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Văcăraş V, Vulturar R, Chiş A, Damian L. Inclusion body myositis, viral infections, and TDP-43: a narrative review. Clin Exp Med 2024; 24:91. [PMID: 38693436 PMCID: PMC11062973 DOI: 10.1007/s10238-024-01353-9] [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: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
The ubiquitous RNA-processing molecule TDP-43 is involved in neuromuscular diseases such as inclusion body myositis, a late-onset acquired inflammatory myopathy. TDP-43 solubility and function are disrupted in certain viral infections. Certain viruses, high viremia, co-infections, reactivation of latent viruses, and post-acute expansion of cytotoxic T cells may all contribute to inclusion body myositis, mainly in an age-shaped immune landscape. The virally induced senescent, interferon gamma-producing cytotoxic CD8+ T cells with increased inflammatory, and cytotoxic features are involved in the occurrence of inclusion body myositis in most such cases, in a genetically predisposed host. We discuss the putative mechanisms linking inclusion body myositis, TDP-43, and viral infections untangling the links between viruses, interferon, and neuromuscular degeneration could shed a light on the pathogenesis of the inclusion body myositis and other TDP-43-related neuromuscular diseases, with possible therapeutic implications.
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Affiliation(s)
- Vitalie Văcăraş
- Department of Neurosciences, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, 43, Victor Babeş St, 400012, Cluj-Napoca, Romania
- Neurology Department of Cluj, County Emergency Hospital, 3-5, Clinicilor St, 400347, Cluj-Napoca, Romania
| | - Romana Vulturar
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, 6, Pasteur St, 400349, Cluj-Napoca, Romania
- Cognitive Neuroscience Laboratory, University Babeş-Bolyai, 30, Fântânele St, 400294, Cluj-Napoca, Romania
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania
| | - Adina Chiş
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, 6, Pasteur St, 400349, Cluj-Napoca, Romania.
- Cognitive Neuroscience Laboratory, University Babeş-Bolyai, 30, Fântânele St, 400294, Cluj-Napoca, Romania.
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania.
| | - Laura Damian
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania
- Department of Rheumatology, Centre for Rare Autoimmune and Autoinflammatory Diseases, Emergency, Clinical County Hospital Cluj, 2-4, Clinicilor St, 400006, Cluj-Napoca, Romania
- CMI Reumatologie Dr. Damian, 6-8, Petru Maior St, 400002, Cluj-Napoca, Romania
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2
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Tomic Vujovic K, Ugrin M, Tosic N, Vukovic V, Marjanovic I, Kostic T, Stankovic S, Otasevic V, Sarac S, Antic D, Pavlovic S, Karan-Djurasevic T. Expression Pattern and Prognostic Significance of the Long Non-Coding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 in Chronic Lymphocytic Leukemia. Int J Mol Sci 2024; 25:922. [PMID: 38255996 PMCID: PMC10815316 DOI: 10.3390/ijms25020922] [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: 11/17/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Dysregulated expression of the long non-coding RNA MALAT1 has been implicated in the pathogenesis and progression of a variety of cancers, including hematological malignancies, but it has been poorly investigated in chronic lymphocytic leukemia (CLL). In this study, the expression of MALAT1 was measured using a quantitative reverse-transcriptase polymerase chain reaction in the peripheral blood mononuclear cells of 114 unselected, newly diagnosed CLL patients in order to analyze its association with clinical, laboratory, and molecular patients' characteristics at diagnosis, as well as its prognostic relevance. MALAT1 was found to be upregulated in CLL patients in comparison to healthy controls, and expression levels were not related to age, leukocyte, lymphocyte and platelet count, serum β2-microglobulin, and IGHV somatic hypermutational status. On the other hand, high MALAT1 expression was associated with several favorable prognostic markers (high hemoglobin, low serum lactate dehydrogenase, earlier clinical stages, CD38-negative status), but also with unfavorable cytogenetics. Furthermore, an association between high MALAT1 levels and longer time to first treatment and overall survival in IGHV-unmutated CLL subtype was observed. In summary, our results imply that high MALAT1 expression at diagnosis may be a predictor of better prognosis and point to MALAT1 expression profiling as a candidate biomarker potentially useful in clinical practice.
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Affiliation(s)
- Kristina Tomic Vujovic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
| | - Milena Ugrin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Natasa Tosic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Vojin Vukovic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
| | - Irena Marjanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Tatjana Kostic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Sanja Stankovic
- Center for Medical Biochemistry, University Clinical Center of Serbia, 11000 Belgrade, Serbia;
- Department of Biochemistry, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Vladimir Otasevic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
| | - Sofija Sarac
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
| | - Darko Antic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (V.O.); (S.S.); (D.A.)
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
| | - Teodora Karan-Djurasevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (M.U.); (N.T.); (I.M.); (T.K.); (S.P.)
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3
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García Morato J, Gloeckner CJ, Kahle PJ. Proteomics elucidating physiological and pathological functions of TDP-43. Proteomics 2023; 23:e2200410. [PMID: 37671599 DOI: 10.1002/pmic.202200410] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Trans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can associate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulated by its low-complexity domain calls for innovative proximity labeling methodologies. In addition to protein partners, the analysis of post-translational modifications showed that they may play a role in the nucleocytoplasmic shuttling, RNA binding, liquid-liquid phase separation and protein aggregation of TDP-43. Here we review the various TDP-43 ribonucleoprotein complexes characterized so far, how they contribute to the diverse functions of TDP-43, and roles of post-translational modifications. Further understanding of the fluid dynamic properties of TDP-43 in ribonucleoprotein complexes, RNA granules, and self-assemblies will advance the understanding of RNA processing in cells and perhaps help to develop novel therapeutic approaches for TDPopathies.
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Affiliation(s)
- Jorge García Morato
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christian Johannes Gloeckner
- Research Group Functional Neuroproteomics, German Center of Neurodegenerative Diseases, Tübingen, Germany
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Tübingen, Tübingen, Germany
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4
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Liau WS, Zhao Q, Bademosi A, Gormal RS, Gong H, Marshall PR, Periyakaruppiah A, Madugalle SU, Zajaczkowski EL, Leighton LJ, Ren H, Musgrove M, Davies J, Rauch S, He C, Dickinson BC, Li X, Wei W, Meunier FA, Fernández-Moya SM, Kiebler MA, Srinivasan B, Banerjee S, Clark M, Spitale RC, Bredy TW. Fear extinction is regulated by the activity of long noncoding RNAs at the synapse. Nat Commun 2023; 14:7616. [PMID: 37993455 PMCID: PMC10665438 DOI: 10.1038/s41467-023-43535-1] [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: 02/24/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules that are involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are localized to the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq, we identified a specific set of lncRNAs that accumulate in the synaptic compartment within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Among these was a splice variant related to the stress-associated lncRNA, Gas5. RNA immunoprecipitation followed by mass spectrometry and single-molecule imaging revealed that this Gas5 isoform, in association with the RNA binding proteins G3BP2 and CAPRIN1, regulates the activity-dependent trafficking and clustering of RNA granules. In addition, we found that cell-type-specific, activity-dependent, and synapse-specific knockdown of the Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and RNA condensates in the synaptic compartment.
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Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Qiongyi Zhao
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Adekunle Bademosi
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rachel S Gormal
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Hao Gong
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ambika Periyakaruppiah
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Mason Musgrove
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua Davies
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Frédéric A Meunier
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Sandra M Fernández-Moya
- Biomedical Centre, Ludwig Maximilian University of Munich, Munich, Germany
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet del Llobregat, 08908, Barcelona, Spain
| | - Michael A Kiebler
- Biomedical Centre, Ludwig Maximilian University of Munich, Munich, Germany
| | | | | | - Michael Clark
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, The University of California, Irvine, CA, USA
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
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5
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Hu Y, Hao T, Yu H, Miao W, Zheng Y, Tao W, Zhuang J, Wang J, Fan Y, Jia S. lhCLIP reveals the in vivo RNA-RNA interactions recognized by hnRNPK. PLoS Genet 2023; 19:e1011006. [PMID: 37851698 PMCID: PMC10635571 DOI: 10.1371/journal.pgen.1011006] [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: 04/13/2023] [Revised: 11/09/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
RNA-RNA interactions play a crucial role in regulating gene expression and various biological processes, but identifying these interactions on a transcriptomic scale remains a challenge. To address this, we have developed a new biochemical technique called pCp-biotin labelled RNA hybrid and ultraviolet crosslinking and immunoprecipitation (lhCLIP) that enables the transcriptome-wide identification of intra- and intermolecular RNA-RNA interactions mediated by a specific RNA-binding protein (RBP). Using lhCLIP, we have uncovered a diverse landscape of intermolecular RNA interactions recognized by hnRNPK in human cells, involving all major classes of noncoding RNAs (ncRNAs) and mRNA. Notably, hnRNPK selectively binds with snRNA U4, U11, and U12, and shapes the secondary structure of these snRNAs, which may impact RNA splicing. Our study demonstrates the potential of lhCLIP as a user-friendly and widely applicable method for discovering RNA-RNA interactions mediated by a particular protein of interest and provides a valuable tool for further investigating the role of RBPs in gene expression and biological processes.
