PD) is characterized by dopaminergic neurodegeneration and an abnormal accumulation of α-synuclein aggregates. A number of genetic factors have been shown to increase the risk of PD. Exploring the underlying molecular mechanisms that mediate PD's transcriptomic diversity can help us understand neurodegenerative pathogenesis. In this study, we identified 9897 A-to-I RNA editing events associated with 6286 genes across 372 PD patients. Of them, 72 RNA editing events altered miRNA binding sites and this may directly affect miRNA regulations of their host genes. However, RNA editing effects on the miRNA regulation of genes are more complex. They can (1) abolish existing miRNA binding sites, which allows miRNAs to regulate other genes; (2) create new miRNA binding sites that may sequester miRNAs from regulating other genes; or (3) occur in the miRNA seed regions and change their targets. The first two processes are also referred to as miRNA competitive binding. In our study, we found 8 RNA editing events that may alter the expression of 1146 other genes via miRNA competition. We also found one RNA editing event that modified a miRNA seed region, which was predicted to disturb the regulation of four genes. Considering the PD-related functions of the affected genes, 25 A-to-I RNA editing biomarkers for PD are proposed, including the 3 editing events in the EIF2AK2, APOL6, and miR-4477b seed regions. These biomarkers may alter the miRNA regulation of 133 PD-related genes. All these analyses reveal the potential mechanisms and regulations of RNA editing in PD pathogenesis.
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Affiliation(s)
- Sijia Wu
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Qiuping Xue
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Xinyu Qin
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Xiaoming Wu
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jacqueline Chyr
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
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34
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Wei ZY, Wang ZX, Li JH, Wen YS, Gao D, Xia SY, Li YN, Pan XB, Liu YS, Jin YY, Chen JH. Host A-to-I RNA editing signatures in intracellular bacterial and single-strand RNA viral infections. Front Immunol 2023; 14:1121096. [PMID: 37081881 PMCID: PMC10112020 DOI: 10.3389/fimmu.2023.1121096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
BackgroundMicrobial infection is accompanied by remodeling of the host transcriptome. Involvement of A-to-I RNA editing has been reported during viral infection but remains to be elucidated during intracellular bacterial infections.ResultsHerein we analyzed A-to-I RNA editing during intracellular bacterial infections based on 18 RNA-Seq datasets of 210 mouse samples involving 7 tissue types and 8 intracellular bacterial pathogens (IBPs), and identified a consensus signature of RNA editing for IBP infections, mainly involving neutrophil-mediated innate immunity and lipid metabolism. Further comparison of host RNA editing patterns revealed remarkable similarities between pneumonia caused by IBPs and single-strand RNA (ssRNA) viruses, such as altered editing enzyme expression, editing site numbers, and levels. In addition, functional enrichment analysis of genes with RNA editing highlighted that the Rab GTPase family played a common and vital role in the host immune response to IBP and ssRNA viral infections, which was indicated by the consistent up-regulated RNA editing of Ras-related protein Rab27a. Nevertheless, dramatic differences between IBP and viral infections were also observed, and clearly distinguished the two types of intracellular infections.ConclusionOur study showed transcriptome-wide host A-to-I RNA editing alteration during IBP and ssRNA viral infections. By identifying and comparing consensus signatures of host A-to-I RNA editing, our analysis implicates the importance of host A-to-I RNA editing during these infections and provides new insights into the diagnosis and treatment of infectious diseases.
