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Zhang Y, Song Z, Wu R, Kong X, Zhang H, Li S, Gong X, Gong S, Cheng J, Yuan F, Wu H, Wang S, Yuan Z. PRRC2B modulates oligodendrocyte progenitor cell development and myelination by stabilizing Sox2 mRNA. Cell Rep 2024; 43:113930. [PMID: 38507412 DOI: 10.1016/j.celrep.2024.113930] [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: 04/24/2023] [Revised: 01/13/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
Oligodendrocyte progenitor cells (OPCs) differentiate into myelin-producing cells and modulate neuronal activity. Defects in OPC development are associated with neurological diseases. N6-methyladenosine (m6A) contributes to neural development; however, the mechanism by which m6A regulates OPC development remains unclear. Here, we demonstrate that PRRC2B is an m6A reader that regulates OPC development and myelination. Nestin-Cre-mediated Prrc2b deletion affects neural stem cell self-renewal and glial differentiation. Moreover, the oligodendroglia lineage-specific deletion of Prrc2b reduces the numbers of OPCs and oligodendrocytes, causing hypomyelination and impaired motor coordination. Integrative methylated RNA immunoprecipitation sequencing, RNA sequencing, and RNA immunoprecipitation sequencing analyses identify Sox2 as the target of PRRC2B. Notably, PRRC2B, displaying separate and cooperative functions with PRRC2A, stabilizes mRNA by binding to m6A motifs in the coding sequence and 3' UTR of Sox2. In summary, we identify the posttranscriptional regulation of PRRC2B in OPC development, extending the understanding of PRRC2 family proteins and providing a therapeutic target for myelin-related disorders.
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Affiliation(s)
- Ying Zhang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Zhihong Song
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Rong Wu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xiangxi Kong
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou 221004, China
| | - Hongye Zhang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Shuoshuo Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xuanwei Gong
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Shenghui Gong
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jinbo Cheng
- Center on Translational Neuroscience, College of Life and Environmental Science, Minzu University of China, Beijing 100081, China; Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang 050000, China
| | - Fang Yuan
- Department of Oncology, The Fifth Medical Center, Chinese PLA General Hospital, Beijing 100071, China
| | - Haitao Wu
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Shukun Wang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
| | - Zengqiang Yuan
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
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2
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Meril S, Bahlsen M, Eisenstein M, Savidor A, Levin Y, Bialik S, Pietrokovski S, Kimchi A. Loss-of-function cancer-linked mutations in the EIF4G2 non-canonical translation initiation factor. Life Sci Alliance 2024; 7:e202302338. [PMID: 38129098 PMCID: PMC10746786 DOI: 10.26508/lsa.202302338] [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: 08/24/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Tumor cells often exploit the protein translation machinery, resulting in enhanced protein expression essential for tumor growth. Since canonical translation initiation is often suppressed because of cell stress in the tumor microenvironment, non-canonical translation initiation mechanisms become particularly important for shaping the tumor proteome. EIF4G2 is a non-canonical translation initiation factor that mediates internal ribosome entry site (IRES)- and uORF-dependent initiation mechanisms, which can be used to modulate protein expression in cancer. Here, we explored the contribution of EIF4G2 to cancer by screening the COSMIC database for EIF4G2 somatic mutations in cancer patients. Functional examination of missense mutations revealed deleterious effects on EIF4G2 protein-protein interactions and, importantly, on its ability to mediate non-canonical translation initiation. Specifically, one mutation, R178Q, led to reductions in protein expression and near-complete loss of function. Two other mutations within the MIF4G domain specifically affected EIF4G2's ability to mediate IRES-dependent translation initiation but not that of target mRNAs with uORFs. These results shed light on both the structure-function of EIF4G2 and its potential tumor suppressor effects.