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Affiliation(s)
- Yuanlang Hu
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, People’s Republic of China
- Ministry of Science and Education, University of Chinese Academy of Sciences-Shenzhen Hospital, Shenzhen, People’s Republic of China
- College of basic medical sciences, Three Gorges University, Yichang, People’s Republic of China
| | - Tao Hao
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, People’s Republic of China
- The Guangdong-Hong Kong-Macao Joint University Laboratory of Metabolic and Molecular Medicine, Jinan University, Guangzhou, People’s Republic of China
| | - Hanwen Yu
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Wenbin Miao
- Ministry of Science and Education, University of Chinese Academy of Sciences-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Yi Zheng
- Ministry of Science and Education, University of Chinese Academy of Sciences-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Weihua Tao
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, People’s Republic of China
- The Guangdong-Hong Kong-Macao Joint University Laboratory of Metabolic and Molecular Medicine, Jinan University, Guangzhou, People’s Republic of China
| | - Jingshen Zhuang
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, People’s Republic of China
| | - Jichang Wang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yujuan Fan
- Ministry of Science and Education, University of Chinese Academy of Sciences-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Shiqi Jia
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, People’s Republic of China
- The Guangdong-Hong Kong-Macao Joint University Laboratory of Metabolic and Molecular Medicine, Jinan University, Guangzhou, People’s Republic of China
- Key Lab of Guangzhou Basic and Translational Research of Pan-vascular Diseases, Guangzhou, People’s Republic of China
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Zhang L, Zheng B, Bai Y, Zhou J, Zhang X, Yang Y, Yu J, Zhao H, Ma D, Wu H, Wen J. Exosomes-transferred LINC00668 Contributes to Thrombosis by Promoting NETs Formation in Inflammatory Bowel Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300560. [PMID: 37590310 PMCID: PMC10558653 DOI: 10.1002/advs.202300560] [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: 01/26/2023] [Revised: 06/03/2023] [Indexed: 08/19/2023]
Abstract
Epidemiological studies show an association between inflammatory bowel disease (IBD) and increased risk of thrombosis. However, how IBD influences thrombosis remains unknown. The current study shows that formation of neutrophil extracellular traps (NETs) significantly increased in the dextran sulfate sodium (DSS)-induced IBD mice, which in turn, contributes to thrombus formation in a NETs-dependent fashion. Furthermore, the exosomes isolated from the plasma of the IBD mice induce arterial and venous thrombosis in vivo. Importantly, proinflammatory factors-exposed intestinal epithelial cells (inflamed IECs) promote neutrophils to release NETs through their secreted exosomes. RNA sequencing revealed that LINC00668 is highly enriched in the inflamed IECs-derived exosomes. Mechanistically, LINC00668 facilitates the translocation of neutrophil elastase (NE) from the cytoplasmic granules to the nucleus via its interaction with NE in a sequence-specific manner, thereby inducing NETs release and thrombus formation. Importantly, berberine (BBR) suppresses the nuclear translocation of NE and subsequent NETs formation by inhibiting the interaction of LINC00668 with NE, thus exerting its antithrombotic effects. This study provides a novel pathobiological mechanism linking IBD and thrombosis by exosome-mediated NETs formation. Targeting LINC00668 can serve as a novel molecular treatment strategy to treat IBD-related thrombosis.
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Affiliation(s)
- Long Zhang
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
| | - Bin Zheng
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
| | - Yang Bai
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
| | - Jing Zhou
- Department of EndocrineThe Second Hospital of Hebei Medical UniversityShijiazhuang050017China
| | - Xin‐hua Zhang
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
- Institution of Chinese Integrative MedicineHebei Medical UniversityShijiazhuang050017China
| | - Yu‐qin Yang
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
| | - Jing Yu
- Department of RespiratoryThe Second Hospital of Hebei Medical UniversityShijiazhuang050017China
| | - Hong‐ye Zhao
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
| | - Dong Ma
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
| | - Han Wu
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
| | - Jin‐kun Wen
- Department of Biochemistry and Molecular BiologyThe Key Laboratory of Neural and Vascular BiologyMinistry of Education of ChinaHebei Medical UniversityShijiazhuang050017China
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7
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Ayala YM. Uncovering Critical Roles for RNA in Neurodegeneration. MISSOURI MEDICINE 2023; 120:374-380. [PMID: 37841575 PMCID: PMC10569393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
RNA-binding proteins, in particular TDP-43, are key players in neurodegenerative disorders, mainly amyotrophic lateral sclerosis and frontotemporal dementia. We aim to elucidate how TDP-43 dysfunction alters cell metabolism and to identify mechanisms linked to aberrant behavior. We find that RNA binding plays a key role in maintaining TDP-43 homeostasis and in controlling cellular organization, two processes of essential importance to TDP-43 pathology. This research will provide insight into pathogenesis and help develop therapeutic interventions.
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Affiliation(s)
- Yuna M Ayala
- Edward A. Doisy Department of Biochemistry & Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
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8
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Zablowsky N, Farack L, Rofall S, Kramer J, Meyer H, Nguyen D, Ulrich AKC, Bader B, Steigemann P. High Throughput FISH Screening Identifies Small Molecules That Modulate Oncogenic lncRNA MALAT1 via GSK3B and hnRNPs. Noncoding RNA 2023; 9:ncrna9010002. [PMID: 36649031 PMCID: PMC9844399 DOI: 10.3390/ncrna9010002] [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: 10/06/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Traditionally, small molecule-based drug discovery has mainly focused on proteins as the drug target. Opening RNA as an additional target space for small molecules offers the possibility to therapeutically modulate disease-driving non-coding RNA targets as well as mRNA of otherwise undruggable protein targets. MALAT1 is a highly conserved long-noncoding RNA whose overexpression correlates with poor overall patient survival in some cancers. We report here a fluorescence in-situ hybridization-based high-content imaging screen to identify small molecules that modulate the oncogenic lncRNA MALAT1 in a cellular setting. From a library of FDA approved drugs and known bioactive molecules, we identified two compounds, including Niclosamide, an FDA-approved drug, that lead to a rapid decrease of MALAT1 nuclear levels with good potency. Mode-of-action studies suggest a novel cellular regulatory pathway that impacts MALAT1 lncRNA nuclear levels by GSK3B activation and the involvement of the RNA modulating family of heterogenous nuclear ribonucleoproteins (hnRNPs). This study is the basis for the identification of novel targets that lead to a reduction of the oncogenic lncRNA MALAT1 in a cancer setting.
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9
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Mehta M, Raguraman R, Ramesh R, Munshi A. RNA binding proteins (RBPs) and their role in DNA damage and radiation response in cancer. Adv Drug Deliv Rev 2022; 191:114569. [PMID: 36252617 PMCID: PMC10411638 DOI: 10.1016/j.addr.2022.114569] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 01/24/2023]
Abstract
Traditionally majority of eukaryotic gene expression is influenced by transcriptional and post-transcriptional events. Alterations in the expression of proteins that act post-transcriptionally can affect cellular signaling and homeostasis. RNA binding proteins (RBPs) are a family of proteins that specifically bind to RNAs and are involved in post-transcriptional regulation of gene expression and important cellular processes such as cell differentiation and metabolism. Deregulation of RNA-RBP interactions and any changes in RBP expression or function can lead to various diseases including cancer. In cancer cells, RBPs play an important role in regulating the expression of tumor suppressors and oncoproteins involved in various cell-signaling pathways. Several RBPs such as HuR, AUF1, RBM38, LIN28, RBM24, tristetrapolin family and Musashi play critical roles in various types of cancers and their aberrant expression in cancer cells makes them an attractive therapeutic target for cancer treatment. In this review we provide an overview of i). RBPs involved in cancer progression and their mechanism of action ii). the role of RBPs, including HuR, in breast cancer progression and DNA damage response and iii). explore RBPs with emphasis on HuR as therapeutic target for breast cancer therapy.
