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Azam S, Armijo KS, Weindel CG, Chapman MJ, Devigne A, Nakagawa S, Hirose T, Carpenter S, Watson RO, Patrick KL. The early macrophage response to pathogens requires dynamic regulation of the nuclear paraspeckle. Proc Natl Acad Sci U S A 2024; 121:e2312587121. [PMID: 38381785 PMCID: PMC10907238 DOI: 10.1073/pnas.2312587121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/10/2024] [Indexed: 02/23/2024] Open
Abstract
To ensure a robust immune response to pathogens without risking immunopathology, the kinetics and amplitude of inflammatory gene expression in macrophages need to be exquisitely well controlled. There is a growing appreciation for stress-responsive membraneless organelles (MLOs) regulating various steps of eukaryotic gene expression in response to extrinsic cues. Here, we implicate the nuclear paraspeckle, a highly ordered biomolecular condensate that nucleates on the Neat1 lncRNA, in tuning innate immune gene expression in murine macrophages. In response to a variety of innate agonists, macrophage paraspeckles rapidly aggregate (0.5 h poststimulation) and disaggregate (2 h poststimulation). Paraspeckle maintenance and aggregation require active transcription and MAPK signaling, whereas paraspeckle disaggregation requires degradation of Neat1 via the nuclear RNA exosome. In response to lipopolysaccharide treatment, Neat1 KO macrophages fail to properly express a large cohort of proinflammatory cytokines, chemokines, and antimicrobial mediators. Consequently, Neat1 KO macrophages cannot control replication of Salmonella enterica serovar Typhimurium or vesicular stomatitis virus. These findings highlight a prominent role for MLOs in orchestrating the macrophage response to pathogens and support a model whereby dynamic assembly and disassembly of paraspeckles reorganizes the nuclear landscape to enable inflammatory gene expression following innate stimuli.
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Affiliation(s)
- Sikandar Azam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Kaitlyn S. Armijo
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Chi G. Weindel
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Morgan J. Chapman
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Alice Devigne
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA95064
| | | | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, Osaka565-0871, Japan
| | - Susan Carpenter
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA95064
| | - Robert O. Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
| | - Kristin L. Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, School of Medicine, Bryan, TX77807
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Zhao M, Liu S, Wang Y, Lv K, Lou P, Zhou P, Zhu J, Li L, Cheng J, Lu Y, Liu J. The mitochondria‒paraspeckle axis regulates the survival of transplanted stem cells under oxidative stress conditions. Theranostics 2024; 14:1517-1533. [PMID: 38389853 PMCID: PMC10879866 DOI: 10.7150/thno.88764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Rationale: Stem cell-based therapies have emerged as promising tools for tissue engineering and regenerative medicine, but their therapeutic efficacy is largely limited by the oxidative stress-induced loss of transplanted cells at injured tissue sites. To address this issue, we aimed to explore the underlying mechanism and protective strategy of ROS-induced MSC loss. Methods: Changes in TFAM (mitochondrial transcription factor A) signaling, mitochondrial function, DNA damage, apoptosis and senescence in MSCs under oxidative stress conditions were assessed using real-time PCR, western blotting and RNA sequencing, etc. The impact of TFAM or lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) knockdown or overexpression on mitochondrial function, DNA damage repair, apoptosis and senescence in MSCs was also analyzed. The effect of mitochondrion-targeted antioxidant (Mito-TEMPO) on the survival of transplanted MSCs was evaluated in a mouse model of renal ischemia/reperfusion (I/R) injury. Results: Mitochondrial ROS (mtROS) bursts caused defects in TFAM signaling and overall mitochondrial function, which further impaired NEAT1 expression and its mediated paraspeckle formation and DNA repair pathways in MSCs, thereby jointly promoting MSC senescence and death under oxidative stress. In contrast, targeted inhibition of the mtROS bursts is a sufficient strategy for attenuating early transplanted MSC loss at injured tissue sites, and coadministration of Mito-TEMPO improved the local retention of transplanted MSCs and reduced oxidative injury in ischemic kidneys. Conclusions: This study identified the critical role of the mitochondria‒paraspeckle axis in regulating cell survival and may provide insights into developing advanced stem cell therapies for tissue engineering and regenerative medicine.