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Affiliation(s)
- Zhi-Yuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Zhi-Xin Wang
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Jia-Huan Li
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yan-Shuo Wen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Di Gao
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Shou-Yue Xia
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yu-Ning Li
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Xu-Bin Pan
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Wuxi Children’s Hospital, Wuxi, Jiangsu, China
| | - Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- *Correspondence: Jian-Huan Chen, ; Yun-Yun Jin,
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- *Correspondence: Jian-Huan Chen, ; Yun-Yun Jin,
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35
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Tassinari V, La Rosa P, Guida E, Colopi A, Caratelli S, De Paolis F, Gallo A, Cenciarelli C, Sconocchia G, Dolci S, Cesarini V. Contribution of A-to-I RNA editing, M6A RNA Methylation, and Alternative Splicing to physiological brain aging and neurodegenerative diseases. Mech Ageing Dev 2023; 212:111807. [PMID: 37023929 DOI: 10.1016/j.mad.2023.111807] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Aging is a physiological and progressive phenomenon in all organisms' life cycle, characterized by the accumulation of degenerative processes triggered by several alterations within molecular pathways. These changes compromise cell fate, resulting in the loss of functions in tissues throughout the body, including the brain. Physiological brain aging has been linked to structural and functional alterations, as well as to an increased risk of neurodegenerative diseases. Post-transcriptional RNA modifications modulate mRNA coding properties, stability, translatability, expanding the coding capacity of the genome, and are involved in all cellular processes. Among mRNA post-transcriptional modifications, the A-to-I RNA editing, m6A RNA Methylation and Alternative Splicing play a critical role in all the phases of a neuronal cell life cycle and alterations in their mechanisms of action significantly contribute to aging and neurodegeneration. Here we review our current understanding of the contribution of A-to-I RNA editing, m6A RNA Methylation, and Alternative Splicing to physiological brain aging process and neurodegenerative diseases.
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Affiliation(s)
- Valentina Tassinari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Eugenia Guida
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Ambra Colopi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Sara Caratelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Francesca De Paolis
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Angela Gallo
- RNA Editing Lab., Oncohaematology Department, Cellular and Gene Therapy Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Cenciarelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Giuseppe Sconocchia
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Susanna Dolci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Valeriana Cesarini
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
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36
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Luo Y, Liang H. Cancer Cells Employ the Most Prolific RNA Editors: A Closer Look at the Single-Cell Level. Cancer Res 2023; 83:351-353. [PMID: 36734079 DOI: 10.1158/0008-5472.can-22-3537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 02/04/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a major source of nucleotide diversification that has significant mechanistic implications in cancer progression and treatment response. However, its activity and prevalence have not yet been systematically determined at a single-cell resolution. Chan and colleagues revealed widespread A-to-I RNA editing events in single cancer cells through an in-depth analysis of a public lung adenocarcinoma single-cell transcriptome dataset. Edits significantly enriched in cancer cells compared to other cell types have the potential to inhibit innate immune response and to predict poor therapeutic response and prognosis in patients treated with targeted therapies. See related article by Chan et al., p. 374.
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Affiliation(s)
- Yikai Luo
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Han Liang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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37
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Chan TW, Dodson JP, Arbet J, Boutros PC, Xiao X. Single-Cell Analysis in Lung Adenocarcinoma Implicates RNA Editing in Cancer Innate Immunity and Patient Prognosis. Cancer Res 2023; 83:374-385. [PMID: 36449563 PMCID: PMC9898195 DOI: 10.1158/0008-5472.can-22-1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/08/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
RNA editing modifies single nucleotides of RNAs, regulating primary protein structure and protein abundance. In recent years, the diversity of proteins and complexity of gene regulation associated with RNA editing dysregulation has been increasingly appreciated in oncology. Large-scale shifts in editing have been observed in bulk tumors across various cancer types. However, RNA editing in single cells and individual cell types within tumors has not been explored. By profiling editing in single cells from lung adenocarcinoma biopsies, we found that the increased editing trend of bulk lung tumors was unique to cancer cells. Elevated editing levels were observed in cancer cells resistant to targeted therapy, and editing sites associated with drug response were enriched. Consistent with the regulation of antiviral pathways by RNA editing, higher editing levels in cancer cells were associated with reduced antitumor innate immune response, especially levels of natural killer cell infiltration. In addition, the level of RNA editing in cancer cells was positively associated with somatic point mutation burden. This observation motivated the definition of a new metric, RNA editing load, reflecting the amount of RNA mutations created by RNA editing. Importantly, in lung cancer, RNA editing load was a stronger predictor of patient survival than DNA mutations. This study provides the first single cell dissection of editing in cancer and highlights the significance of RNA editing load in cancer prognosis. SIGNIFICANCE RNA editing analysis in single lung adenocarcinoma cells uncovers RNA mutations that correlate with tumor mutation burden and cancer innate immunity and reveals the amount of RNA mutations that strongly predicts patient survival. See related commentary by Luo and Liang, p. 351.