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Affiliation(s)
- Meghna Mehta
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Anupama Munshi
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA.
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10
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Altered TDP-43 Structure and Function: Key Insights into Aberrant RNA, Mitochondrial, and Cellular and Systemic Metabolism in Amyotrophic Lateral Sclerosis. Metabolites 2022; 12:metabo12080709. [PMID: 36005581 PMCID: PMC9415507 DOI: 10.3390/metabo12080709] [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: 07/13/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 12/10/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neuromuscular disorder with no cure available and limited treatment options. ALS is a highly heterogeneous disease, whereby patients present with vastly different phenotypes. Despite this heterogeneity, over 97% of patients will exhibit pathological TAR-DNA binding protein-43 (TDP-43) cytoplasmic inclusions. TDP-43 is a ubiquitously expressed RNA binding protein with the capacity to bind over 6000 RNA and DNA targets—particularly those involved in RNA, mitochondrial, and lipid metabolism. Here, we review the unique structure and function of TDP-43 and its role in affecting the aforementioned metabolic processes in ALS. Considering evidence published specifically in TDP-43-relevant in vitro, in vivo, and ex vivo models we posit that TDP-43 acts in a positive feedback loop with mRNA transcription/translation, stress granules, cytoplasmic aggregates, and mitochondrial proteins causing a relentless cycle of disease-like pathology eventuating in neuronal toxicity. Given its undeniable presence in ALS pathology, TDP-43 presents as a promising target for mechanistic disease modelling and future therapeutic investigations.
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11
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Duan L, Zaepfel BL, Aksenova V, Dasso M, Rothstein JD, Kalab P, Hayes LR. Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export. Cell Rep 2022; 40:111106. [PMID: 35858577 PMCID: PMC9345261 DOI: 10.1016/j.celrep.2022.111106] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/26/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022] Open
Abstract
Nuclear clearance of the RNA-binding protein TDP-43 is a hallmark of neurodegeneration and an important therapeutic target. Our current understanding of TDP-43 nucleocytoplasmic transport does not fully explain its predominantly nuclear localization or mislocalization in disease. Here, we show that TDP-43 exits nuclei by passive diffusion, independent of facilitated mRNA export. RNA polymerase II blockade and RNase treatment induce TDP-43 nuclear efflux, suggesting that nuclear RNAs sequester TDP-43 in nuclei and limit its availability for passive export. Induction of TDP-43 nuclear efflux by short, GU-rich oligomers (presumably by outcompeting TDP-43 binding to endogenous nuclear RNAs), and nuclear retention conferred by splicing inhibition, demonstrate that nuclear TDP-43 localization depends on binding to GU-rich nuclear RNAs. Indeed, RNA-binding domain mutations markedly reduce TDP-43 nuclear localization and abolish transcription blockade-induced nuclear efflux. Thus, the nuclear abundance of GU-RNAs, dictated by the balance of transcription, pre-mRNA processing, and RNA export, regulates TDP-43 nuclear localization.
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Affiliation(s)
- Lauren Duan
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin L Zaepfel
- Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Petr Kalab
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Lindsey R Hayes
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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12
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Integrated lncRNA function upon genomic and epigenomic regulation. Mol Cell 2022; 82:2252-2266. [PMID: 35714586 DOI: 10.1016/j.molcel.2022.05.027] [Citation(s) in RCA: 172] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/09/2022] [Accepted: 05/23/2022] [Indexed: 12/20/2022]
Abstract
Although some long noncoding (lnc)RNAs are known since the 1950s, the past 25 years have uncovered myriad lncRNAs with diverse sequences, structures, and functions. The advent of high-throughput and sensitive technologies has further uncovered the vast heterogeneity of lncRNA-interacting molecules and patterns of expressed lncRNAs. We propose a unifying functional theme for the expansive family of lncRNAs. At an elementary level, the genomic program of gene expression is elicited via canonical transcription and post-transcriptional mRNA assembly, turnover, and translation. Building upon this regulation, an epigenomic program refines the basic genomic control by modifying chromatin architecture as well as DNA and RNA chemistry. Superimposed over the genomic and epigenomic programs, lncRNAs create an additional regulatory dimension: by interacting with the proteins and nucleic acids that regulate gene expression in the nucleus and cytoplasm, lncRNAs help establish robust, nimble, and specific transcriptional and post-transcriptional control. We describe our present understanding of lncRNA-coordinated control of protein programs and cell fate and discuss challenges and opportunities as we embark on the next 25 years of lncRNA discovery.
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13
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Yao PA, Wu Y, Zhao K, Li Y, Cao J, Xing C. The feedback loop of ANKHD1/lncRNA MALAT1/YAP1 strengthens the radioresistance of CRC by activating YAP1/AKT signaling. Cell Death Dis 2022; 13:103. [PMID: 35110552 PMCID: PMC8810793 DOI: 10.1038/s41419-022-04554-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/22/2021] [Accepted: 01/17/2022] [Indexed: 12/19/2022]
Abstract
Innate radioresistance substantially limits the effectiveness of radiotherapy for colorectal cancer (CRC); thus, a strategy to enhance the radiosensitivity of CRC is urgently needed. Herein, we reported that ankyrin repeat and KH domain containing 1 (ANKHD1) serves as a key regulator of radioresistance in CRC. ANKHD1 was highly expressed in CRC tissues and was highly correlated with Yes-associated protein 1 (YAP1) in CRC. Our results first revealed that ANKHD1 knockdown could increase the radiosensitivity of CRC by regulating DNA-damage repair, both in vitro and in vivo. Furthermore, the interactive regulation between ANKHD1 or YAP1 and lncRNA MALAT1 was revealed by RIP and RNA pull-down assays. Moreover, our results also demonstrated that MALAT1 silencing can radiosensitize CRC cells to IR through YAP1/AKT axis, similar to ANKHD1 silencing. Taken together, we report a feedback loop of ANKHD1/MALAT1/YAP1 that synergistically promotes the transcriptional coactivation of YAP1 and in turn enhances the radioresistance of CRC by regulating DNA-damage repair, probably via the YAP1/AKT axis. Our results suggested that targeting the YAP1/AKT axis downstream of ANKHD1/MALAT1/YAP1 may enhance the radiosensitivity of CRC.
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Affiliation(s)
- Ping-An Yao
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yong Wu
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Kui Zhao
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yecheng Li
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Jianping Cao
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, 215123, China. .,State Key Laboratory of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China.
| | - Chungen Xing
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, 215004, China.
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14
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Zhang X, Zhu YN, Chen B, Kang L. A Gypsy element contributes to the nuclear retention and transcriptional regulation of the resident lncRNA in locusts. RNA Biol 2022; 19:206-220. [PMID: 35067197 PMCID: PMC8786324 DOI: 10.1080/15476286.2021.2024032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The majority of long noncoding RNAs (lncRNAs) contain transposable elements (TEs). PAHAL, a nuclear-retained lncRNA that is inserted by a Gypsy retrotransposon, has been shown to be a vital regulator of phenylalanine hydroxylase (PAH) gene expression that controls dopamine biosynthesis and behavioural aggregation in the migratory locust. However, the role of the Gypsy retrotransposon in the transcriptional regulation of PAHAL remains unknown. Here, we identified a Gypsy retrotransposon (named Gypsy element) as an inverted long terminal repeat located in the 3′ end of PAHAL, representing a feature shared by many other lncRNAs in the locust genome. The embedded Gypsy element contains a RNA nuclear localization signal motif, which promotes the stable accumulation of PAHAL in the nucleus. The Gypsy element also provides high-affinity SRSF2 binding sites for PAHAL that induce the recruitment of SRSF2, resulting in the PAHAL-mediated transcriptional activation of PAH. Thus, our data demonstrate that TEs provide discrete functional domains for lncRNA organization and highlight the contribution of TEs to the regulatory significance of lncRNAs.