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Affiliation(s)
- Sara Meril
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marcela Bahlsen
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Miriam Eisenstein
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- https://ror.org/0316ej306 The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- https://ror.org/0316ej306 The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Shani Bialik
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shmuel Pietrokovski
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Kimchi
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Huang W, Luo T, Lan M, Zhou W, Zhang M, Wu L, Lu Z, Fan L. Identification and Characterization of a ceRNA Regulatory Network Involving LINC00482 and PRRC2B in Peripheral Blood Mononuclear Cells: Implications for COPD Pathogenesis and Diagnosis. Int J Chron Obstruct Pulmon Dis 2024; 19:419-430. [PMID: 38348310 PMCID: PMC10860591 DOI: 10.2147/copd.s437046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/01/2024] [Indexed: 02/15/2024] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide, characterized by intense lung infiltrations of immune cells (macrophages and monocytes). While existing studies have highlighted the crucial role of the competitive endogenous RNA (ceRNA) regulatory network in COPD development, the complexity and characteristics of the ceRNA network in monocytes remain unexplored. Methods We downloaded messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) microarray data from GSE146560, GSE102915, and GSE71220 in the Gene Expression Omnibus (GEO) database. This data was used to identify differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), and lncRNAs (DElncRNAs). Predicted miRNAs that bind to DElncRNAs were intersected with DEmiRNAs, forming a set of intersecting miRNAs. This set was then used to predict potential binding mRNAs, intersected with DEmRNAs, and underwent functional enrichment analysis using R software and the STRING database. The resulting triple regulatory network and hub genes were constructed using Cytoscape. Comparative Toxicomics Database (CTD) was utilized for disease correlation predictions, and ROC curve analysis assessed diagnostic accuracy. Results Our study identified 5 lncRNAs, 4 miRNAs, and 149 mRNAs as differentially expressed. A lncRNA-miRNA-mRNA regulatory network was constructed, and hub genes were selected through hub analysis. Enrichment analysis highlighted terms related to cell movement and gene expression regulation. We established a LINC00482-has-miR-6088-PRRC2B ceRNA network with diagnostic relevance for COPD. ROC analysis demonstrated the diagnostic value of these genes. Moreover, a positive correlation between LINC00482 and PRRC2B expression was observed in COPD PBMCs. The CTD database indicated their involvement in inflammatory responses. Conclusion In summary, our study not only identified pivotal hub genes in peripheral blood mononuclear cells (PBMCs) of COPD but also constructed a ceRNA regulatory network. This contributes to understanding the pathophysiological processes of COPD through bioinformatics analysis, expanding our knowledge of COPD, and providing a foundation for potential diagnostic and therapeutic targets for COPD.
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Affiliation(s)
- Wenjie Huang
- Department of Reproductive Medicine, Guangzhou Women and Children’s Medical Center Liuzhou Hospital, Liuzhou, Guangxi, 545616, People’s Republic of China
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, 545001, People’s Republic of China
| | - Ting Luo
- Department of Reproductive Medicine, Guangzhou Women and Children’s Medical Center Liuzhou Hospital, Liuzhou, Guangxi, 545616, People’s Republic of China
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, 545001, People’s Republic of China
| | - Mengqiu Lan
- Clinical Laboratory Science, Liuzhou Municipal Liutie Central Hospital, Liuzhou, Guangxi, 545007, People’s Republic of China
| | - Wenting Zhou
- Department of Reproductive Medicine, Guangzhou Women and Children’s Medical Center Liuzhou Hospital, Liuzhou, Guangxi, 545616, People’s Republic of China
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, 545001, People’s Republic of China
| | - Ming Zhang
- Department of Reproductive Medicine, Guangzhou Women and Children’s Medical Center Liuzhou Hospital, Liuzhou, Guangxi, 545616, People’s Republic of China
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, 545001, People’s Republic of China
| | - Lihong Wu
- Clinical Laboratory Science, Liuzhou Municipal Liutie Central Hospital, Liuzhou, Guangxi, 545007, People’s Republic of China
| | - Zhenni Lu
- Clinical Laboratory Science, Liuzhou Municipal Liutie Central Hospital, Liuzhou, Guangxi, 545007, People’s Republic of China
| | - Li Fan
- Department of Reproductive Medicine, Guangzhou Women and Children’s Medical Center Liuzhou Hospital, Liuzhou, Guangxi, 545616, People’s Republic of China
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, 545001, People’s Republic of China
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Anastasakis DG, Benhalevy D, Çuburu N, Altan-Bonnet N, Hafner M. Epigenetic repression of antiviral genes by SARS-CoV-2 NSP1. PLoS One 2024; 19:e0297262. [PMID: 38277395 PMCID: PMC10817131 DOI: 10.1371/journal.pone.0297262] [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: 08/31/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the innate immune machinery through multiple viral proteins, including nonstructural protein 1 (NSP1). While NSP1 is known to suppress translation of host mRNAs, the mechanisms underlying its immune evasion properties remain elusive. By integrating RNA-seq, ribosome footprinting, and ChIP-seq in A549 cells we found that NSP1 predominantly represses transcription of immune-related genes by favoring Histone 3 Lysine 9 dimethylation (H3K9me2). G9a/GLP H3K9 methyltransferase inhibitor UNC0638 restored expression of antiviral genes and restricted SARS-CoV-2 replication. Our multi-omics study unravels an epigenetic mechanism underlying host immune evasion by SARS-CoV-2 NSP1. Elucidating the factors involved in this phenomenon, may have implications for understanding and treating viral infections and other immunomodulatory diseases.