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Affiliation(s)
- Tracey W. Chan
- Bioinformatics interdepartmental program, University of California, Los Angeles, CA, USA
| | - Jack P. Dodson
- Bioinformatics interdepartmental program, University of California, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, CA, USA,Department of Integrative Biology and Physiology, University of California, Los Angeles, California, CA, USA
| | - Jaron Arbet
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, CA, USA
| | - Paul C. Boutros
- Bioinformatics interdepartmental program, University of California, Los Angeles, CA, USA,Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, CA, USA,Molecular Biology Institute, University of California, Los Angeles, California, CA, USA,Institute for Quantitative and Computational Sciences, University of California, Los Angeles, California, CA, USA,Institute for Precision Health, University of California, Los Angeles, California, CA
| | - Xinshu Xiao
- Bioinformatics interdepartmental program, University of California, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, CA, USA,Molecular Biology Institute, University of California, Los Angeles, California, CA, USA,Department of Integrative Biology and Physiology, University of California, Los Angeles, California, CA, USA,Correspondence: Xinshu Xiao, ; 310-206-6522, 611 Charles E. Young Drive South, Terasaki Life Sciences Building, 2000E, UCLA, Los Angeles, CA, 90095
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38
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Pecori R, Chillón I, Lo Giudice C, Arnold A, Wüst S, Binder M, Marcia M, Picardi E, Papavasiliou FN. ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts. Front Cell Dev Biol 2023; 10:1080626. [PMID: 36684421 PMCID: PMC9852825 DOI: 10.3389/fcell.2022.1080626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Despite hundreds of RNA modifications described to date, only RNA editing results in a change in the nucleotide sequence of RNA molecules compared to the genome. In mammals, two kinds of RNA editing have been described so far, adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. Recent improvements in RNA sequencing technologies have led to the discovery of a continuously growing number of editing sites. These methods are powerful but not error-free, making routine validation of newly-described editing sites necessary. During one of these validations on DDX58 mRNA, along with A-to-I RNA editing sites, we encountered putative U-to-C editing. These U-to-C edits were present in several cell lines and appeared regulated in response to specific environmental stimuli. The same findings were also observed for the human long intergenic non-coding RNA p21 (hLincRNA-p21). A more in-depth analysis revealed that putative U-to-C edits result from A-to-I editing on overlapping antisense RNAs that are transcribed from the same loci. Such editing events, occurring on overlapping genes transcribed in opposite directions, have recently been demonstrated to be immunogenic and have been linked with autoimmune and immune-related diseases. Our findings, also confirmed by deep transcriptome data, demonstrate that such loci can be recognized simply through the presence of A-to-I and U-to-C mismatches within the same locus, reflective A-to-I editing both in the sense-oriented transcript and in the cis-natural antisense transcript (cis-NAT), implying that such clusters could be a mark of functionally relevant ADAR1 editing events.