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Affiliation(s)
- Xia Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Ya Nan Zhu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Bing Chen
- School of Life Sciences, Hebei University, Baoding, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,School of Life Sciences, Hebei University, Baoding, China.,Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing, China
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15
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Cao Y, Zhu H, Liu W, Wang L, Yin W, Tan J, Zhou Q, Xin Z, Huang H, Xie D, Zhao M, Jiang X, Peng J, Ren C. Multi-Omics Analysis Based on Genomic Instability for Prognostic Prediction in Lower-Grade Glioma. Front Genet 2022; 12:758596. [PMID: 35069679 PMCID: PMC8766732 DOI: 10.3389/fgene.2021.758596] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Lower-grade gliomas (LGGs) are a heterogeneous set of gliomas. One of the primary sources of glioma heterogeneity is genomic instability, a novel characteristic of cancer. It has been reported that long noncoding RNAs (lncRNAs) play an essential role in regulating genomic stability. However, the potential relationship between genomic instability and lncRNA in LGGs and its prognostic value is unclear. Methods: In this study, the LGG samples from The Cancer Genome Atlas (TCGA) were divided into two clusters by integrating the lncRNA expression profile and somatic mutation data using hierarchical clustering. Then, with the differentially expressed lncRNAs between these two clusters, we identified genomic instability-related lncRNAs (GInLncRNAs) in the LGG samples and analyzed their potential function and pathway by co-expression network. Cox and least absolute shrinkage and selection operator (LASSO) regression analyses were conducted to establish a GInLncRNA prognostic signature (GInLncSig), which was assessed by internal and external verification, correlation analysis with somatic mutation, independent prognostic analysis, clinical stratification analysis, and model comparisons. We also established a nomogram to predict the prognosis more accurately. Finally, we performed multi-omics-based analyses to explore the relationship between risk scores and multi-omics data, including immune characteristics, N6-methyladenosine (m6A), stemness index, drug sensitivity, and gene set enrichment analysis (GSEA). Results: We identified 52 GInLncRNAs and screened five from them to construct the GInLncSig model (CRNDE, AC025171.5, AL390755.1, AL049749.1, and TGFB2-AS1), which could independently and accurately predict the outcome of patients with LGG. The GInLncSig model was significantly associated with somatic mutation and outperformed other published signatures. GSEA revealed that metabolic pathways, immune pathways, and cancer pathways were enriched in the high-risk group. Multi-omics-based analyses revealed that T-cell functions, m6A statuses, and stemness characteristics were significantly disparate between two risk subgroups, and immune checkpoints such as PD-L1, PDCD1LG2, and HAVCR2 were significantly highly expressed in the high-risk group. The expression of GInLncSig prognostic genes dramatically correlated with the sensitivity of tumor cells to chemotherapy drugs. Conclusion: A novel signature composed of five GInLncRNAs can be utilized to predict prognosis and impact the immune status, m6A status, and stemness characteristics in LGG. Furthermore, these lncRNAs may be potential and alternative therapeutic targets.
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Affiliation(s)
- Yudong Cao
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hecheng Zhu
- Changsha Kexin Cancer Hospital, Changsha, China
| | - Weidong Liu
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China
| | - Lei Wang
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China
| | - Wen Yin
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jun Tan
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Quanwei Zhou
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaoqi Xin
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hailong Huang
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Dongcheng Xie
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zhao
- Changsha Kexin Cancer Hospital, Changsha, China
| | - Xingjun Jiang
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jiahui Peng
- Department of Medical Ultrasonics, Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Caiping Ren
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China
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16
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Yao ZT, Yang YM, Sun MM, He Y, Liao L, Chen KS, Li B. New insights into the interplay between long non-coding RNAs and RNA-binding proteins in cancer. Cancer Commun (Lond) 2022; 42:117-140. [PMID: 35019235 PMCID: PMC8822594 DOI: 10.1002/cac2.12254] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
With the development of proteomics and epigenetics, a large number of RNA‐binding proteins (RBPs) have been discovered in recent years, and the interaction between long non‐coding RNAs (lncRNAs) and RBPs has also received increasing attention. It is extremely important to conduct in‐depth research on the lncRNA‐RBP interaction network, especially in the context of its role in the occurrence and development of cancer. Increasing evidence has demonstrated that lncRNA‐RBP interactions play a vital role in cancer progression; therefore, targeting these interactions could provide new insights for cancer drug discovery. In this review, we discussed how lncRNAs can interact with RBPs to regulate their localization, modification, stability, and activity and discussed the effects of RBPs on the stability, transport, transcription, and localization of lncRNAs. Moreover, we explored the regulation and influence of these interactions on lncRNAs, RBPs, and downstream pathways that are related to cancer development, such as N6‐methyladenosine (m6A) modification of lncRNAs. In addition, we discussed how the lncRNA‐RBP interaction network regulates cancer cell phenotypes, such as proliferation, apoptosis, metastasis, drug resistance, immunity, tumor environment, and metabolism. Furthermore, we summarized the therapeutic strategies that target the lncRNA‐RBP interaction network. Although these treatments are still in the experimental stage and various theories and processes are still being studied, we believe that these strategies may provide new ideas for cancer treatment.
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Affiliation(s)
- Zi-Ting Yao
- Ministry of Education Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
| | - Yan-Ming Yang
- Ministry of Education Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
| | - Miao-Miao Sun
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450001, P. R. China
| | - Yan He
- Ministry of Education Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China.,Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510700, P. R. China
| | - Long Liao
- Ministry of Education Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, Guangdong, 510632, P. R. China.,Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510700, P. R. China
| | - Kui-Sheng Chen
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450001, P. R. China
| | - Bin Li
- Ministry of Education Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, Guangdong, 510632, P. R. China.,Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510700, P. R. China
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17
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Puvvula PK, Buczkowski S, Moon AM. hnRNPK-derived cell-penetrating peptide inhibits cancer cell survival. Mol Ther Oncolytics 2021; 23:342-354. [PMID: 34820504 PMCID: PMC8586514 DOI: 10.1016/j.omto.2021.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/28/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022] Open
Abstract
hnRNPK is a multifunctional protein that plays an important role in cancer cell proliferation and metastasis via its RNA- and DNA-binding properties. Previously we showed that cell-penetrating peptides derived from the RGG RNA-binding domain of SAFA (hnRNPU) disrupt cancer cell proliferation and survival. Here we explore the efficacy of a peptide derived from the RGG domain of hnRNPK. This peptide acts in a dominant-negative manner on several hnRNPK functions to induce death of multiple types of cancer cells. The peptide phenocopies the effect of hnRNPK knockdown on its mRNA-stability targets such as KLF4 and EGR1 and alters the levels and locations of long non-coding RNAs (lncRNAs) and proteins required for nuclear and paraspeckle formation and function. The RGG-derived peptide also decreases euchromatin as evidenced by loss of active marks and polymerase II occupancy. Our findings reveal the potential therapeutic utility of the hnRNPK RGG-derived peptide in a range of cancers.
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Affiliation(s)
- Pavan Kumar Puvvula
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Corresponding author: Pavan Kumar Puvvula, PhD, Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
| | - Stephanie Buczkowski
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
| | - Anne M. Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, NY, USA
- Corresponding author: Anne M. Moon, MD, PhD, Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
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18
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Ma X, Ying Y, Xie H, Liu X, Wang X, Li J. The Regulatory Role of RNA Metabolism Regulator TDP-43 in Human Cancer. Front Oncol 2021; 11:755096. [PMID: 34778070 PMCID: PMC8581290 DOI: 10.3389/fonc.2021.755096] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022] Open
Abstract
TAR-DNA-binding protein-43 (TDP-43) is a member of hnRNP family and acts as both RNA and DNA binding regulator, mediating RNA metabolism and transcription regulation in various diseases. Currently, emerging evidence gradually elucidates the crucial role of TDP-43 in human cancers like it is previously widely researched in neurodegeneration diseases. A series of RNA metabolism events, including mRNA alternative splicing, transport, stability, miRNA processing, and ncRNA regulation, are all confirmed to be closely involved in various carcinogenesis and tumor progressions, which are all partially regulated and interacted by TDP-43. Herein we conducted the first overall review about TDP-43 and cancers to systematically summarize the function and precise mechanism of TDP-43 in different human cancers. We hope it would provide basic knowledge and concepts for tumor target therapy and biomarker diagnosis in the future.