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Affiliation(s)
- Meng Zhao
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Shuyun Liu
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yizhuo Wang
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ke Lv
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Peng Lou
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Pingya Zhou
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiaying Zhu
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Lan Li
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jingqiu Cheng
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yanrong Lu
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jingping Liu
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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Fan Z, Yang G, Luo R, Qu X, Ye X, Wang J, Yan Z, Shu M, Zhang W, Liu R. Sublethal heat treatment enhances lactic acid uptake in macrophages via MCT1, leading to reduced paraspeckle formation and a subsequent decrease in macrophage pyroptosis. Front Immunol 2024; 14:1290185. [PMID: 38274825 PMCID: PMC10808517 DOI: 10.3389/fimmu.2023.1290185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Heat ablation is one of the key modalities in treating liver cancer, yet the residual cancer tissues suffering sublethal heat treatment possess a potential for increased malignancy. This study conducts a comprehensive analysis of cellular dynamics, metabolic shifts, and macrophage polarization within the tumor microenvironment following sublethal heat treatment. Methods We observed significant acidification in tumor cell supernatants, attributed to increased lactic acid production. The study focused on how this pH shift, crucial in tumor progression and resistance, influences macrophage polarization, especially towards the M2 phenotype known for tumor-promoting functions. We also examined the upregulation of MCT1 expression post sublethal heat treatment and its primary role in lactic acid transport. Results Notably, the study found minimal disparity in MCT1 expression between hepatocellular carcinoma patients and healthy liver tissues, highlighting the complexity of cancer biology. The research further revealed an intricate relationship between lactic acid, MCT1, and the inhibition of macrophage pyroptosis, offering significant insights for therapeutic strategies targeting the tumor immune environment. Post sublethal heat treatment, a reduction in paraspeckle under lactic acid exposure was observed, indicating diverse cellular impacts. Additionally, PKM2 was identified as a key molecule in this context, with decreased levels after sublethal heat treatment in the presence of lactic acid. Discussion Collectively, these findings illuminate the intertwined mechanisms of sublethal heat treatments, metabolic alterations, and immune modulation in the tumor milieu, providing a deeper understanding of the complex interplay in cancer biology and treatment.
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Affiliation(s)
- Zhuoyang Fan
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guowei Yang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Xudong Qu
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodan Ye
- Department of Radiology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Jianhua Wang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiping Yan
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minfeng Shu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Zhang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rong Liu
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Interventional Radiology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
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Takakuwa H, Yamazaki T, Souquere S, Adachi S, Yoshino H, Fujiwara N, Yamamoto T, Natsume T, Nakagawa S, Pierron G, Hirose T. Shell protein composition specified by the lncRNA NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles. Nat Cell Biol 2023; 25:1664-1675. [PMID: 37932453 DOI: 10.1038/s41556-023-01254-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 09/12/2023] [Indexed: 11/08/2023]
Abstract
Many membraneless organelles (MLOs) formed through phase separation play crucial roles in various cellular processes. Although these MLOs co-exist in cells, how they maintain their independence without coalescence or engulfment remains largely unknown. Here, we investigated the molecular mechanism by which paraspeckles with core-shell architecture scaffolded by NEAT1_2 long noncoding RNAs exist as distinct MLOs. We identified NEAT1 deletion mutants that assemble paraspeckles that are incorporated into nuclear speckles. Several paraspeckle proteins, including SFPQ, HNRNPF and BRG1, prevent this incorporation and thus contribute to the segregation of paraspeckles from nuclear speckles. Shell localization of these proteins in the paraspeckles, which is determined by NEAT1_2 long noncoding RNA domains, is required for this segregation process. Conversely, U2-related spliceosomal proteins are involved in internalizing the paraspeckles into nuclear speckles. This study shows that the paraspeckle shell composition dictates the independence of MLOs in the nucleus, providing insights into the importance of the shell in defining features and functions of MLOs.
