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Milcamps R, Michiels T. Involvement of paraspeckle components in viral infections. Nucleus 2024; 15:2350178. [PMID: 38717150 PMCID: PMC11086011 DOI: 10.1080/19491034.2024.2350178] [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: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Paraspeckles are non-membranous subnuclear bodies, formed through the interaction between the architectural long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) and specific RNA-binding proteins, including the three Drosophila Behavior/Human Splicing (DBHS) family members (PSPC1 (Paraspeckle Component 1), SFPQ (Splicing Factor Proline and Glutamine Rich) and NONO (Non-POU domain-containing octamer-binding protein)). Paraspeckle components were found to impact viral infections through various mechanisms, such as induction of antiviral gene expression, IRES-mediated translation, or viral mRNA polyadenylation. A complex involving NEAT1 RNA and paraspeckle proteins was also found to modulate interferon gene transcription after nuclear DNA sensing, through the activation of the cGAS-STING axis. This review aims to provide an overview on how these elements actively contribute to the dynamics of viral infections.
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Affiliation(s)
- Romane Milcamps
- Université catholique de Louvain, de Duve Institute, Brussels, Belgium
| | - Thomas Michiels
- Université catholique de Louvain, de Duve Institute, Brussels, Belgium
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2
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Ronchetti D, Traini V, Silvestris I, Fabbiano G, Passamonti F, Bolli N, Taiana E. The pleiotropic nature of NONO, a master regulator of essential biological pathways in cancers. Cancer Gene Ther 2024; 31:984-994. [PMID: 38493226 PMCID: PMC11257950 DOI: 10.1038/s41417-024-00763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
NONO is a member of the Drosophila behavior/human splicing (DBHS) family of proteins. NONO is a multifunctional protein that acts as a "molecular scaffold" to carry out versatile biological activities in many aspects of gene regulation, cell proliferation, apoptosis, migration, DNA damage repair, and maintaining cellular circadian rhythm coupled to the cell cycle. Besides these physiological activities, emerging evidence strongly indicates that NONO-altered expression levels promote tumorigenesis. In addition, NONO can undergo various post-transcriptional or post-translational modifications, including alternative splicing, phosphorylation, methylation, and acetylation, whose impact on cancer remains largely to be elucidated. Overall, altered NONO expression and/or activities are a common feature in cancer. This review provides an integrated scenario of the current understanding of the molecular mechanisms and the biological processes affected by NONO in different tumor contexts, suggesting that a better elucidation of the pleiotropic functions of NONO in physiology and tumorigenesis will make it a potential therapeutic target in cancer. In this respect, due to the complex landscape of NONO activities and interactions, we highlight caveats that must be considered during experimental planning and data interpretation of NONO studies.
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Affiliation(s)
- Domenica Ronchetti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Valentina Traini
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Ilaria Silvestris
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppina Fabbiano
- Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Passamonti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Niccolò Bolli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Taiana
- Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy.
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Gu L, Yue X, Niu S, Ma J, Liu S, Pan M, Song L, Su Q, Tan Y, Li Y, Chang J. Systematical identification of key genes and regulatory genetic variants associated with prognosis of esophageal squamous cell carcinoma. Mol Carcinog 2024; 63:1013-1023. [PMID: 38380955 DOI: 10.1002/mc.23704] [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: 12/20/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) stands as a highly lethal malignancy characterized by pronounced recurrence and metastasis, resulting in a bleak 5-year survival rate. Despite extensive investigations, encompassing genome-wide association studies, the identification of robust prognostic markers has remained elusive. In this study, leveraging four independent data sets comprising 404 ESCC patients, we conducted a systematic analysis to unveil pivotal genes influencing overall survival. our meta-analysis identified 278 genes significantly associated with ESCC prognosis. Further exploration of the prognostic landscape involved an examination of expression quantitative trait loci for these genes, leading to the identification of six tag single nucleotide polymorphisms predictive of overall survival in a cohort of 904 ESCC patients. Notably, functional annotation spotlighted rs11227223, residing in the enhancer region of nuclear paraspeckle assembly transcript 1 (NEAT1), as a crucial variant likely exerting a substantive biological role. Through a series of biochemistry experiments, we conclusively demonstrated that the rs11227223-T allele, indicative of a poorer prognosis, augmented NEAT1 expression. Our results underscore the substantive role of NEAT1 and its regulatory variant in prognostic predictions for ESCC. This comprehensive analysis not only advances our comprehension of ESCC prognosis but also unveils a potential avenue for targeted interventions, offering promise for enhanced clinical outcomes.
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Affiliation(s)
- Linglong Gu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinying Yue
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Siyuan Niu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jialing Ma
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shasha Liu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Miaoxin Pan
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lina Song
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qianqian Su
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqian Tan
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yueping Li
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Trifault B, Mamontova V, Cossa G, Ganskih S, Wei Y, Hofstetter J, Bhandare P, Baluapuri A, Nieto B, Solvie D, Ade CP, Gallant P, Wolf E, Larsen DH, Munschauer M, Burger K. Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts. Nucleic Acids Res 2024; 52:3050-3068. [PMID: 38224452 PMCID: PMC11014278 DOI: 10.1093/nar/gkae022] [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: 07/13/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024] Open
Abstract
RNA-binding proteins emerge as effectors of the DNA damage response (DDR). The multifunctional non-POU domain-containing octamer-binding protein NONO/p54nrb marks nuclear paraspeckles in unperturbed cells, but also undergoes re-localization to the nucleolus upon induction of DNA double-strand breaks (DSBs). However, NONO nucleolar re-localization is poorly understood. Here we show that the topoisomerase II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-inducible antisense intergenic non-coding RNA (asincRNA) in human cancer cells. Such transcripts originate from distinct nucleolar intergenic spacer regions and form DNA-RNA hybrids to tether NONO to the nucleolus in an RNA recognition motif 1 domain-dependent manner. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of a subset of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signalling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair.