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Affiliation(s)
- Xueyou Ma
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Yufan Ying
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Haiyun Xie
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Xiaoyan Liu
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao Wang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Jiangfeng Li
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
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19
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HnRNP K mislocalisation is a novel protein pathology of frontotemporal lobar degeneration and ageing and leads to cryptic splicing. Acta Neuropathol 2021; 142:609-627. [PMID: 34274995 PMCID: PMC8423707 DOI: 10.1007/s00401-021-02340-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 02/08/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (HnRNPs) are a group of ubiquitously expressed RNA-binding proteins implicated in the regulation of all aspects of nucleic acid metabolism. HnRNP K is a member of this highly versatile hnRNP family. Pathological redistribution of hnRNP K to the cytoplasm has been linked to the pathogenesis of several malignancies but, until now, has been underexplored in the context of neurodegenerative disease. Here we show hnRNP K mislocalisation in pyramidal neurons of the frontal cortex to be a novel neuropathological feature that is associated with both frontotemporal lobar degeneration and ageing. HnRNP K mislocalisation is mutually exclusive to TDP-43 and tau pathological inclusions in neurons and was not observed to colocalise with mitochondrial, autophagosomal or stress granule markers. De-repression of cryptic exons in RNA targets following TDP-43 nuclear depletion is an emerging mechanism of potential neurotoxicity in frontotemporal lobar degeneration and the mechanistically overlapping disorder amyotrophic lateral sclerosis. We silenced hnRNP K in neuronal cells to identify the transcriptomic consequences of hnRNP K nuclear depletion. Intriguingly, by performing RNA-seq analysis we find that depletion of hnRNP K induces 101 novel cryptic exon events. We validated cryptic exon inclusion in an SH-SY5Y hnRNP K knockdown and in FTLD brain exhibiting hnRNP K nuclear depletion. We, therefore, present evidence for hnRNP K mislocalisation to be associated with FTLD and for this to induce widespread changes in splicing.
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20
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Hallegger M, Chakrabarti AM, Lee FCY, Lee BL, Amalietti AG, Odeh HM, Copley KE, Rubien JD, Portz B, Kuret K, Huppertz I, Rau F, Patani R, Fawzi NL, Shorter J, Luscombe NM, Ule J. TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell 2021; 184:4680-4696.e22. [PMID: 34380047 PMCID: PMC8445024 DOI: 10.1016/j.cell.2021.07.018] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 04/12/2021] [Accepted: 07/15/2021] [Indexed: 11/20/2022]
Abstract
Mutations causing amyotrophic lateral sclerosis (ALS) often affect the condensation properties of RNA-binding proteins (RBPs). However, the role of RBP condensation in the specificity and function of protein-RNA complexes remains unclear. We created a series of TDP-43 C-terminal domain (CTD) variants that exhibited a gradient of low to high condensation propensity, as observed in vitro and by nuclear mobility and foci formation. Notably, a capacity for condensation was required for efficient TDP-43 assembly on subsets of RNA-binding regions, which contain unusually long clusters of motifs of characteristic types and density. These "binding-region condensates" are promoted by homomeric CTD-driven interactions and required for efficient regulation of a subset of bound transcripts, including autoregulation of TDP-43 mRNA. We establish that RBP condensation can occur in a binding-region-specific manner to selectively modulate transcriptome-wide RNA regulation, which has implications for remodeling RNA networks in the context of signaling, disease, and evolution.
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Affiliation(s)
- Martina Hallegger
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Anob M Chakrabarti
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Genetics, Evolution and Environment, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Flora C Y Lee
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Bo Lim Lee
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aram G Amalietti
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Hana M Odeh
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jack D Rubien
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Klara Kuret
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Ina Huppertz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Frédérique Rau
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Genetics, Evolution and Environment, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK; Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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21
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Lu Y, Yan Y, Li B, Liu M, Liang Y, Ye Y, Cheng W, Li J, Jiao J, Chang S. A Novel Prognostic Model for Oral Squamous Cell Carcinoma: The Functions and Prognostic Values of RNA-Binding Proteins. Front Oncol 2021; 11:592614. [PMID: 34395233 PMCID: PMC8362834 DOI: 10.3389/fonc.2021.592614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The biological roles and clinical significance of RNA-binding proteins (RBPs) in oral squamous cell carcinoma (OSCC) are not fully understood. We investigated the prognostic value of RBPs in OSCC using several bioinformatic strategies. MATERIALS AND METHODS OSCC data were obtained from a public online database, the Limma R package was used to identify differentially expressed RBPs, and functional enrichment analysis was performed to elucidate the biological functions of the above RBPs in OSCC. We performed protein-protein interaction (PPI) network and Cox regression analyses to extract prognosis-related hub RBPs. Next, we established and validated a prognostic model based on the hub RBPs using Cox regression and risk score analyses. RESULTS We found that the differentially expressed RBPs were closely related to the defense response to viruses and multiple RNA processes. We identified 10 prognosis-related hub RBPs (ZC3H12D, OAS2, INTS10, ACO1, PCBP4, RNASE3, PTGES3L-AARSD1, RNASE13, DDX4, and PCF11) and effectively predicted the overall survival of OSCC patients. The area under the receiver operating characteristic (ROC) curve (AUC) of the risk score model was 0.781, suggesting that our model exhibited excellent prognostic performance. Finally, we built a nomogram integrating the 10 RBPs. The internal validation cohort results showed a reliable predictive capability of the nomogram for OSCC. CONCLUSION We established a novel 10-RBP-based model for OSCC that could enable precise individual treatment and follow-up management strategies in the future.
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Affiliation(s)
- Yingjuan Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- RNA Biomedical Institute, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yongcong Yan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- RNA Biomedical Institute, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Hepatobiliary Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bowen Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- RNA Biomedical Institute, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mo Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yancan Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- RNA Biomedical Institute, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yushan Ye
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Weiqi Cheng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jinsong Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiuyang Jiao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shaohai Chang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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22
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Aliperti V, Skonieczna J, Cerase A. Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders. Noncoding RNA 2021; 7:36. [PMID: 34204536 PMCID: PMC8293397 DOI: 10.3390/ncrna7020036] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Development is a complex process regulated both by genetic and epigenetic and environmental clues. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in several tissues including the brain. Altered expression of lncRNAs has been linked to several neurodegenerative, neurodevelopmental and mental disorders. The identification and characterization of lncRNAs that are deregulated or mutated in neurodevelopmental and mental health diseases are fundamental to understanding the complex transcriptional processes in brain function. Crucially, lncRNAs can be exploited as a novel target for treating neurological disorders. In our review, we first summarize the recent advances in our understanding of lncRNA functions in the context of cell biology and then discussing their association with selected neuronal development and neurological disorders.
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Affiliation(s)
- Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Justyna Skonieczna
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
| | - Andrea Cerase
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
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23
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Huang Y, Qiao Y, Zhao Y, Li Y, Yuan J, Zhou J, Sun H, Wang H. Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms. Brief Bioinform 2021; 22:6287336. [PMID: 34056657 DOI: 10.1093/bib/bbab195] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of major biological processes and their functional modes are dictated by their subcellular localization. Relative nuclear enrichment of lncRNAs compared to mRNAs is a prevalent phenomenon but the molecular mechanisms governing their nuclear retention in cells remain largely unknown. Here in this study, we harness the recently released eCLIP data for a large number of RNA-binding proteins (RBPs) in K562 and HepG2 cells and utilize multiple bioinformatics methods to comprehensively survey the roles of RBPs in lncRNA nuclear retention. We identify an array of splicing RBPs that bind to nuclear-enriched lincRNAs (large intergenic non-coding RNAs) thus may act as trans-factors regulating their nuclear retention. Further analyses reveal that these RBPs may bind with distinct core motifs, flanking sequence compositions, or secondary structures to drive lincRNA nuclear retention. Moreover, network analyses uncover potential co-regulatory RBP clusters and the physical interaction between HNRNPU and SAFB2 proteins in K562 cells is further experimentally verified. Altogether, our analyses reveal previously unknown factors and mechanisms that govern lincRNA nuclear localization in cells.