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Affiliation(s)
- Riccardo Pecori
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany,Helmholtz Institute for Translational Oncology (HI-TRON), Mainz, Germany,*Correspondence: Riccardo Pecori, ; Fotini Nina Papavasiliou,
| | - Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Claudio Lo Giudice
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
| | - Annette Arnold
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany
| | - Sandra Wüst
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response,” German Cancer Research Centre (DKFZ), Research Program Infection, Inflammation and Cancer, Division Virus Associated Carcinogenesis (F170), Heidelberg, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response,” German Cancer Research Centre (DKFZ), Research Program Infection, Inflammation and Cancer, Division Virus Associated Carcinogenesis (F170), Heidelberg, Germany
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
| | - Fotini Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany,*Correspondence: Riccardo Pecori, ; Fotini Nina Papavasiliou,
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Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance. Commun Biol 2022; 5:1400. [PMID: 36543858 PMCID: PMC9772385 DOI: 10.1038/s42003-022-04338-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Posttranscriptional modification plays an important role in key embryonic processes. Adenosine-to-inosine RNA editing, a common example of such modifications, is widespread in human adult tissues and has various functional impacts and clinical consequences. However, whether it persists in a consistent pattern in most human embryos, and whether it supports embryonic development, are poorly understood. To address this problem, we compiled the largest human embryonic editome from 2,071 transcriptomes and identified thousands of recurrent embryonic edits (>=50% chances of occurring in a given stage) for each early developmental stage. We found that these recurrent edits prefer exons consistently across stages, tend to target genes related to DNA replication, and undergo organized loss in abnormal embryos and embryos from elder mothers. In particular, these recurrent edits are likely to enhance maternal mRNA clearance, a possible mechanism of which could be introducing more microRNA binding sites to the 3'-untranslated regions of clearance targets. This study suggests a potentially important, if not indispensable, role of RNA editing in key human embryonic processes such as maternal mRNA clearance; the identified editome can aid further investigations.
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40
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Fonzino A, Pesole G, Picardi E. Profiling RNA Editing in Single Cells. Methods Mol Biol 2022; 2584:347-370. [PMID: 36495460 DOI: 10.1007/978-1-0716-2756-3_18] [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] [Indexed: 12/13/2022]
Abstract
RNA editing is a widespread molecular phenomenon occurring in a variety of organisms. In humans, it mainly involves the deamination of adenosine to inosine (A-to-I) in double-stranded RNAs by ADAR enzymes. A-to-I RNA editing has been investigated in different tissues as well as in diverse experimental and pathological conditions. By contrast, its biological role in single cells has not been explored in depth. Recent methodologies for cell sorting in combination with deep sequencing technologies have enabled the study of eukaryotic transcriptomes at single cell resolution, paving the way to the profiling of their epitranscriptomic dynamics.Here we describe a step-by-step protocol to detect and characterize A-to-I events occurring in publicly available single-cell RNAseq experiments from human alpha and beta pancreatic cells.
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Affiliation(s)
- Adriano Fonzino
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.
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41
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Wu K, Wang D, Wang J, Zhou Y. Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs. Virol Sin 2022; 37:813-822. [PMID: 36075564 PMCID: PMC9444306 DOI: 10.1016/j.virs.2022.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/01/2022] [Indexed: 12/27/2022] Open
Abstract
The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a positive-stranded RNA genome. Current proteomic studies of SARS-CoV-2 mainly focus on the proteins encoded by its genomic RNA (gRNA) or canonical subgenomic RNAs (sgRNAs). Here, we systematically investigated the translation landscape of SARS-CoV-2, especially its noncanonical sgRNAs. We first constructed a strict pipeline, named vipep, for identifying reliable peptides derived from RNA viruses using RNA-seq and mass spectrometry data. We applied vipep to analyze 24 sets of mass spectrometry data related to SARS-CoV-2 infection. In addition to known canonical proteins, we identified many noncanonical sgRNA-derived peptides, which stably increase after viral infection. Furthermore, we explored the potential functions of those proteins encoded by noncanonical sgRNAs and found that they can bind to viral RNAs and may have immunogenic activity. The generalized vipep pipeline is applicable to any RNA viruses and these results have expanded the SARS-CoV-2 translation map, providing new insights for understanding the functions of SARS-CoV-2 sgRNAs.