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Affiliation(s)
- Barbara Trifault
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Victoria Mamontova
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Daniel Solvie
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Kaspar Burger
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [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] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
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Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
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6
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Xi H, Ma L, Yin X, Yang P, Li X, Li L. X-linked intellectual developmental disorder with onset of neonatal heart failure: A case report and literature review. Mol Genet Metab Rep 2024; 38:101054. [PMID: 38469091 PMCID: PMC10926201 DOI: 10.1016/j.ymgmr.2024.101054] [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] [Received: 11/15/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 03/13/2024] Open
Abstract
X-linked intellectual developmental disorder is a rare X-linked genetic disease, manifested as heart disease, intellectual impairment, and developmental disorders. We report a male infant who presented with dyspnea after birth. Physical examination on admission revealed poor responsiveness, deep eye sockets, a small mandible, abnormalities of the outer ears, and reduced limb muscle tone. The child was moaning with shortness of breath and a positive three-concave sign without pulmonary rales. The heart sounds were weak with a grade 2/6 diastolic heart murmur. Echocardiography showed an enlarged heart with increased trabeculae in the left ventricular muscle wall. X-linked mental retardation syndrome type 34(MRXS34, OMIM# 300967) was diagnosed after exome sequencing showed a c.1131G > A hemizygous variant in the NONO gene. After timely therapy including respiratory support, cardiac glycosides, and diuresis, the child's condition improved and he was discharged at one month of age. A literature review showed that, to date, 22 live births with X-linked mental retardation have been reported. The NONO-related phenotype can be summarized as a neurological and cardiac developmental disorder, which may be accompanied by multisystem malformations. The present case enriches the knowledge of X-linked intellectual developmental syndromes.
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Affiliation(s)
- Hongmin Xi
- Neonatology Department, The Affiliated Hospital of Qingdao University, NO.16Jiangsu Road, Shinan district, Qingdao 266003, Shandong, China
| | - Lili Ma
- Neonatology Department, The Affiliated Hospital of Qingdao University, NO.16Jiangsu Road, Shinan district, Qingdao 266003, Shandong, China
| | - Xiangyun Yin
- Neonatology Department, The Affiliated Hospital of Qingdao University, NO.16Jiangsu Road, Shinan district, Qingdao 266003, Shandong, China
| | - Ping Yang
- Neonatology Department, The Affiliated Hospital of Qingdao University, NO.16Jiangsu Road, Shinan district, Qingdao 266003, Shandong, China
| | - Xianghong Li
- Neonatology Department, The Affiliated Hospital of Qingdao University, NO.16Jiangsu Road, Shinan district, Qingdao 266003, Shandong, China
| | - Liangliang Li
- Neonatology Department, The Affiliated Hospital of Qingdao University, NO.16Jiangsu Road, Shinan district, Qingdao 266003, Shandong, China
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7
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Schulz D, Feulner L, Santos Rubenich D, Heimer S, Rohrmüller S, Reinders Y, Falchetti M, Wetzel M, Braganhol E, Lummertz da Rocha E, Schäfer N, Stöckl S, Brockhoff G, Wege AK, Fritsch J, Pohl F, Reichert TE, Ettl T, Bauer RJ. Subcellular localization of PD-L1 and cell-cycle-dependent expression of nuclear PD-L1 variants: implications for head and neck cancer cell functions and therapeutic efficacy. Mol Oncol 2024; 18:431-452. [PMID: 38103190 PMCID: PMC10850815 DOI: 10.1002/1878-0261.13567] [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: 08/08/2023] [Revised: 11/24/2023] [Accepted: 12/13/2023] [Indexed: 12/18/2023] Open
Abstract
The programmed cell death 1 ligand 1 (PD-L1)/programmed cell death protein 1 (PD-1) axis is primarily associated with immunosuppression in cytotoxic T lymphocytes (CTLs). However, mounting evidence is supporting the thesis that PD-L1 not only functions as a ligand but mediates additional cellular functions in tumor cells. Moreover, it has been demonstrated that PD-L1 is not exclusively localized at the cellular membrane. Subcellular fractionation revealed the presence of PD-L1 in various cellular compartments of six well-characterized head and neck cancer (HNC) cell lines, including the nucleus. Via Western blotting, we detected PD-L1 in its well-known glycosylated/deglycosylated state at 40-55 kDa. In addition, we detected previously unknown PD-L1 variants with a molecular weight at approximately 70 and > 150 kDa exclusively in nuclear protein fractions. These in vitro findings were confirmed with primary tumor samples from head and neck squamous cell carcinoma (HNSCC) patients. Furthermore, we demonstrated that nuclear PD-L1 variant expression is cell-cycle-dependent. Immunofluorescence staining of PD-L1 in different cell cycle phases of synchronized HNC cells supported these observations. Mechanisms of nuclear PD-L1 trafficking remain less understood; however, proximity ligation assays showed a cell-cycle-dependent interaction of the cytoskeletal protein vimentin with PD-L1, whereas vimentin could serve as a potential shuttle for nuclear PD-L1 transportation. Mass spectrometry after PD-L1 co-immunoprecipitation, followed by gene ontology analysis, indicated interaction of nuclear PD-L1 with proteins involved in DNA remodeling and messenger RNA (mRNA) splicing. Our results in HNC cells suggest a highly complex regulation of PD-L1 and multiple tumor cell-intrinsic functions, independent of immune regulation. These observations bear significant implications for the therapeutic efficacy of immune checkpoint inhibition.