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Affiliation(s)
- Yile Huang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yulong Qiao
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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24
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Vasudeva K, Dutta A, Munshi A. Role of lncRNAs in the Development of Ischemic Stroke and Their Therapeutic Potential. Mol Neurobiol 2021; 58:3712-3728. [PMID: 33818737 DOI: 10.1007/s12035-021-02359-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/11/2021] [Indexed: 12/20/2022]
Abstract
Stroke is a major cause of premature mortality and disability around the world. Therefore, identification of cellular and molecular processes implicated in the pathogenesis and progression of ischemic stroke has become a priority. Long non-coding RNAs (lncRNAs) are emerging as significant players in the pathophysiology of cerebral ischemia. They are involved in different signalling pathways of cellular processes like cell apoptosis, autophagy, angiogenesis, inflammation, and cell death, impacting the progression of cerebral damage. Exploring the functions of these lncRNAs and their mechanism of action may help in the development of promising treatment strategies. In this review, the current knowledge of lncRNAs in ischemic stroke, focusing on the mechanism by which they cause cellular apoptosis, inflammation, and microglial activation, has been summarized. Very few lncRNAs have been functionally annotated. Therefore, the therapies based on lncRNAs still face many hurdles since the potential targets are likely to increase with the identification of new ones. Majority of experiments involving the identification and function of lncRNAs have been carried out in animal models, and the role of lncRNAs in human stroke presents a challenge. However, mitigating these issues through more rational experimental design might lead to the development of lncRNA-based stroke therapies to treat ischemic stroke.
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Affiliation(s)
- Kanika Vasudeva
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India
| | - Anyeasha Dutta
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India.
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25
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Sas-Nowosielska H, Magalska A. Long Noncoding RNAs-Crucial Players Organizing the Landscape of the Neuronal Nucleus. Int J Mol Sci 2021; 22:ijms22073478. [PMID: 33801737 PMCID: PMC8037058 DOI: 10.3390/ijms22073478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
The ability to regulate chromatin organization is particularly important in neurons, which dynamically respond to external stimuli. Accumulating evidence shows that lncRNAs play important architectural roles in organizing different nuclear domains like inactive chromosome X, splicing speckles, paraspeckles, and Gomafu nuclear bodies. LncRNAs are abundantly expressed in the nervous system where they may play important roles in compartmentalization of the cell nucleus. In this review we will describe the architectural role of lncRNAs in the nuclei of neuronal cells.
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26
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Long non-coding RNA HAL suppresses the migration and invasion of serous ovarian cancer by inhibiting EMT signaling pathway. Biosci Rep 2021; 40:222072. [PMID: 32039453 PMCID: PMC7056446 DOI: 10.1042/bsr20194496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To investigate the specific function of long non-coding RNA HAL in serous ovarian cancer (SOC) and to further clarify the regulation of HAL on EMT pathway. MATERIALS AND METHODS The expression of HAL and TWIST1 was detected by qRT-PCR. CCK8 assay, wound healing assay, transwell assay and flow cytometry were used to detect the HAL function on proliferation, migration, invasion and apoptosis in SOC cells. Western blot was used to calculate protein level of Vimentin, N-cadherin and E-cadherin. The effect of HAL on tumorigenesis of SOC was confirmed by xenograft nude mice model. RESULTS HAL was significantly decreased in SOC tissues and cells. Overexpression of HAL inhibited the proliferation, migration and invasion of SKOV3 cells, but promoted apoptosis. Furthermore, overexpression of HAL decreased the mRNA and protein levels of TWIST1 via a binding between HAL and TWIST1. Forced expression of TWIST1 reversed the inhibitory role of HAL on SOC cells' migration and invasion. The in vivo tumor growth assay showed that HAL suppressed SOC tumorigenesis with inhibiting EMT pathway. CONCLUSIONS Our research emphasized HAL acting as a tumor-inhibiting gene by regulating EMT signaling pathway, thus providing some novel experimental basis for clinical treatment of SOC.
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27
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Chen Y, Li Z, Chen X, Zhang S. Long non-coding RNAs: From disease code to drug role. Acta Pharm Sin B 2021; 11:340-354. [PMID: 33643816 PMCID: PMC7893121 DOI: 10.1016/j.apsb.2020.10.001] [Citation(s) in RCA: 260] [Impact Index Per Article: 86.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Enormous studies have corroborated that long non-coding RNAs (lncRNAs) extensively participate in crucial physiological processes such as metabolism and immunity, and are closely related to the occurrence and development of tumors, cardiovascular diseases, nervous system disorders, nephropathy, and other diseases. The application of lncRNAs as biomarkers or intervention targets can provide new insights into the diagnosis and treatment of diseases. This paper has focused on the emerging research into lncRNAs as pharmacological targets and has reviewed the transition of lncRNAs from the role of disease coding to acting as drug candidates, including the current status and progress in preclinical research. Cutting-edge strategies for lncRNA modulation have been summarized, including the sources of lncRNA-related drugs, such as genetic technology and small-molecule compounds, and related delivery methods. The current progress of clinical trials of lncRNA-targeting drugs is also discussed. This information will form a latest updated reference for research and development of lncRNA-based drugs.
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Key Words
- AD, Alzheimer's disease
- ANRIL, antisense noncoding RNA gene at the INK4 locus
- ASO, antisense oligonucleotide
- ASncmtRNA
- ASncmtRNA, antisense noncoding mitochondrial RNA
- BCAR4, breast cancer anti-estrogen resistance 4
- BDNF-AS, brain-derived neurotrophic factor antisense
- CASC9, cancer susceptibility candidate 9
- CDK, cyclin dependent kinase 1
- CHRF, cardiac hypertrophy related factor
- CRISPR, clustered regularly interspaced short palindromic repeats
- Clinical trials
- DACH1, dachshund homolog 1
- DANCR, differentiation antagonizing non-protein coding RNA
- DKD, diabetic kidney disease
- DPF, diphenyl furan
- Delivery
- EBF3-AS, early B cell factor 3-antisense
- ENE, element for nuclear expression
- Erbb4-IR, Erb-B2 receptor tyrosine kinase 4-immunoreactivity
- FDA, U.S. Food and Drug Administration
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GAS5, growth arrest specific 5
- Gene therapy
- HISLA, HIF-1α-stabilizing long noncoding RNA
- HOTAIR, HOX transcript antisense intergenic RNA
- HULC, highly upregulated in liver cancer
- LIPCAR, long intergenic noncoding RNA predicting cardiac remodeling
- LNAs, locked nucleic acids
- LncRNAs
- MALAT1, metastasis associated lung adenocarcinoma transcript 1
- MEG3, maternally expressed gene 3
- MHRT, myosin heavy chain associated RNA transcripts
- MM, multiple myeloma
- NEAT1, nuclear enriched abundant transcript 1
- NKILA, NF-kappaB interacting lncRNA
- NPs, nanoparticles
- Norad, non-coding RNA activated by DNA damage
- OIP5-AS1, opa-interacting protein 5 antisense transcript 1
- PD, Parkinson's disease
- PEG, polyethylene glycol
- PNAs, peptide nucleic acids
- PTO, phosphorothioate
- PVT1, plasmacytoma variant translocation 1
- RGD, arginine-glycine-aspartic acid peptide
- RISC, RNA-induced silencing complex
- SALRNA1, senescence associated long non-coding RNA 1
- SNHG1, small nucleolar RNA host gene 1
- Small molecules
- SncmtRNA, sense noncoding mitochondrial RNA
- THRIL, TNF and HNRNPL related immunoregulatory
- TTTY15, testis-specific transcript, Y-linked 15
- TUG1, taurine-upregulated gene 1
- TWIST1, twist family BHLH transcription factor 1
- Targeted drug
- TncRNA, trophoblast-derived noncoding RNA
- Translational medicine
- UCA1, urothelial carcinoma-associated 1
- UTF1, undifferentiated transcription factor 1
- XIST, X-inactive specific transcript
- lincRNA-p21, long intergenic noncoding RNA p21
- lncRNAs, long non-coding RNAs
- mtlncRNA, mitochondrial long noncoding RNA
- pHLIP, pH-low insertion peptide
- sgRNA, single guide RNA
- siRNAs, small interfering RNAs
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Bridges MC, Daulagala AC, Kourtidis A. LNCcation: lncRNA localization and function. J Cell Biol 2021; 220:e202009045. [PMID: 33464299 PMCID: PMC7816648 DOI: 10.1083/jcb.202009045] [Citation(s) in RCA: 653] [Impact Index Per Article: 217.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Subcellular localization of RNAs has gained attention in recent years as a prevalent phenomenon that influences numerous cellular processes. This is also evident for the large and relatively novel class of long noncoding RNAs (lncRNAs). Because lncRNAs are defined as RNA transcripts >200 nucleotides that do not encode protein, they are themselves the functional units, making their subcellular localization critical to their function. The discovery of tens of thousands of lncRNAs and the cumulative evidence involving them in almost every cellular activity render assessment of their subcellular localization essential to fully understanding their biology. In this review, we summarize current knowledge of lncRNA subcellular localization, factors controlling their localization, emerging themes, including the role of lncRNA isoforms and the involvement of lncRNAs in phase separation bodies, and the implications of lncRNA localization on their function and on cellular behavior. We also discuss gaps in the current knowledge as well as opportunities that these provide for novel avenues of investigation.