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Affiliation(s)
- Hiro Takakuwa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
| | | | - Shungo Adachi
- Department of Proteomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hyura Yoshino
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Naoko Fujiwara
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
| | - Tohru Natsume
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology, Tokyo, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Gerard Pierron
- Centre National de la Recherche Scientifique, UMR-9196, Gustave Roussy, Villejuif, France
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
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Mitamura R, Nakano M, Isono M, Kurosawa K, Fukami T, Nakajima M. NEAT1_2 and DAZAP1, Paraspeckle Components, Interact with PXR to Negatively Regulate CYP3A4 Induction. Drug Metab Dispos 2023; 51:1230-1237. [PMID: 37349114 DOI: 10.1124/dmd.122.001065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/22/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
Human pregnane X receptor (PXR) is a major nuclear receptor that upregulates the expression of drug-metabolizing enzymes such as CYP3A4. In our recent study, it was revealed that PXR interacts with DAZ-associated protein 1 (DAZAP1), which is an essential component of the paraspeckle, a membraneless nuclear body, and the interaction was disassociated by rifampicin, a ligand of PXR. The purpose of this study was to clarify the roles of paraspeckles in PXR-mediated transcriptional regulation. Immunoprecipitation assays using PXR-overexpressing HepG2 (ShP51) cells revealed that PXR interacts with not only DAZAP1 but also NEAT1_2, a long noncoding RNA included in the paraspeckle, and that the interaction between PXR and NEAT1_2 was disassociated by rifampicin. These results suggest that PXR is trapped in paraspeckles and that the activation of PXR by its ligands facilitates its disassociation from paraspeckles. Induction of CYP3A4 by rifampicin was significantly enhanced by the knockdown of NEAT1_2 or DAZAP1 in ShP51 cells and their parental HepG2 cells. A luciferase assay using a plasmid containing the PXR response elements of CYP3A4 revealed that the increased CYP3A4 induction by siNEAT1_2 or siDAZAP1 was due to the increased transactivation by PXR. These results suggest that paraspeckles play a role in trapping nuclear PXR in the absence of the ligand to negatively regulate transactivation of its downstream gene. Collectively, this is the first study to demonstrate that the paraspeckle components NEAT1_2 and DAZAP1 negatively regulate CYP3A4 induction by PXR. SIGNIFICANCE STATEMENT: This study revealed that PXR interacts with paraspeckle components NEAT1_2 and DAZAP1 to suppress CYP3A4 induction by PXR, and the interaction is dissociated by PXR ligands. This finding provides a novel concept that paraspeckles formed by liquid-liquid phase separation potentially affect drug metabolism via negative regulation of PXR function.
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Affiliation(s)
- Rei Mitamura
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (R.M., Ma.N., M.I., K.K., T.F., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (Ma.N., K.K., T.F., Mi.N.), Kanazawa University, Kanazawa, Japan
| | - Masataka Nakano
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (R.M., Ma.N., M.I., K.K., T.F., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (Ma.N., K.K., T.F., Mi.N.), Kanazawa University, Kanazawa, Japan
| | - Motoki Isono
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (R.M., Ma.N., M.I., K.K., T.F., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (Ma.N., K.K., T.F., Mi.N.), Kanazawa University, Kanazawa, Japan
| | - Kiamu Kurosawa
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (R.M., Ma.N., M.I., K.K., T.F., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (Ma.N., K.K., T.F., Mi.N.), Kanazawa University, Kanazawa, Japan
| | - Tatsuki Fukami
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (R.M., Ma.N., M.I., K.K., T.F., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (Ma.N., K.K., T.F., Mi.N.), Kanazawa University, Kanazawa, Japan
| | - Miki Nakajima
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (R.M., Ma.N., M.I., K.K., T.F., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (Ma.N., K.K., T.F., Mi.N.), Kanazawa University, Kanazawa, Japan