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Affiliation(s)
- Daniela Schulz
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Laura Feulner
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Dominique Santos Rubenich
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
- Postgraduation program in BiosciencesFederal University of Health Sciences from Porto AlegreBrazil
| | - Sina Heimer
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
| | - Sophia Rohrmüller
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Yvonne Reinders
- Leibniz‐Institute for Analytical Sciences, ISAS e.V.DortmundGermany
| | - Marcelo Falchetti
- Department of Microbiology, Immunology and ParasitologyFederal University of Santa CatarinaFlorianópolisBrazil
| | - Martin Wetzel
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Elizandra Braganhol
- Department of Basic Health SciencesFederal University of Health Sciences from Porto AlegreBrazil
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and ParasitologyFederal University of Santa CatarinaFlorianópolisBrazil
| | - Nicole Schäfer
- Department of Orthopaedic Surgery, Experimental OrthopaedicsUniversity of RegensburgGermany
- Department of Orthopaedic Surgery, Experimental Orthopaedics, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Sabine Stöckl
- Department of Orthopaedic Surgery, Experimental OrthopaedicsUniversity of RegensburgGermany
- Department of Orthopaedic Surgery, Experimental Orthopaedics, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
| | - Gero Brockhoff
- Department of Gynecology and ObstetricsUniversity Medical Center RegensburgGermany
| | - Anja K. Wege
- Department of Gynecology and ObstetricsUniversity Medical Center RegensburgGermany
| | - Jürgen Fritsch
- Department of Infection Prevention and Infectious DiseasesUniversity Medical Center RegensburgGermany
| | - Fabian Pohl
- Department of RadiotherapyUniversity Medical Center RegensburgGermany
| | - Torsten E. Reichert
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
| | - Tobias Ettl
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
| | - Richard J. Bauer
- Department of Oral and Maxillofacial SurgeryUniversity Hospital RegensburgGermany
- Department of Oral and Maxillofacial Surgery, Experimental Oral and Maxillofacial Surgery, Center for Medical BiotechnologyUniversity Hospital RegensburgGermany
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Rashid MU, Coombs KM. Chloride Intracellular Channel Protein 1 (CLIC1) Is a Critical Host Cellular Factor for Influenza A Virus Replication. Viruses 2024; 16:129. [PMID: 38257829 PMCID: PMC10819074 DOI: 10.3390/v16010129] [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: 11/25/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
(1) Background: Influenza A Virus (IAV) uses host cellular proteins during replication in host cells. IAV infection causes elevated expression of chloride intracellular channel protein 1 (CLIC1) in lung epithelial cells, but the importance of this protein in IAV replication is unknown. (2) In this study, we determined the role of CLIC1 in IAV replication by investigating the effects of CLIC1 knockdown (KD) on IAV viral protein translation, genomic RNA transcription, and host cellular proteome dysregulation. (3) Results: CLIC1 KD in A549 human lung epithelial cells resulted in a significant decrease in progeny supernatant IAV, but virus protein expression was unaffected. However, a significantly larger number of viral RNAs accumulated in CLIC1 KD cells. Treatment with a CLIC1 inhibitor also caused a significant reduction in IAV replication, suggesting that CLIC1 is an important host factor in IAV replication. SomaScan®, which measures 1322 proteins, identified IAV-induced dysregulated proteins in wild-type cells and in CLIC1 KD cells. The expression of 116 and 149 proteins was significantly altered in wild-type and in CLIC1 KD cells, respectively. A large number of the dysregulated proteins in CLIC1 KD cells were associated with cellular transcription and predicted to be inhibited during IAV replication. (4) Conclusions: This study suggests that CLIC1 is involved in later stages of IAV replication. Further investigation should clarify mechanism(s) for the development of anti-IAV drugs targeting CLIC1 protein.
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Affiliation(s)
- Mahamud-ur Rashid
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Room 543 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg, MB R3E OJ9, Canada
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Room 543 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg, MB R3E OJ9, Canada
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, Room 513, John Buhler Research Centre, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
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Yu D, Huang CJ, Tucker HO. Established and Evolving Roles of the Multifunctional Non-POU Domain-Containing Octamer-Binding Protein (NonO) and Splicing Factor Proline- and Glutamine-Rich (SFPQ). J Dev Biol 2024; 12:3. [PMID: 38248868 PMCID: PMC10801543 DOI: 10.3390/jdb12010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
It has been more than three decades since the discovery of multifunctional factors, the Non-POU-Domain-Containing Octamer-Binding Protein, NonO, and the Splicing Factor Proline- and Glutamine-Rich, SFPQ. Some of their functions, including their participation in transcriptional and posttranscriptional regulation as well as their contribution to paraspeckle subnuclear body organization, have been well documented. In this review, we focus on several other established roles of NonO and SFPQ, including their participation in the cell cycle, nonhomologous end-joining (NHEJ), homologous recombination (HR), telomere stability, childhood birth defects and cancer. In each of these contexts, the absence or malfunction of either or both NonO and SFPQ leads to either genome instability, tumor development or mental impairment.
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Affiliation(s)
- Danyang Yu
- Department of Biology, New York University in Shanghai, Shanghai 200122, China;
| | - Ching-Jung Huang
- Department of Biology, New York University in Shanghai, Shanghai 200122, China;
| | - Haley O. Tucker
- Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA
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Chen Y, Lu Y, Yang L, Ma W, Dong Y, Zhou S, Liu N, Gan W, Li D. LncRNA like NMRK2 mRNA functions as a key molecular scaffold to enhance mitochondrial respiration of NONO-TFE3 rearranged renal cell carcinoma in an NAD + kinase-independent manner. J Exp Clin Cancer Res 2023; 42:252. [PMID: 37770905 PMCID: PMC10537463 DOI: 10.1186/s13046-023-02837-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND NONO-TFE3 rearranged renal cell carcinoma (NONO-TFE3 rRCC) is one of a subtype of TFE3 rRCCs with high malignancy and poor prognosis. Compared with clear cell RCC, NONO-TFE3 rRCC shows a preference for mitochondrial respiration. We recently identified that the upregulation of nicotinamide ribokinase 2 (NMRK2) was associated with enhanced mitochondrial respiration and tumor progression in TFE3 rRCC. METHODS A tumor-bearing mouse model was established to verify the pro-oncogenic effect of NMRK2 on NONO-TFE3 rRCC. Then the expression of NMRK2 RNA and protein was detected in cell lines and patient specimens. The NMRK2 transcripts were Sanger-sequenced and blasted at NCBI website. We constructed dCas13b-HA system to investigate the factors binding with NMRK2 RNA. We also used molecular experiments like RIP-seq, IP-MS, FISH and fluorescence techniques to explore the mechanisms that long non-coding RNA (lncRNA) like NMRK2 mRNA promoted the mitochondrial respiration of NONO-TFE3 rRCC. The efficacy of the combination of shRNA (NMRK2)-lentivirus and metformin on NONO-TFE3 rRCC was assessed by CCK-8 assay. RESULTS In this study, we confirmed that NMRK2 showed transcriptional-translational conflict and functioned as lncRNA like mRNA in the NONO-TFE3 rRCC. Furthermore, we revealed the molecular mechanism that NONO-TFE3 fusion suppressed the translation of NMRK2 mRNA. Most importantly, three major pathways were shown to explain the facilitation effects of lncRNA like NMRK2 mRNA on the mitochondrial respiration of NONO-TFE3 rRCC in an NAD+ kinase-independent manner. Finally, the efficacy of combination of shRNA (NMRK2)-lentivirus and metformin on NONO-TFE3 rRCC was demonstrated to be superior than either agent alone. CONCLUSIONS Overall, our data comprehensively demonstrated the mechanisms for the enhanced mitochondrial respiration in NONO-TFE3 rRCC and proposed lncRNA like NMRK2 mRNA as a therapy target for NONO-TFE3 rRCC.
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Affiliation(s)
- Yi Chen
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Yanwen Lu
- Department of Urology, Affiliated Drum Tower Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Lei Yang
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226000, China
| | - Wenliang Ma
- Department of Urology, Affiliated Drum Tower Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Yuhan Dong
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Shuoming Zhou
- Department of Urology, Affiliated Drum Tower Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Ning Liu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210001, China.
| | - Weidong Gan
- Department of Urology, Affiliated Drum Tower Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210008, China.
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China.
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China.