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Affiliation(s)
- Kai Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Dehe Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junhao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China,TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, 430072, China,Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China,Corresponding author
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42
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Lo Giudice C, Zambelli F, Chiara M, Pavesi G, Tangaro M, Picardi E, Pesole G. UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions. Nucleic Acids Res 2022; 51:D337-D344. [PMID: 36399486 PMCID: PMC9825521 DOI: 10.1093/nar/gkac1016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Since 1996, we have developed and maintained UTRdb, a specialized database of UTR sequences. Here we present UTRdb 2.0, a major update of UTRdb featuring an extensive collection of eukaryotic 5' and 3' UTR sequences, including over 26 million entries from over 6 million genes and 573 species, enriched with a curated set of functional annotations. Annotations include CAGE tags and polyA signals to label the completeness of 5' and 3'UTRs, respectively. In addition, uORFs and IRES are annotated in 5'UTRs as well as experimentally validated miRNA targets in 3'UTRs. Further annotations include evolutionarily conserved blocks, Rfam motifs, ADAR-mediated RNA editing events, and m6A modifications. A web interface allowing a flexible selection and retrieval of specific subsets of UTRs, selected according to a combination of criteria, has been implemented which also provides comprehensive download facilities. UTRdb 2.0 is accessible at http://utrdb.cloud.ba.infn.it/utrdb/.
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Affiliation(s)
- Claudio Lo Giudice
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, 70126 Bari, Italy
| | - Federico Zambelli
- Department of Biosciences, University of Milan, 20133 Milan, Italy,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, 20133 Milan, Italy,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, 20133 Milan, Italy,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Marco Antonio Tangaro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, 70126 Bari, Italy,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Graziano Pesole
- To whom correspondence should be addressed. Tel: +39 0805443588;
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43
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Abstract
The field of epitranscriptomics has expanded dramatically in recent years, both in the number of identified RNA modifications and the number of researchers studying them. As knowledge of post-transcriptional modifications continues to expand, numerous new methods have been developed to detect these modifications. Additionally, modifications are being extended to therapeutic settings, such as with recent mRNA vaccines. With this increase in knowledge and use, the community is recognizing the necessity for user-friendly databases to (i) store information from both high- and low-throughput studies and (ii) provide prediction software on how RNA modifications contribute to RNA function and disease. This mini-review highlights select RNA modification databases and their key attributes with the aim of providing a resource to researchers in the field of epitranscriptomics.
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Affiliation(s)
- Jillian Ramos
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, Colorado 80045, USA
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44
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Huang W, Sun YM, Pan Q, Fang K, Chen XT, Zeng ZC, Chen TQ, Zhu SX, Huang LB, Luo XQ, Wang WT, Chen YQ. The snoRNA-like lncRNA LNC-SNO49AB drives leukemia by activating the RNA-editing enzyme ADAR1. Cell Discov 2022; 8:117. [PMID: 36316318 PMCID: PMC9622897 DOI: 10.1038/s41421-022-00460-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/18/2022] [Indexed: 01/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are usually 5' capped and 3' polyadenylated, similar to most typical mRNAs. However, recent studies revealed a type of snoRNA-related lncRNA with unique structures, leading to questions on how they are processed and how they work. Here, we identify a novel snoRNA-related lncRNA named LNC-SNO49AB containing two C/D box snoRNA sequences, SNORD49A and SNORD49B; and show that LNC-SNO49AB represents an unreported type of lncRNA with a 5'-end m7G and a 3'-end snoRNA structure. LNC-SNO49AB was found highly expressed in leukemia patient samples, and silencing LNC-SNO49AB dramatically suppressed leukemia progression in vitro and in vivo. Subcellular location indicated that the LNC-SNO49AB is mainly located in nucleolus and interacted with the nucleolar protein fibrillarin. However, we found that LNC-SNO49AB does not play a role in 2'-O-methylation regulation, a classical function of snoRNA; instead, its snoRNA structure affected the lncRNA stability. We further demonstrated that LNC-SNO49AB could directly bind to the adenosine deaminase acting on RNA 1(ADAR1) and promoted its homodimerization followed by a high RNA A-to-I editing activity. Transcriptome profiling shows that LNC-SNO49AB and ADAR1 knockdown respectively share very similar patterns of RNA modification change in downstream signaling pathways, especially in cell cycle pathways. These findings suggest a previously unknown class of snoRNA-related lncRNAs, which function via a manner in nucleolus independently on snoRNA-guide rRNA modification. This is the first report that a lncRNA regulates genome-wide RNA A-to-I editing by enhancing ADAR1 dimerization to facilitate hematopoietic malignancy, suggesting that LNC-SNO49AB may be a novel target in therapy directed to leukemia.