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Affiliation(s)
- Dimitrios G. Anastasakis
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel Benhalevy
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicolas Çuburu
- Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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Zhang T, Xue Y, Su S, Altouma V, Ho K, Martindale JL, Lee SK, Shen W, Park A, Zhang Y, De S, Gorospe M, Wang W. RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames. Nucleic Acids Res 2024; 52:885-905. [PMID: 38000373 PMCID: PMC10810208 DOI: 10.1093/nar/gkad1122] [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: 06/20/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
RNA-binding proteins (RBPs) with intrinsically disordered regions (IDRs) are linked to multiple human disorders, but their mechanisms of action remain unclear. Here, we report that one such protein, Nocte, is essential for Drosophila eye development by regulating a critical gene expression cascade at translational level. Knockout of nocte in flies leads to lethality, and its eye-specific depletion impairs eye size and morphology. Nocte preferentially enhances translation of mRNAs with long upstream open reading frames (uORFs). One of the key Nocte targets, glass mRNA, encodes a transcription factor critical for differentiation of photoreceptor neurons and accessory cells, and re-expression of Glass largely rescued the eye defects caused by Nocte depletion. Mechanistically, Nocte counteracts long uORF-mediated translational suppression by promoting translation reinitiation downstream of the uORF. Nocte interacts with translation factors eIF3 and Rack1 through its BAT2 domain, and a Nocte mutant lacking this domain fails to promote translation of glass mRNA. Notably, de novo mutations of human orthologs of Nocte have been detected in schizophrenia patients. Our data suggest that Nocte family of proteins can promote translation reinitiation to overcome long uORFs-mediated translational suppression, and disruption of this function can lead to developmental defects and neurological disorders.
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Affiliation(s)
- Tianyi Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Valerie Altouma
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Katherine Ho
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung-Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Aaron Park
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Sokol-Borrelli SL, Reilly SM, Holmes MJ, Orchanian SB, Massmann MD, Sharp KG, Cabo LF, Alrubaye HS, Martorelli Di Genova B, Lodoen MB, Sullivan WJ, Boyle JP. A transcriptional network required for bradyzoite development in Toxoplasma gondii is dispensable for recrudescent disease. Nat Commun 2023; 14:6078. [PMID: 37770433 PMCID: PMC10539341 DOI: 10.1038/s41467-023-40948-w] [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: 02/23/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
Identification of regulators of Toxoplasma gondii bradyzoite development and cyst formation is the most direct way to address the importance of parasite development in long-term persistence and reactivation of this parasite. Here we show that a T. gondii gene (named Regulator of Cystogenesis 1; ROCY1) is sufficient for T. gondii bradyzoite formation in vitro and in vivo. ROCY1 encodes an RNA binding protein that has a preference for 3' regulatory regions of hundreds of T. gondii transcripts, and its RNA-binding domains are required to mediate bradyzoite development. Female mice infected with ΔROCY1 parasites have reduced (>90%) cyst burden. While viable parasites can be cultivated from brain tissue for up to 6 months post-infection, chronic brain-resident ΔROCY1 parasites have reduced oral infectivity compared to wild type. Despite clear defects in bradyzoite formation and oral infectivity, ΔROCY1 parasites were able to reactivate with similar timing and magnitude as wild type parasites for up to 5 months post-infection. Therefore while ROCY1 is a critical regulator of the bradyzoite developmental pathway, it is not required for parasite reactivation, raising new questions about the persisting life stage responsible for causing recrudescent disease.
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Affiliation(s)
- Sarah L Sokol-Borrelli
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah M Reilly
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael J Holmes
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 462022, USA
| | - Stephanie B Orchanian
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | - Mackenzie D Massmann
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Katherine G Sharp
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah F Cabo
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hisham S Alrubaye
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruno Martorelli Di Genova
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Melissa B Lodoen
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | - William J Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 462022, USA
| | - Jon P Boyle
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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