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Xu X, Wang J, Wang W, Zhang Y, Wan B, Miao Z, Xu X. 5hmC modification regulates R-loop accumulation in response to stress. Front Psychiatry 2023; 14:1198502. [PMID: 37363169 PMCID: PMC10289295 DOI: 10.3389/fpsyt.2023.1198502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
R-loop, an RNA-DNA hybrid structure, arises as a transcriptional by-product and has been implicated in DNA damage and genomic instability when excessive R-loop is accumulated. Although previous study demonstrated that R-loop is associated with ten-eleven translocation (Tet) proteins, which oxidize 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), the sixth base of DNA. However, the relationship between R-loop and DNA 5hmC modification remains unclear. In this study, we found that chronic restraint stress increased R-loop accumulation and decreased 5hmC modification in the prefrontal cortex (PFC) of the stressed mice. The increase of DNA 5hmC modification by vitamin C was accompanied with the decrease of R-loop levels; on the contrary, the decrease of DNA 5hmC modification by a small compound SC-1 increased the R-loop levels, indicating that 5hmC modification inversely regulates R-loop accumulation. Further, we showed that Tet deficiency-induced reduction of DNA 5hmC promoted R-loop accumulation. In addition, Tet proteins immunoprecipitated with Non-POU domain-containing octamer-binding (NONO) proteins. The deficiency of Tet proteins or NONO increased R-loop levels, but silencing Tet proteins and NONO did not further increase the increase accumulation, suggesting that NONO and Tet proteins formed a complex to inhibit R-loop formation. It was worth noting that NONO protein levels decreased in the PFC of stressed mice with R-loop accumulation. The administration of antidepressant fluoxetine to stressed mice increased NONO protein levels, and effectively decreased R-loop accumulation and DNA damage. In conclusion, we showed that DNA 5hmC modification negatively regulates R-loop accumulation by the NONO-Tet complex under stress. Our findings provide potential therapeutic targets for depression.
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Affiliation(s)
- Xingyun Xu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Junjie Wang
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Wenjuan Wang
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Yutong Zhang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Bo Wan
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Zhigang Miao
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Xingshun Xu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Soochow University, Suzhou, Jiangsu, China
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12
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Pruunsild P, Bengtson CP, Loss I, Lohrer B, Bading H. Expression of the primate-specific LINC00473 RNA in mouse neurons promotes excitability and CREB-regulated transcription. J Biol Chem 2023; 299:104671. [PMID: 37019214 DOI: 10.1016/j.jbc.2023.104671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The LINC00473 (Lnc473) gene has previously been shown to be associated with cancer and psychiatric disorders. Its expression is elevated in several types of tumors and decreased in the brains of patients diagnosed with schizophrenia or major depression. In neurons, Lnc473 transcription is strongly responsive to synaptic activity, suggesting a role in adaptive, plasticity-related mechanisms. However, the function of Lnc473 is largely unknown. Here, using a recombinant adeno-associated viral vector, we introduced a primate-specific human Lnc473 RNA into mouse primary neurons. We show that this resulted in a transcriptomic shift comprising downregulation of epilepsy-associated genes and a rise in cAMP response element binding protein (CREB) activity, which was driven by augmented CREB-regulated transcription coactivator 1 (CRTC1) nuclear localization. Moreover, we demonstrate that ectopic Lnc473 expression increased neuronal excitability as well as network excitability. These findings suggest that primates may possess a lineage-specific activity-dependent modulator of CREB-regulated neuronal excitability.
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13
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Jacksi M, Schad E, Buday L, Tantos A. Absence of Scaffold Protein Tks4 Disrupts Several Signaling Pathways in Colon Cancer Cells. Int J Mol Sci 2023; 24:ijms24021310. [PMID: 36674824 PMCID: PMC9861885 DOI: 10.3390/ijms24021310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Tks4 is a large scaffold protein in the EGFR signal transduction pathway that is involved in several cellular processes, such as cellular motility, reactive oxygen species-dependent processes, and embryonic development. It is also implicated in a rare developmental disorder, Frank-ter Haar syndrome. Loss of Tks4 resulted in the induction of an EMT-like process, with increased motility and overexpression of EMT markers in colorectal carcinoma cells. In this work, we explored the broader effects of deletion of Tks4 on the gene expression pattern of HCT116 colorectal carcinoma cells by transcriptome sequencing of wild-type and Tks4 knockout (KO) cells. We identified several protein coding genes with altered mRNA levels in the Tks4 KO cell line, as well as a set of long non-coding RNAs, and confirmed these changes with quantitative PCR on a selected set of genes. Our results show a significant perturbation of gene expression upon the deletion of Tks4, suggesting the involvement of different signal transduction pathways over the well-known EGFR signaling.
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Affiliation(s)
- Mevan Jacksi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Department of Molecular Biology, Semmelweis University Medical School, 1094 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence:
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Jiang D, Jiang C, Sui C, Wu X, Hu Y, Lee C, Cong X, Li J, Du Y, Qi J. Swine NONO is an essential factor to inhibit pseudorabies virus infection. Vet Microbiol 2022; 275:109582. [DOI: 10.1016/j.vetmic.2022.109582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/09/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022]
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15
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Ronchetti D, Favasuli VK, Silvestris I, Todoerti K, Torricelli F, Bolli N, Ciarrocchi A, Taiana E, Neri A. Expression levels of NONO, a nuclear protein primarily involved in paraspeckles function, are associated with several deregulated molecular pathways and poor clinical outcome in multiple myeloma. Discov Oncol 2022; 13:124. [PMID: 36367609 PMCID: PMC9652193 DOI: 10.1007/s12672-022-00582-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
PURPOSE The NONO protein belongs to the multifunctional family of proteins that can bind DNA, RNA and proteins. It is located in the nucleus of most mammalian cells and can affect almost every step of gene regulation. Dysregulation of NONO has been found in many types of cancer; however, data regarding its expression and relevance in Multiple Myeloma (MM) are virtually absent. METHODS We took advantage of a large cohort of MM patients enrolled in the Multiple Myeloma Research Foundation CoMMpass study to elucidate better the clinical and biological relevance of NONO expression in the context of the MM genomic landscape and transcriptome. RESULTS NONO is overexpressed in pathological samples compared to normal controls. In addition, higher NONO expression levels are significant independent prognostic markers of worse clinical outcome in MM. Our results indicate that NONO deregulation may play a pathogenetic role in MM by affecting cell cycle, DNA repair mechanisms, and influencing translation by regulating ribosome biogenesis and assembly. Furthermore, our data suggest NONO involvement in the metabolic reprogramming of glucose metabolism from respiration to aerobic glycolysis, a phenomenon known as the 'Warburg Effect' that supports rapid cancer cell growth, survival, and invasion. CONCLUSION These findings strongly support the need of future investigations for the understanding of the mechanisms of deregulation and the biological role and activity of NONO in MM.