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Affiliation(s)
- Wei Huang
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Yu-Meng Sun
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Qi Pan
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Ke Fang
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xiao-Tong Chen
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Zhan-Cheng Zeng
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Tian-Qi Chen
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Shun-Xin Zhu
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Li-Bin Huang
- grid.412615.50000 0004 1803 6239The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xue-Qun Luo
- grid.412615.50000 0004 1803 6239The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Wen-Tao Wang
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Yue-Qin Chen
- grid.12981.330000 0001 2360 039XGuangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
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Zhou X, Bao P, Zhang X, Guo X, Liang C, Chu M, Wu X, Yan P. Genome-wide detection of RNA editing events during the hair follicles cycle of Tianzhu white yak. BMC Genomics 2022; 23:737. [PMID: 36316632 PMCID: PMC9624038 DOI: 10.1186/s12864-022-08951-5] [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: 04/08/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The hair coat is available for the yak to live in the harsh environment of the plateau. Besides, improving the hair production of yak is necessary for its textile industry development. Hair grows from hair follicles (HFs). The HFs undergo periodic growth after birth and are regulated by the complex gene regulatory network. However, the molecular mechanism of HFs regeneration in the Tianzhu white yak remains unclear. RNA editing is a post-transcriptional mechanism that regulates gene expression and produces new transcripts. Hence, we investigated the influence of the A-to-I RNA editing events on the HFs cycle of the Tianzhu white yak. RESULTS We finally identified 54,707 adenosine-to-inosine (A-to-I) RNA editing sites (RESs) from RNA sequencing data of the HFs cycle in the Tianzhu white yak. Annotation results showed RESs caused missense amino acid changes in 7 known genes. And 202 A-to-I editing sites altered 23 target genes of 140 microRNAs. A total of 1,722 differential RESs were identified during the HFs cycle of Tianzhu white yak. GO and KEGG enrichment analysis revealed several signaling pathways and GO terms involved skin development, hair growth, and HFs cycle. Such as genes with differential RNA editing levels were significantly enriched in the peroxisome, metabolic pathways, Notch signaling pathway, and PPAR signaling pathway. Besides, the editing sites in HFs development-related genes FAS, APCDD1, WWOX, MPZL3, RUNX1, KANK2, DCN, DSC2, LEPR, HEPHL1, and PTK2B were suggested as the potential RESs involving HFs development. CONCLUSION This study investigated the global A-to-I RNA editing events during the HFs cycle of yak skin tissue and expanded the knowledge of A-to-I RNA editing on the HFs cycle. Furthermore, this study revealed that RNA editing-influenced genes may regulate the HFs cycle by participating in the HFs development-related pathways. The findings might provide new insight into the regulation of RNA editing in hair growth.