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Cubillos-Zapata C, Martínez-García MÁ, Díaz-García E, García-Tovar S, Campos-Rodríguez F, Sánchez-de-la-Torre M, Nagore E, Martorell-Calatayud A, Blasco LH, Pastor E, Abad-Capa J, Montserrat JM, Cabriada-Nuño V, Cano-Pumarega I, Corral-Peñafiel J, Arias E, Mediano O, Somoza-González M, Dalmau-Arias J, Almendros I, Farré R, Gozal D, García-Río F. Obstructive sleep apnoea is related to melanoma aggressiveness through paraspeckle protein-1 upregulation. Eur Respir J 2023; 61:13993003.00707-2022. [PMID: 36265878 DOI: 10.1183/13993003.00707-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/26/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND In patients with obstructive sleep apnoea (OSA), intermittent hypoxia induces overexpression of paraspeckle component (PSPC)1, a master modulator of transforming growth factor (TGF)-β signalling, which promotes cell cancer progression through epithelial-mesenchymal transition (EMT) and acquisition of cancer stem cell (CSC)-like features. However, the persistence of intermittent hypoxia-induced effects on PSPC1, and their consequences in cancer patients are not known. To this effect, circulating PSPC1 levels were compared in patients with cutaneous melanoma with or without OSA, and their relationship with tumour aggressiveness along with the in vitro effects of soluble PSPC1 and intermittent hypoxia on melanoma cell aggressiveness mechanisms were assessed. METHODS In 292 cutaneous melanoma patients, sleep studies and serum levels of PSPC1 and TGF-β were evaluated. The effect of PSPC1 on expression of EMT and CSC transcription factors was assessed using melanoma cell lines with patient sera under both normoxia and intermittent hypoxia conditions. RESULTS PSPC1 levels were higher in patients with moderate-severe OSA compared with mild OSA or non-OSA patients. Serum levels of PSPC1 were associated with several cutaneous melanoma clinical aggressiveness indicators. Both intermittent hypoxia exposures and serum from OSA patients upregulated TGF-β expression and amplified the expression of transcription factors associated with EMT activation and acquisition of CSC characteristics. CONCLUSION In cutaneous melanoma patients, OSA severity is associated with higher PSPC1 serum levels, which jointly with intermittent hypoxia would enhance the self-reprogramming capabilities of EMT and CSC feature acquisition of melanoma cells, promoting their intrinsic aggressiveness.
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Affiliation(s)
- Carolina Cubillos-Zapata
- Grupo de Enfermedades Respiratorias, Servicio de Neumología, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Miguel Ángel Martínez-García
- Grupo de Enfermedades Respiratorias, Servicio de Neumología, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Respiratory Department, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Elena Díaz-García
- Grupo de Enfermedades Respiratorias, Servicio de Neumología, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sara García-Tovar
- Grupo de Enfermedades Respiratorias, Servicio de Neumología, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Francisco Campos-Rodríguez
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Respiratory Department, Hospital Universitario de Valme, IBIS, Seville, Spain
| | - Manuel Sánchez-de-la-Torre
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Precision Medicine in Chronic Diseases, Hospital Universitari Arnau de Vilanova-Santa Maria, IRB Lleida, Department of Nursing and Physiotherapy, Faculty of Nursing and Physiotherapy, University of Lleida, Lleida, Spain
| | - Eduardo Nagore
- Dermatology Department, Instituto Valenciano de Oncología, Valencia, Spain
| | | | - Luis Hernández Blasco
- Respiratory Department, ISABIAL, Hospital General Universitario de Alicante, Alicante, Spain
- Departamento Medicina Clinica, Universidad Miguel Hernandez, Elche, Spain
| | - Esther Pastor
- Respiratory Department, Hospital san Juan de Alicante, Alicante, Spain
| | - Jorge Abad-Capa
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Respiratory Department, Hospital Germans Trias i Pujol, Centro de investigacion Biomedica, Madrid, Spain
| | - Josep María Montserrat
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Respiratory Department, Hospital Clinic - IDIBAPS, Barcelona, Spain
| | | | | | - Jaime Corral-Peñafiel
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Respiratory Department, Hospital Universitario S. Pedro Alcántara, Cáceres, Spain
| | - Eva Arias
- Respiratory Department, Hospital 12 de Octubre, Madrid, Spain
| | - Olga Mediano
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Respiratory Department, Hospital Universitario de Guadalajara, Guadalajara, Spain
| | | | - Joan Dalmau-Arias
- Dermatology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Isaac Almendros
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ramón Farré
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - David Gozal
- Department of Child Health, University of Missouri School of Medicine, Columbia, MO, USA
| | - Francisco García-Río
- Grupo de Enfermedades Respiratorias, Servicio de Neumología, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
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Reddy D, Bhattacharya S, Levy M, Zhang Y, Gogol M, Li H, Florens L, Workman JL. Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep 2023; 24:e55345. [PMID: 36354291 PMCID: PMC9827562 DOI: 10.15252/embr.202255345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