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Affiliation(s)
- Domenica Ronchetti
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
| | - Vanessa Katia Favasuli
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
| | - Ilaria Silvestris
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
| | - Katia Todoerti
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122, Milan, Italy
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Niccolò Bolli
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, 42123, Reggio Emilia, Italy
| | - Elisa Taiana
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122, Milan, Italy.
| | - Antonino Neri
- Scientific Directorate, Azienda USL-IRCCS Reggio Emilia, 42123, Reggio Emilia, Italy
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Ryu JE, Jung TY, Park SH, Park JH, Kim HS. Reversible acetylation modulates p54nrb/NONO-mediated expression of the interleukin 8 gene. Biochem Biophys Res Commun 2022; 622:50-56. [DOI: 10.1016/j.bbrc.2022.06.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
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Trifault B, Mamontova V, Burger K. In vivo Proximity Labeling of Nuclear and Nucleolar Proteins by a Stably Expressed, DNA Damage-Responsive NONO-APEX2 Fusion Protein. Front Mol Biosci 2022; 9:914873. [PMID: 35733943 PMCID: PMC9207311 DOI: 10.3389/fmolb.2022.914873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular stress can induce DNA lesions that threaten the stability of genes. The DNA damage response (DDR) recognises and repairs broken DNA to maintain genome stability. Intriguingly, components of nuclear paraspeckles like the non-POU domain containing octamer-binding protein (NONO) participate in the repair of DNA double-strand breaks (DSBs). NONO is a multifunctional RNA-binding protein (RBP) that facilitates the retention and editing of messenger (m)RNA as well as pre-mRNA processing. However, the role of NONO in the DDR is poorly understood. Here, we establish a novel human U2OS cell line that expresses NONO fused to the engineered ascorbate peroxidase 2 (U2OS:NONO-APEX2-HA). We show that NONO-APEX2-HA accumulates in the nucleolus in response to DNA damage. Combining viability assays, subcellular localisation studies, coimmunoprecipitation experiments and in vivo proximity labeling, we demonstrate that NONO-APEX2-HA is a stably expressed fusion protein that mimics endogenous NONO in terms of expression, localisation and bona fide interactors. We propose that in vivo proximity labeling in U2OS:NONO-APEX2-HA cells is capable for the assessment of NONO interactomes by downstream assays. U2OS:NONO-APEX2-HA cells will likely be a valuable resource for the investigation of NONO interactome dynamics in response to DNA damage and other stimuli.
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Bufton JC, Powers KT, Szeto JYA, Toelzer C, Berger I, Schaffitzel C. Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation. Nucleic Acids Res 2022; 50:5934-5947. [PMID: 35640974 PMCID: PMC9177958 DOI: 10.1093/nar/gkac421] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/01/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
UPF3 is a key nonsense-mediated mRNA decay (NMD) factor required for mRNA surveillance and eukaryotic gene expression regulation. UPF3 exists as two paralogs (A and B) which are differentially expressed depending on cell type and developmental stage and believed to regulate NMD activity based on cellular requirements. UPF3B mutations cause intellectual disability. The underlying molecular mechanisms remain elusive, as many of the mutations lie in the poorly characterized middle-domain of UPF3B. Here, we show that UPF3A and UPF3B share structural and functional homology to paraspeckle proteins comprising an RNA-recognition motif-like domain (RRM-L), a NONA/paraspeckle-like domain (NOPS-L), and extended α-helical domain. These domains are essential for RNA/ribosome-binding, RNA-induced oligomerization and UPF2 interaction. Structures of UPF2's third middle-domain of eukaryotic initiation factor 4G (MIF4GIII) in complex with either UPF3B or UPF3A reveal unexpectedly intimate binding interfaces. UPF3B's disease-causing mutation Y160D in the NOPS-L domain displaces Y160 from a hydrophobic cleft in UPF2 reducing the binding affinity ∼40-fold compared to wildtype. UPF3A, which is upregulated in patients with the UPF3B-Y160D mutation, binds UPF2 with ∼10-fold higher affinity than UPF3B reliant mainly on NOPS-L residues. Our characterization of RNA- and UPF2-binding by UPF3's middle-domain elucidates its essential role in NMD.
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Affiliation(s)
- Joshua C Bufton
- School of Biochemistry, University of Bristol; University Walk, Bristol BS8 1TD, UK
| | - Kyle T Powers
- School of Biochemistry, University of Bristol; University Walk, Bristol BS8 1TD, UK
| | - Jenn-Yeu A Szeto
- School of Biochemistry, University of Bristol; University Walk, Bristol BS8 1TD, UK
| | - Christine Toelzer
- School of Biochemistry, University of Bristol; University Walk, Bristol BS8 1TD, UK
| | - Imre Berger
- School of Biochemistry, University of Bristol; University Walk, Bristol BS8 1TD, UK.,Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
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Compartment-Specific Proximity Ligation Expands the Toolbox to Assess the Interactome of the Long Non-Coding RNA NEAT1. Int J Mol Sci 2022; 23:ijms23084432. [PMID: 35457249 PMCID: PMC9027746 DOI: 10.3390/ijms23084432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 12/23/2022] Open
Abstract
The nuclear paraspeckle assembly transcript 1 (NEAT1) locus encodes two long non-coding (lnc)RNA isoforms that are upregulated in many tumours and dynamically expressed in response to stress. NEAT1 transcripts form ribonucleoprotein complexes with numerous RNA-binding proteins (RBPs) to assemble paraspeckles and modulate the localisation and activity of gene regulatory enzymes as well as a subset of messenger (m)RNA transcripts. The investigation of the dynamic composition of NEAT1-associated proteins and mRNAs is critical to understand the function of NEAT1. Interestingly, a growing number of biochemical and genetic tools to assess NEAT1 interactomes has been reported. Here, we discuss the Hybridisation Proximity (HyPro) labeling technique in the context of NEAT1. HyPro labeling is a recently developed method to detect spatially ordered interactions of RNA-containing nuclear compartments in cultured human cells. After introducing NEAT1 and paraspeckles, we describe the advantages of the HyPro technology in the context of other methods to study RNA interactomes, and review the key findings in mapping NEAT1-associated RNA transcripts and protein binding partners. We further discuss the limitations and potential improvements of HyPro labeling, and conclude by delineating its applicability in paraspeckles-related cancer research.