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Affiliation(s)
- Xuelan Zhou
- grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050 Lanzhou, P.R. China ,grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050 Lanzhou, P.R. China
| | - Pengjia Bao
- grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050 Lanzhou, P.R. China ,grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050 Lanzhou, P.R. China
| | - Xiaolan Zhang
- grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050 Lanzhou, P.R. China ,grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050 Lanzhou, P.R. China
| | - Xian Guo
- grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050 Lanzhou, P.R. China ,grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050 Lanzhou, P.R. China
| | - Chunnian Liang
- grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050 Lanzhou, P.R. China ,grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050 Lanzhou, P.R. China
| | - Min Chu
- grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050 Lanzhou, P.R. China ,grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050 Lanzhou, P.R. China
| | - Xiaoyun Wu
- grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050 Lanzhou, P.R. China ,grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050 Lanzhou, P.R. China
| | - Ping Yan
- grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050 Lanzhou, P.R. China ,grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050 Lanzhou, P.R. China
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Lesch E, Schilling MT, Brenner S, Yang Y, Gruss O, Knoop V, Schallenberg-Rüdinger M. Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells. Nucleic Acids Res 2022; 50:9966-9983. [PMID: 36107771 PMCID: PMC9508816 DOI: 10.1093/nar/gkac752] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/10/2022] [Accepted: 08/29/2022] [Indexed: 11/12/2022] Open
Abstract
RNA editing processes are strikingly different in animals and plants. Up to thousands of specific cytidines are converted into uridines in plant chloroplasts and mitochondria whereas up to millions of adenosines are converted into inosines in animal nucleo-cytosolic RNAs. It is unknown whether these two different RNA editing machineries are mutually incompatible. RNA-binding pentatricopeptide repeat (PPR) proteins are the key factors of plant organelle cytidine-to-uridine RNA editing. The complete absence of PPR mediated editing of cytosolic RNAs might be due to a yet unknown barrier that prevents its activity in the cytosol. Here, we transferred two plant mitochondrial PPR-type editing factors into human cell lines to explore whether they could operate in the nucleo-cytosolic environment. PPR56 and PPR65 not only faithfully edited their native, co-transcribed targets but also different sets of off-targets in the human background transcriptome. More than 900 of such off-targets with editing efficiencies up to 91%, largely explained by known PPR-RNA binding properties, were identified for PPR56. Engineering two crucial amino acid positions in its PPR array led to predictable shifts in target recognition. We conclude that plant PPR editing factors can operate in the entirely different genetic environment of the human nucleo-cytosol and can be intentionally re-engineered towards new targets.
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Affiliation(s)
- Elena Lesch
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
| | - Maximilian T Schilling
- Institut für Genetik, Abteilung Zellteilung, Universität Bonn , Karlrobert-Kreiten-Str. 13 , D-53115 Bonn , Germany
| | - Sarah Brenner
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
| | - Yingying Yang
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
| | - Oliver J Gruss
- Institut für Genetik, Abteilung Zellteilung, Universität Bonn , Karlrobert-Kreiten-Str. 13 , D-53115 Bonn , Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn , Kirschallee 1 , D-53115 Bonn , Germany
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ADAR2 Protein Is Associated with Overall Survival in GBM Patients and Its Decrease Triggers the Anchorage-Independent Cell Growth Signature. Biomolecules 2022; 12:biom12081142. [PMID: 36009036 PMCID: PMC9405742 DOI: 10.3390/biom12081142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Epitranscriptomic mechanisms, such as A-to-I RNA editing mediated by ADAR deaminases, contribute to cancer heterogeneity and patients’ stratification. ADAR enzymes can change the sequence, structure, and expression of several RNAs, affecting cancer cell behavior. In glioblastoma, an overall decrease in ADAR2 RNA level/activity has been reported. However, no data on ADAR2 protein levels in GBM patient tissues are available; and most data are based on ADARs overexpression experiments. Methods: We performed IHC analysis on GBM tissues and correlated ADAR2 levels and patients’ overall survival. We silenced ADAR2 in GBM cells, studied cell behavior, and performed a gene expression/editing analysis. Results: GBM tissues do not all show a low/no ADAR2 level, as expected by previous studies. Although, different amounts of ADAR2 protein were observed in different patients, with a low level correlating with a poor patient outcome. Indeed, reducing the endogenous ADAR2 protein in GBM cells promotes cell proliferation and migration and changes the cell’s program to an anchorage-independent growth mode. In addition, deep-seq data and bioinformatics analysis indicated multiple RNAs are differently expressed/edited upon siADAR2. Conclusion: ADAR2 protein is an important deaminase in GBM and its amount correlates with patient prognosis.