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Affiliation(s)
| | | | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC
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Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq. Sci Rep 2021; 11:1175. [PMID: 33441968 PMCID: PMC7806670 DOI: 10.1038/s41598-020-80846-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein–RNA complexes and poly-A pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non poly-A RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of poly-A pulldown. Our study demonstrates that ~ 68% of the total POP-seq peaks exhibited an overlap with publicly available protein–RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein–RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e−16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein–RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
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Goyal B, Yadav SRM, Awasthee N, Gupta S, Kunnumakkara AB, Gupta SC. Diagnostic, prognostic, and therapeutic significance of long non-coding RNA MALAT1 in cancer. Biochim Biophys Acta Rev Cancer 2021; 1875:188502. [PMID: 33428963 DOI: 10.1016/j.bbcan.2021.188502] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/30/2020] [Accepted: 01/02/2021] [Indexed: 12/20/2022]
Abstract
Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is a widely studied lncRNA in cancer. Although dispensable for normal physiology, MALAT1 is important for cancer-related pathways regulation. It is localized in the nuclear speckles periphery along with centrally located pre-RNA splicing factors. MALAT1 associated cancer signaling pathways include MAPK/ERK, PI3K/AKT, β-catenin/Wnt, Hippo, VEGF, YAP, etc. Molecular tools such as immunoprecipitation, RNA pull-down, reporter assay, Northern blotting, microarray, and q-RT-PCR has been used to elucidate MALAT1's function in cancer pathogenesis. MALAT1 can regulate multiple steps in the development of tumours. The diagnostic and prognostic significance of MALAT1 has been demonstrated in cancers of the breast, cervix, colorectum, gallbladder, lung, ovary, pancreas, prostate, glioma, hepatocellular carcinoma, and multiple myeloma. MALAT1 has also emerged as a novel therapeutic target for solid as well as hematological malignancies. In experimental models, siRNA and antisense oligonucleotide (ASO) based strategy has been used for targeting MALAT1. The lncRNA has also been targeted for the chemosensitization and radiosensitization of cancer cells. However, most studies have been performed in preclinical models. How the cross-talk of MALAT1 with other signaling pathways affect cancer pathogenesis is the focus of this article. The diagnostic, prognostic, and therapeutic significance of MALAT1 in multiple cancer types are discussed.
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Affiliation(s)
- Bela Goyal
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Shashi Ranjan Mani Yadav
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Nikee Awasthee
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Sweety Gupta
- Department of Radiation Oncology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Ajaikumar B Kunnumakkara
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, India
| | - Subash Chandra Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Liao H, Chen Q, Xiao J. Reflections on the Role of Malat1 in Gynecological Cancer. Cancer Manag Res 2020; 12:13489-13500. [PMID: 33408521 PMCID: PMC7779295 DOI: 10.2147/cmar.s286804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
Non-coding RNAs (ncRNAs) have received significant attention over the last few years. Malat1, as one of the most extensively studied ncRNAs, is believed to be not only a potential biomarker for disease diagnosis and prognosis, but also a candidate drug target for gynecological cancers. This potential is supported by a growing body of experimental evidence demonstrating that Malat1 participates in the occurrence, progression, and metastasis of tumors. Research has also shown that Malat1 can influence patient survival by regulating a range of target genes and signaling pathways. However, previous review articles have generally failed to consider the role of Malat1 in gynecological cancer in detail. In the present review, we summarize recent progress in research relating to the clinical relevance of Malat1 and the molecular mechanisms underlying the action of this ncRNA. Besides, we put forward some action points for further research after taking into consideration the sub-location and other essential properties of Malat1, which might enable us to have a better understanding of the potential of this molecule regarding clinical diagnosis and treatment.
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Affiliation(s)
- Huiyan Liao
- The 2nd Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, People's Republic of China
| | - Qi Chen
- The 6th Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, People's Republic of China
| | - Jing Xiao
- Department of Gynecology, the University Town Branch, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510120, People's Republic of China
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Mechanisms of Long Noncoding RNA Nuclear Retention. Trends Biochem Sci 2020; 45:947-960. [DOI: 10.1016/j.tibs.2020.07.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/27/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
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Kang D, Lee Y, Lee JS. RNA-Binding Proteins in Cancer: Functional and Therapeutic Perspectives. Cancers (Basel) 2020; 12:cancers12092699. [PMID: 32967226 PMCID: PMC7563379 DOI: 10.3390/cancers12092699] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary RNA-binding proteins (RBPs) play central roles in regulating posttranscriptional expression of genes. Many of them are known to be deregulated in a wide variety of cancers. Dysregulated RBPs influence the expression levels of target RNAs related to cancer phenotypes, such as proliferation, apoptosis, angiogenesis, senescence, and EMT/invasion/metastasis. Thus, understanding the molecular functions of RBPs and their roles in cancer-related phenotypes can lead to improved therapeutic strategies. Abstract RNA-binding proteins (RBPs) crucially regulate gene expression through post-transcriptional regulation, such as by modulating microRNA (miRNA) processing and the alternative splicing, alternative polyadenylation, subcellular localization, stability, and translation of RNAs. More than 1500 RBPs have been identified to date, and many of them are known to be deregulated in cancer. Alterations in the expression and localization of RBPs can influence the expression levels of oncogenes, tumor-suppressor genes, and genome stability-related genes. RBP-mediated gene regulation can lead to diverse cancer-related cellular phenotypes, such as proliferation, apoptosis, angiogenesis, senescence, and epithelial-mesenchymal transition (EMT)/invasion/metastasis. This regulation can also be associated with cancer prognosis. Thus, RBPs can be potential targets for the development of therapeutics for the cancer treatment. In this review, we describe the molecular functions of RBPs, their roles in cancer-related cellular phenotypes, and various approaches that may be used to target RBPs for cancer treatment.
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Affiliation(s)
- Donghee Kang
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
- Program in Biomedical Science & Engineering, Inha University Graduate School, Incheon 22212, Korea
| | - Yerim Lee
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
| | - Jae-Seon Lee
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
- Program in Biomedical Science & Engineering, Inha University Graduate School, Incheon 22212, Korea
- Correspondence: ; Tel.: +82-32-860-9832
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LncRNA Malat1 inhibition of TDP43 cleavage suppresses IRF3-initiated antiviral innate immunity. Proc Natl Acad Sci U S A 2020; 117:23695-23706. [PMID: 32907941 DOI: 10.1073/pnas.2003932117] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) involved in the regulation of antiviral innate immune responses need to be further identified. By functionally screening the lncRNAs in macrophages, here we identified lncRNA Malat1, abundant in the nucleus but significantly down-regulated after viral infection, as a negative regulator of antiviral type I IFN (IFN-I) production. Malat1 directly bound to the transactive response DNA-binding protein (TDP43) in the nucleus and prevented activation of TDP43 by blocking the activated caspase-3-mediated TDP43 cleavage to TDP35. The cleaved TDP35 increased the nuclear IRF3 protein level by binding and degrading Rbck1 pre-mRNA to prevent IRF3 proteasomal degradation upon viral infection, thus selectively promoting antiviral IFN-I production. Deficiency of Malat1 enhanced antiviral innate responses in vivo, accompanying the increased IFN-I production and reduced viral burden. Importantly, the reduced MALAT1, augmented IRF3, and increased IFNA mRNA were found in peripheral blood mononuclear cells (PBMCs) from systemic lupus erythematosus (SLE) patients. Therefore, the down-regulation of MALAT1 in virus-infected cells or in human cells from autoimmune diseases will increase host resistance against viral infection or lead to autoinflammatory interferonopathies via the increased type I IFN production. Our results demonstrate that the nuclear Malat1 suppresses antiviral innate responses by targeting TDP43 activation via RNA-RBP interactive network, adding insight to the molecular regulation of innate responses and autoimmune pathogenesis.