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The caspase-2 substrate p54nrb exhibits a multifaceted role in tumor cell death susceptibility via gene regulatory functions. Cell Death Dis 2022; 13:386. [PMID: 35444189 PMCID: PMC9021192 DOI: 10.1038/s41419-022-04829-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 12/18/2022]
Abstract
Caspase-2 represents an evolutionary conserved caspase, which plays a role in genotoxic stress-induced apoptosis, ageing-related metabolic changes, and in deleting aneuploid cells in tumors. Genetic deletion of caspase-2 leads to increased tumor susceptibility in vivo. The exact downstream signaling mechanism by which caspase-2 accomplishes its specific tumor suppressor functions is not clear. Caspase-2, uniquely among caspases, resides in the nucleus and other cellular compartments. In this study, we identify a nuclear caspase-2 specific substrate, p54nrb, which is selectively cleaved by caspase-2 at D422, leading to disruption of the C-terminal site, the putative DNA binding region of the protein. P54nrb is an RNA and DNA binding protein, which plays a role in RNA editing, transport, and transcriptional regulation of genes. Overexpression of p54nrb is observed in several human tumor types, such as cervix adenocarcinoma, melanoma, and colon carcinoma. In contrast, the loss of p54nrb in tumor cell lines leads to increased cell death susceptibility and striking decrease in tumorigenic potential. By employing high resolution quantitative proteomics, we demonstrate that the loss/cleavage of p54nrb results in altered expression of oncogenic genes, among which the downregulation of the tumorigenic protease cathepsin-Z and the anti-apoptotic gelsolin can be detected universally across three tumor cell types, including adenocarcinoma, melanoma and colon carcinoma. Finally, we demonstrate that p54nrb interacts with cathepsin-Z and gelsolin DNA, but not RNA. Taken together, this study uncovers a so far not understood mechanism of caspase-2 tumor suppressor function in human tumor cells. ![]()
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SFPQ-ABL1 and BCR-ABL1 utilize different signalling networks to drive B-cell acute lymphoblastic leukaemia. Blood Adv 2022; 6:2373-2387. [PMID: 35061886 PMCID: PMC9006296 DOI: 10.1182/bloodadvances.2021006076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
SFPQ-ABL1 is localized to the nuclear compartment and is a relatively weaker driver of cellular proliferation compared with BCR-ABL1. SFPQ-ABL1 and BCR-ABL1 activate distinct signaling networks, both of which converge on inhibiting apoptosis and driving proliferation.
Philadelphia-like (Ph-like) acute lymphoblastic leukemia (ALL) is a high-risk subtype of B-cell ALL characterized by a gene expression profile resembling Philadelphia chromosome–positive ALL (Ph+ ALL) in the absence of BCR-ABL1. Tyrosine kinase–activating fusions, some involving ABL1, are recurrent drivers of Ph-like ALL and are targetable with tyrosine kinase inhibitors (TKIs). We identified a rare instance of SFPQ-ABL1 in a child with Ph-like ALL. SFPQ-ABL1 expressed in cytokine-dependent cell lines was sufficient to transform cells and these cells were sensitive to ABL1-targeting TKIs. In contrast to BCR-ABL1, SFPQ-ABL1 localized to the nuclear compartment and was a weaker driver of cellular proliferation. Phosphoproteomics analysis showed upregulation of cell cycle, DNA replication, and spliceosome pathways, and downregulation of signal transduction pathways, including ErbB, NF-κB, vascular endothelial growth factor (VEGF), and MAPK signaling in SFPQ-ABL1–expressing cells compared with BCR-ABL1–expressing cells. SFPQ-ABL1 expression did not activate phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling and was associated with phosphorylation of G2/M cell cycle proteins. SFPQ-ABL1 was sensitive to navitoclax and S-63845 and promotes cell survival by maintaining expression of Mcl-1 and Bcl-xL. SFPQ-ABL1 has functionally distinct mechanisms by which it drives ALL, including subcellular localization, proliferative capacity, and activation of cellular pathways. These findings highlight the role that fusion partners have in mediating the function of ABL1 fusions.
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Huang R, Wang S, Zhu R, Xian S, Huang Z, Cheng L, Zhang J. Identification of Key eRNAs for Spinal Cord Injury by Integrated Multinomial Bioinformatics Analysis. Front Cell Dev Biol 2021; 9:728242. [PMID: 34708039 PMCID: PMC8542800 DOI: 10.3389/fcell.2021.728242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Spinal cord injury (SCI) is a severe neurological deficit affecting both young and older people worldwide. The potential role of key enhancer RNAs (eRNAs) in SCI remains elusive, which is a prominent challenge in the trauma repair process. This study aims to investigate the roles of key eRNAs, transcription factors (TFs), signaling pathways, and small-molecule inhibitors in SCI using multi-omics bioinformatics analysis. Methods: Microarray data of peripheral blood mononuclear cell (PBMC) samples from 27 healthy volunteers and 25 chronic-phase SCI patients were retrieved from the Gene Expression Omnibus database. Differentially expressed transcription factors (DETFs), differentially expressed enhancer RNAs (DEeRNAs), and differentially expressed target genes (DETGs) were identified using the Linear Models for Microarray Data (limma) package. Fraction of immune cells was estimated using CIBERSORT algorithm. Gene Set Variation Analysis (GSVA) was applied to identify the downstream signaling pathways. The eRNA regulatory network was constructed based on the correlation results. Connectivity Map (CMap) database was used to find potential drugs for SCI patients. The cellular communication analysis was performed to explore the molecular regulation mechanism of SCI based on single-cell RNA sequencing (scRNA-seq) data. Chromatin immunoprecipitation sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data were used to validate the key regulatory mechanisms. scRNA-seq dataset was used to validate the cell subtype localization of the key eRNAs. Results: In total, 21 DETFs, 24 DEeRNAs, and 829 DETGs were identified. A regulatory network of 13 DETFs, six DEeRNAs, seven DETGs, two hallmark pathways, two immune cells, and six immune pathways was constructed. The link of Splicing factor proline and glutamine rich (SFPQ) (TF) and vesicular overexpressed in cancer prosurvival protein 1 (VOPP1) (eRNA) (R = 0.990, p < 0.001, positive), VOPP1 (eRNA) and epidermal growth factor receptor (EGFR) (target gene) (R = 0.974, p < 0.001, positive), VOPP1, and T helper (Th) cells (R = -0.987, p < 0.001, negative), and VOPP1 and hallmark coagulation (R = 0.937, p < 0.001, positive) was selected. Trichostatin A was considered the best compound target to SCI-related eRNAs (specificity = 0.471, p < 0.001). Conclusion: VOPP1, upregulated by SFPQ, strengthened the transient expression of EGFR. Th cells and coagulation were the potential downstream pathways of VOPP1. This regulatory network and potential inhibitors provide novel diagnostic biomarkers and therapeutic targets for SCI.