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Fu T, Chan TW, Bahn JH, Kim TH, Rowat AC, Xiao X. Multifaceted role of RNA editing in promoting loss-of-function of PODXL in cancer. iScience 2022; 25:104836. [PMID: 35992085 PMCID: PMC9382340 DOI: 10.1016/j.isci.2022.104836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
PODXL, a protein that is dysregulated in multiple cancers, plays an important role in promoting cancer metastasis. In this study, we report that RNA editing promotes the inclusion of a PODXL alternative exon. The resulting edited PODXL long isoform is more prone to protease digestion and has the strongest effects on reducing cell migration and cisplatin chemoresistance among the three PODXL isoforms (short, unedited long, and edited long isoforms). Importantly, the editing level of the PODXL recoding site and the inclusion level of the PODXL alternative exon are strongly associated with overall patient survival in Kidney Renal Clear Cell Carcinoma (KIRC). Supported by significant enrichment of exonic RNA editing sites in alternatively spliced exons, we hypothesize that exonic RNA editing sites may enhance proteomic diversity through alternative splicing, in addition to amino acid changes, a previously under-appreciated aspect of RNA editing function.
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Affiliation(s)
- Ting Fu
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tracey W. Chan
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tae-Hyung Kim
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amy C. Rowat
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Bannister S, Kim B, Domínguez-Andrés J, Kilic G, Ansell BRE, Neeland MR, Moorlag SJCFM, Matzaraki V, Vlahos A, Shepherd R, Germano S, Bahlo M, Messina NL, Saffery R, Netea MG, Curtis N, Novakovic B. Neonatal BCG vaccination is associated with a long-term DNA methylation signature in circulating monocytes. SCIENCE ADVANCES 2022; 8:eabn4002. [PMID: 35930640 PMCID: PMC9355358 DOI: 10.1126/sciadv.abn4002] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/23/2022] [Indexed: 05/21/2023]
Abstract
Trained immunity describes the capacity of innate immune cells to develop heterologous memory in response to certain exogenous exposures. This phenomenon mediates, at least in part, the beneficial off-target effects of the BCG vaccine. Using an in vitro model of trained immunity, we show that BCG exposure induces a persistent change in active histone modifications, DNA methylation, transcription, and adenosine-to-inosine RNA modification in human monocytes. By profiling DNA methylation of circulating monocytes from infants in the MIS BAIR clinical trial, we identify a BCG-associated DNA methylation signature that persisted more than 12 months after neonatal BCG vaccination. Genes associated with this epigenetic signature are involved in viral response pathways, consistent with the reported off-target protection against viral infections in neonates, adults, and the elderly. Our findings indicate that the off-target effects of BCG in infants are accompanied by epigenetic remodeling of circulating monocytes that lasts more than 1 year.
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Affiliation(s)
- Samantha Bannister
- Infectious Diseases, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Unit, The Royal Children’s Hospital, Parkville, VIC, Australia
| | - Bowon Kim
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500HB Nijmegen, Netherlands
| | - Gizem Kilic
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500HB Nijmegen, Netherlands
| | - Brendan R. E. Ansell
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Melanie R. Neeland
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Simone J. C. F. M. Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500HB Nijmegen, Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500HB Nijmegen, Netherlands
| | - Amanda Vlahos
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Rebecca Shepherd
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Susie Germano
- Infectious Diseases, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Nicole L. Messina
- Infectious Diseases, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Richard Saffery
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500HB Nijmegen, Netherlands
- Department for Immunology and Metabolism, Life and Medical Science Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Nigel Curtis
- Infectious Diseases, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Unit, The Royal Children’s Hospital, Parkville, VIC, Australia
- Corresponding author. (B.N.); (N.C.)
| | - Boris Novakovic
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Corresponding author. (B.N.); (N.C.)
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Guo Y, Van der Heijden YF, Maruri F, Jiang L, Morrison R, Sterling TR. RNA editing in Mycobacterium tuberculosis. Microbiol Res 2022; 264:127174. [DOI: 10.1016/j.micres.2022.127174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022]
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