Paraspeckles are subnuclear RNA-protein structures that are implicated in important processes including cellular stress response, differentiation, and cancer progression. However, it is unclear how paraspeckles impart their physiological effect at the molecular level. Through biochemical analyses, we show that paraspeckles interact with the SWI/SNF chromatin-remodeling complex. This is specifically mediated by the direct interaction of the long-non-coding RNA NEAT1 of the paraspeckles with ARID1B of the cBAF-type SWI/SNF complex. Strikingly, ARID1B depletion, in addition to resulting in loss of interaction with the SWI/SNF complex, decreases the binding of paraspeckle proteins to chromatin modifiers, transcription factors, and histones. Functionally, the loss of ARID1B and NEAT1 influences the transcription and the alternative splicing of a common set of genes. Our findings reveal that dynamic granules such as the paraspeckles may leverage the specificity of epigenetic modifiers to impart their regulatory effect, thus providing a molecular basis for their function.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | | | - Ying Zhang
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | - Hua Li
- Stowers Institute for Medical ResearchKansas CityMOUSA
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Yamamoto K. [Leukemia-associated gene ASXL1 involved in paraspeckle formation]. Rinsho Ketsueki 2023; 64:719-730. [PMID: 37673622 DOI: 10.11406/rinketsu.64.719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Somatic mutations in the ASXL1 gene are commonly observed in myeloid neoplasms. Pathogenic ASXL1 mutations induce the expression of C-terminally truncated mutant ASXL1 protein. We have shown that wild-type ASXL1 is a phase-separating protein involved in the formation of paraspeckles, one of the best known membraneless organelles (MLOs). Mutant ASXL1 lacks the intrinsically disordered region, which is important for phase separation and fails to support paraspeckle formation. Additionally, paraspeckles are disrupted in hematopoietic cells derived from ASXL1-MT knockin mice. The disruption of paraspeckles in hematopoietic cells results in a dysfunction of the hematopoietic reconstitution capacity. Therefore, this review presents our findings and summarizes the knowledge of phase separation and MLOs as a hot topic in cell biology.
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Affiliation(s)
- Keita Yamamoto
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo
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Yamada A, Toya H, Tanahashi M, Kurihara M, Mito M, Iwasaki S, Kurosaka S, Takumi T, Fox A, Kawamura Y, Miura K, Nakagawa S. Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat. RNA 2022; 28:1128-1143. [PMID: 35654483 PMCID: PMC9297846 DOI: 10.1261/rna.079135.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Paraspeckles are mammalian-specific nuclear bodies built on the long noncoding RNA NEAT1_2 The molecular mechanisms of paraspeckle formation have been mainly studied using human or mouse cells, and it is not known if the same molecular components are involved in the formation of paraspeckles in other mammalian species. We thus investigated the expression pattern of NEAT1_2 in naked mole-rats (nNEAT1_2), which exhibit extreme longevity and lower susceptibility to cancer. In the intestine, nNEAT1_2 is widely expressed along the entire intestinal epithelium, which is different from the expression of mNeat1_2 that is restricted to the cells of the distal tip in mice. Notably, the expression of FUS, a FET family RNA binding protein, essential for the formation of paraspeckles both in humans and mice, was absent in the distal part of the intestinal epithelium in naked mole-rats. Instead, mRNAs of other FET family proteins EWSR1 and TAF15 were expressed in the distal region. Exogenous expression of these proteins in Fus-deficient murine embryonic fibroblast cells rescued the formation of paraspeckles. These observations suggest that nNEAT1_2 recruits a different set of RNA binding proteins in a cell type-specific manner during the formation of paraspeckles in different organisms.
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Affiliation(s)
- Akihiro Yamada
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Hikaru Toya
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Mayuko Tanahashi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Misuzu Kurihara
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | | | - Toru Takumi
- RIKEN Brain Science Institute, Saitama 351-0198, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe 670-0017, Japan
| | - Archa Fox
- School of Human Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Yoshimi Kawamura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kyoko Miura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto 860-8556, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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