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Affiliation(s)
- Runzhi Huang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai, China
| | - Rui Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Shuyuan Xian
- Tongji University School of Medicine, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liming Cheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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23
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SFPQ rescues F508del-CFTR expression and function in cystic fibrosis bronchial epithelial cells. Sci Rep 2021; 11:16645. [PMID: 34404863 PMCID: PMC8371023 DOI: 10.1038/s41598-021-96141-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/05/2021] [Indexed: 01/19/2023] Open
Abstract
Cystic fibrosis (CF) occurs as a result of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which lead to misfolding, trafficking defects, and impaired function of the CFTR protein. Splicing factor proline/glutamine-rich (SFPQ) is a multifunctional nuclear RNA-binding protein (RBP) implicated in the regulation of gene expression pathways and intracellular trafficking. Here, we investigated the role of SFPQ in the regulation of the expression and function of F508del-CFTR in CF lung epithelial cells. We find that the expression of SFPQ is reduced in F508del-CFTR CF epithelial cells compared to WT-CFTR control cells. Interestingly, the overexpression of SFPQ in CF cells increases the expression as well as rescues the function of F508del-CFTR. Further, comprehensive transcriptome analyses indicate that SFPQ plays a key role in activating the mutant F508del-CFTR by modulating several cellular signaling pathways. This is the first report on the role of SFPQ in the regulation of expression and function of F508del-CFTR in CF lung disease. Our findings provide new insights into SFPQ-mediated molecular mechanisms and point to possible novel epigenetic therapeutic targets for CF and related pulmonary diseases.
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24
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Fijen C, Rothenberg E. The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair. DNA Repair (Amst) 2021; 105:103170. [PMID: 34256335 DOI: 10.1016/j.dnarep.2021.103170] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/08/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Formation of biomolecular condensates is increasingly recognized as a mechanism employed by cells to deal with stress and to optimize enzymatic reactions. Recent studies have characterized several DNA repair foci as phase-separated condensates, behaving like liquid droplets. Concomitantly, the apparent importance of long non-coding RNAs and RNA-binding proteins for the repair of double-strand breaks has raised many questions about their exact contribution to the repair process. Here we discuss how RNA molecules can participate in condensate formation and how RNA-binding proteins can act as molecular scaffolds. We furthermore summarize our current knowledge about how properties of condensates can influence the choice of repair pathway (homologous recombination or non-homologous end joining) and identify the open questions in this field of emerging importance.
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Affiliation(s)
- Carel Fijen
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
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25
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The periphilin 1-like BFAR isoform 3 is highly expressed in transcriptionally silent oocytes and involved in RNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119086. [PMID: 34175335 DOI: 10.1016/j.bbamcr.2021.119086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 05/22/2021] [Accepted: 06/19/2021] [Indexed: 11/22/2022]
Abstract
The mouse 3110001I22Rik gene located in the first intron of Bfar is considered as a Bfar variant coding for the BFARv3 protein. However, it differs from other BFAR isoforms and resembles periphilin 1 (PPHLN1) due to its two (Lge1 and serine-rich) conserved domains. We identified the BFARv3/EGFP-interacting proteins by co-immunoprecipitation coupled to mass spectrometry, which revealed 40S ribosomal proteins (RPS3, RPS14, RPS19, RPS25, RPS27), histones (H1.2, H1.4, H3.3C), proteins involved in RNA processing and splicing (SFPQ, SNRPA1, HNRNPA3, NONO, KHDRBS3), calcium signaling (HPCAL1, PTK2B), as well as HSD17B4, GRB14, POSTN, and MYO10. Co-immunoprecipitation revealed that both Lge1 and Ser-rich domains of BFARv3 were necessary for binding to RNA-interacting factors NONO and SFPQ, known to be components of paraspeckles. Reciprocal co-immunoprecipitation and the proximity ligation assay confirmed that both BFARv3 and PPHLN1 could interact with NONO and SFPQ, suggesting a new function for PPHLN1 as well. BFARv3 and its Lge1 or Ser-rich-deficient mutants preferentially localize in the nucleus. We found an accumulation of BFARv3/EGFP (but not its mutated forms) in the nuclear granules, which was enhanced in response to arsenite treatment and ionizing radiation. Although Bfar v3 is expressed ubiquitously in mouse tissues, its expression is the highest in metaphase II oocytes. The BFARv3 interactome suggests its role in RNA metabolism, which is critical for the transcriptionally silent MII oocyte. Mouse BFARv3 has no ortholog in the human genome, thus it may contribute to the differences between these two species observed in oocyte maturation and early embryonic development.
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26
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Cerrito MG, Grassilli E. Identifying Novel Actionable Targets in Colon Cancer. Biomedicines 2021; 9:biomedicines9050579. [PMID: 34065438 PMCID: PMC8160963 DOI: 10.3390/biomedicines9050579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer is the fourth cause of death from cancer worldwide, mainly due to the high incidence of drug-resistance toward classic chemotherapeutic and newly targeted drugs. In the last decade or so, the development of novel high-throughput approaches, both genome-wide and chemical, allowed the identification of novel actionable targets and the development of the relative specific inhibitors to be used either to re-sensitize drug-resistant tumors (in combination with chemotherapy) or to be synthetic lethal for tumors with specific oncogenic mutations. Finally, high-throughput screening using FDA-approved libraries of “known” drugs uncovered new therapeutic applications of drugs (used alone or in combination) that have been in the clinic for decades for treating non-cancerous diseases (re-positioning or re-purposing approach). Thus, several novel actionable targets have been identified and some of them are already being tested in clinical trials, indicating that high-throughput approaches, especially those involving drug re-positioning, may lead in a near future to significant improvement of the therapy for colon cancer patients, especially in the context of a personalized approach, i.e., in defined subgroups of patients whose tumors carry certain mutations.