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Farooqi AA, Legaki E, Gazouli M, Rinaldi S, Berardi R. MALAT1 as a Versatile Regulator of Cancer: Overview of the updates from Predatory role as Competitive Endogenous RNA to Mechanistic Insights. Curr Cancer Drug Targets 2020; 21:CCDT-EPUB-108738. [PMID: 32748748 DOI: 10.2174/1568009620999200730183110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022]
Abstract
The central dogma of molecular biology, has remained a cornerstone of classical molecular biology. However, serendipitously discovered microRNAs (miRNAs) in nematodes paradigmatically shifted our current knowledge of the intricate mechanisms during transitions from transcription to translation. The discovery of miRNA captured considerable attention and appreciation, and we had witnessed an explosion in the field of non-coding RNAs. Ground-breaking discoveries in the field of non-coding RNAs have helped in better characterization of microRNAs and long non-coding RNAs (LncRNAs). There is an ever-increasing list of miRNA targets that are regulated by MALAT1 to stimulate or repress the expression of target genes. However, in this review, our main focus is to summarize mechanistic insights on MALAT1-mediated regulation of oncogenic signaling pathways. We have discussed how MALAT1 modulated TGF/SMAD and Hippo pathways in various cancers. We have also comprehensively summarized how JAK/STAT and Wnt/β-catenin pathways stimulated MALAT1 expression and consequentially how MALAT1 potentiated these signaling cascades to promote cancer. MALAT1 research has undergone substantial broadening. However, there is still a need to identify additional mechanisms. MALAT1 is involved in the multi-layered regulation of multiple transduction cascades, and detailed analysis of different pathways will be advantageous in getting a step closer to individualized medicine.
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Affiliation(s)
- Ammad Ahmad Farooqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 54000. Pakistan
| | - Evangelia Legaki
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens,. Greece
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens,. Greece
| | - Silvia Rinaldi
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti Umberto I -GM Lancisi -G Salesi di Ancona, Via Conca 71, 60126 Ancona. Italy
| | - Rossana Berardi
- Clinica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti Umberto I -GM Lancisi -G Salesi di Ancona, Via Conca 71, 60126 Ancona. Italy
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Nguyen TM, Alchalabi S, Oluwatoyosi A, Ropri AS, Herschkowitz JI, Rosen JM. New twists on long noncoding RNAs: from mobile elements to motile cancer cells. RNA Biol 2020; 17:1535-1549. [PMID: 32522127 DOI: 10.1080/15476286.2020.1760535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The purpose of this review is to highlight several areas of lncRNA biology and cancer that we hope will provide some new insights for future research. These include the relationship of lncRNAs and the epithelial to mesenchymal transition (EMT) with a focus on transcriptional and alternative splicing mechanisms and mRNA stability through miRNAs. In addition, we highlight the potential role of enhancer e-lncRNAs, the importance of transposable elements in lncRNA biology, and finally the emerging area of using antisense oligonucleotides (ASOs) and small molecules to target lncRNAs and their therapeutic implications.
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Affiliation(s)
- Tuan M Nguyen
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School , Boston, MA, USA.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, MA, USA
| | - Sumayya Alchalabi
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Adewunmi Oluwatoyosi
- Department of Molecular & Cellular Biology, Baylor College of Medicine , Houston, TX, USA
| | - Ali S Ropri
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Jason I Herschkowitz
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Jeffrey M Rosen
- Department of Molecular & Cellular Biology, Baylor College of Medicine , Houston, TX, USA
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Zhao Y, Teng H, Yao F, Yap S, Sun Y, Ma L. Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs. Cancers (Basel) 2020; 12:cancers12061458. [PMID: 32503290 PMCID: PMC7352683 DOI: 10.3390/cancers12061458] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in many physiological and pathological processes, such as development, aging, immunity, and cancer. Mechanistically, lncRNAs exert their functions through interaction with proteins, genomic DNA, and other RNA, leading to transcriptional and post-transcriptional regulation of gene expression, either in cis or in trans; it is often difficult to distinguish between these two regulatory mechanisms. A variety of approaches, including RNA interference, antisense oligonucleotides, CRISPR-based methods, and genetically engineered mouse models, have yielded abundant information about lncRNA functions and underlying mechanisms, albeit with many discrepancies. In this review, we elaborate on the challenges in ascribing functions to lncRNAs based on the features of lncRNAs, including the genomic location, copy number, domain structure, subcellular localization, stability, evolution, and expression pattern. We also describe a framework for the investigation of lncRNA functions and mechanisms of action. Rigorous characterization of cancer-implicated lncRNAs is critical for the identification of bona fide anticancer targets.
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Affiliation(s)
- Yang Zhao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
| | - Fan Yao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
| | - Shannon Yap
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: ; Tel.: +1-713-792-6590
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Arun G, Aggarwal D, Spector DL. MALAT1 Long Non-Coding RNA: Functional Implications. Noncoding RNA 2020; 6:E22. [PMID: 32503170 PMCID: PMC7344863 DOI: 10.3390/ncrna6020022] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
The mammalian genome is pervasively transcribed and the functional significance of many long non-coding RNA (lncRNA) transcripts are gradually being elucidated. Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is one of the most well-studied lncRNAs. MALAT1 is a highly conserved nuclear retained lncRNA that is abundantly expressed in cells and tissues and has been shown to play a role in regulating genes at both the transcriptional and post-transcriptional levels in a context-dependent manner. However, Malat1 has been shown to be dispensable for normal development and viability in mice. Interestingly, accumulating evidence suggests that MALAT1 plays an important role in numerous diseases including cancer. Here, we discuss the current state-of-knowledge in regard to MALAT1 with respect to its function, role in diseases, and the potential therapeutic opportunities for targeting MALAT1 using antisense oligonucleotides and small molecules.
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Affiliation(s)
- Gayatri Arun
- Envisagenics, 101 Avenue of the Americas, New York, NY 10013, USA;
| | - Disha Aggarwal
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, NY 11794, USA;
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
| | - David L. Spector
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, NY 11794, USA;
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
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Fazal FM, Chang HY. Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:31-45. [PMID: 32482897 PMCID: PMC7426137 DOI: 10.1101/sqb.2019.84.040352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNAs are trafficked and localized with exquisite precision inside the cell. Studies of candidate messenger RNAs have shown the vital importance of RNA subcellular location in development and cellular function. New sequencing- and imaging-based methods are providing complementary insights into subcellular localization of RNAs transcriptome-wide. APEX-seq and ribosome profiling as well as proximity-labeling approaches have revealed thousands of transcript isoforms are localized to distinct cytotopic locations, including locations that defy biochemical fractionation and hence were missed by prior studies. Sequences in the 3' and 5' untranslated regions (UTRs) serve as "zip codes" to direct transcripts to particular locales, and it is clear that intronic and retrotransposable sequences within transcripts have been co-opted by cells to control localization. Molecular motors, nuclear-to-cytosol RNA export, liquid-liquid phase separation, RNA modifications, and RNA structure dynamically shape the subcellular transcriptome. Location-based RNA regulation continues to pose new mysteries for the field, yet promises to reveal insights into fundamental cell biology and disease mechanisms.
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Affiliation(s)
- Furqan M Fazal
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
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RNA-Binding Proteins as Important Regulators of Long Non-Coding RNAs in Cancer. Int J Mol Sci 2020; 21:ijms21082969. [PMID: 32340118 PMCID: PMC7215867 DOI: 10.3390/ijms21082969] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
The majority of the genome is transcribed into pieces of non-(protein) coding RNA, among which long non-coding RNAs (lncRNAs) constitute a large group of particularly versatile molecules that govern basic cellular processes including transcription, splicing, RNA stability, and translation. The frequent deregulation of numerous lncRNAs in cancer is known to contribute to virtually all hallmarks of cancer. An important regulatory mechanism of lncRNAs is the post-transcriptional regulation mediated by RNA-binding proteins (RBPs). So far, however, only a small number of known cancer-associated lncRNAs have been found to be regulated by the interaction with RBPs like human antigen R (HuR), ARE/poly(U)-binding/degradation factor 1 (AUF1), insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), and tristetraprolin (TTP). These RBPs regulate, by various means, two aspects in particular, namely the stability and the localization of lncRNAs. Importantly, these RBPs themselves are commonly deregulated in cancer and might thus play a major role in the deregulation of cancer-related lncRNAs. There are, however, still many open questions, for example regarding the context specificity of these regulatory mechanisms that, in part, is based on the synergistic or competitive interaction between different RBPs. There is also a lack of knowledge on how RBPs facilitate the transport of lncRNAs between different cellular compartments.
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