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27
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Zhang J, Rui Y, Gao M, Wang L, Yan BC. Expression of Long Non-coding RNA RGD1566344 in the Brain Cortex of Male Mice After Focal Cerebral Ischemia-Reperfusion and the Neuroprotective Effect of a Non-coding RNA RGD1566344 Inhibitor. Cell Mol Neurobiol 2021; 41:705-716. [PMID: 32424772 DOI: 10.1007/s10571-020-00877-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
Abstract
Ischemic stroke (IS) remains a major cause of disability and death. The changes in long non-coding RNA (lncRNA) RGD1566344 expression in the mouse cerebral cortex, including the infarct and penumbra regions after IS, are not clear. Less is known about the impact and underlying mechanisms of RGD1566344 in IS. In this study, we found that RGD1566344 levels were elevated in the ischemic infarct and penumbra regions 12 h after middle cerebral artery occlusion/reperfusion (MCAO/R) in male mice and in PC12 cells with oxygen glucose deprivation/reperfusion (OGD/R). The inhibition of RGD1566344 by small interference RNA (siRNA) significantly alleviated apoptosis in OGD/R PC12 cells. In cell transfection, quantitative real-time PCR, and Western blot experiments, we demonstrated the possible interaction of non-POU domain-containing octamer-binding protein (NONO) with RGD1566344. The NONO level in OGD/R PC12 cells was obviously increased after inhibiting the RGD1566344 treatment; subsequently the protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway was activated. This demonstrated the effect of the RGD1566344-NONO-AKT axis on neural protection after IS. These results revealed a new molecular mechanism of lncRNA RGD1566344 inhibitors through targeting NONO/AKT/mTOR signaling to protect against ischemic neuronal injury, providing strong evidence for the development of promising therapeutic strategies against IS.
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Affiliation(s)
- Jie Zhang
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, People's Republic of China
- Department of Neurology, Affiliated Hospital, Yangzhou University, Yangzhou, 225001, People's Republic of China
| | - Yanggang Rui
- Department of Neurology, Xuyi People's Hospital, Huai'an, 211700, People's Republic of China
| | - Manman Gao
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, People's Republic of China
| | - Li Wang
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, People's Republic of China
| | - Bing Chun Yan
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, People's Republic of China.
- Department of Neurology, Affiliated Hospital, Yangzhou University, Yangzhou, 225001, People's Republic of China.
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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28
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Zhang L, Vickers TA, Sun H, Liang XH, Crooke ST. Binding of phosphorothioate oligonucleotides with RNase H1 can cause conformational changes in the protein and alter the interactions of RNase H1 with other proteins. Nucleic Acids Res 2021; 49:2721-2739. [PMID: 33577678 PMCID: PMC7969025 DOI: 10.1093/nar/gkab078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023] Open
Abstract
We recently found that toxic PS-ASOs can cause P54nrb and PSF nucleolar mislocalization in an RNase H1-dependent manner. To better understand the underlying mechanisms of these observations, here we utilize different biochemical approaches to demonstrate that PS-ASO binding can alter the conformations of the bound proteins, as illustrated using recombinant RNase H1, P54nrb, PSF proteins and various isolated domains. While, in general, binding of PS-ASOs or ASO/RNA duplexes stabilizes the conformations of these proteins, PS-ASO binding may also cause the unfolding of RNase H1, including both the hybrid binding domain and the catalytic domain. The extent of conformational change correlates with the binding affinity of PS-ASOs to the proteins. Consequently, PS-ASO binding to RNase H1 induces the interaction of RNase H1 with P54nrb or PSF in a 2′-modification and sequence dependent manner, and toxic PS-ASOs tend to induce more interactions than non-toxic PS-ASOs. PS-ASO binding also enhances the interaction between P54nrb and PSF. However, the interaction between RNase H1 and P32 protein can be disrupted upon binding of PS-ASOs. Together, these results suggest that stronger binding of PS-ASOs can cause greater conformational changes of the bound proteins, subsequently affecting protein–protein interactions. These observations thus provide deeper understanding of the molecular basis of PS-ASO-induced protein mislocalization or degradation observed in cells and advance our understanding of why some PS-ASOs are cytotoxic.
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Affiliation(s)
- Lingdi Zhang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Vickers
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Antisense Drug discovery, Ionis Pharmaceuticals, Inc. Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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29
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Role of promoters in regulating alternative splicing. Gene 2021; 782:145523. [PMID: 33667606 DOI: 10.1016/j.gene.2021.145523] [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: 10/25/2020] [Revised: 12/31/2020] [Accepted: 02/09/2021] [Indexed: 01/19/2023]
Abstract
Alternative splicing (AS) plays a critical role in enhancing proteome complexity in higher eukaryotes. Almost all the multi intron-containing genes undergo AS in humans. Splicing mainly occurs co-transcriptionally, where RNA polymerase II (RNA pol II) plays a crucial role in coordinating transcription and pre-mRNA splicing. Aberrant AS leads to non-functional proteins causative in various pathophysiological conditions such as cancers, neurodegenerative diseases, and muscular dystrophies. Transcription and pre-mRNA splicing are deeply interconnected and can influence each other's functions. Several studies evinced that specific promoters employed by RNA pol II dictate the RNA processing decisions. Promoter-specific recruitment of certain transcriptional factors or transcriptional coactivators influences splicing, and the extent to which these factors affect splicing has not been discussed in detail. Here, in this review, various DNA-binding proteins and their influence on promoter-specific AS are extensively discussed. Besides, this review highlights how the promoter-specific epigenetic changes might regulate AS.
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30
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Malnar M, Rogelj B. SFPQ regulates the accumulation of RNA foci and dipeptide repeat proteins from the expanded repeat mutation in C9orf72. J Cell Sci 2021; 134:jcs.256602. [PMID: 33495278 PMCID: PMC7904093 DOI: 10.1242/jcs.256602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022] Open
Abstract
The expanded GGGGCC repeat mutation in the C9orf72 gene is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The expansion is transcribed to sense and antisense RNA, which form RNA foci and bind cellular proteins. This mechanism of action is considered cytotoxic. Translation of the expanded RNA transcripts also leads to the accumulation of toxic dipeptide repeat proteins (DPRs). The RNA-binding protein splicing factor proline and glutamine rich (SFPQ), which is being increasingly associated with ALS and FTD pathology, binds to sense RNA foci. Here, we show that SFPQ plays an important role in the C9orf72 mutation. Overexpression of SFPQ resulted in higher numbers of both sense and antisense RNA foci and DPRs in transfected human embryonic kidney (HEK) cells. Conversely, reduced SPFQ levels resulted in lower numbers of RNA foci and DPRs in both transfected HEK cells and C9orf72 mutation-positive patient-derived fibroblasts and lymphoblasts. Therefore, we have revealed a role of SFPQ in regulating the C9orf72 mutation that has implications for understanding and developing novel therapeutic targets for ALS and FTD. This article has an associated First Person interview with the first author of the paper. Summary: Expression level modulation of the core paraspeckle protein SFPQ regulates sense and antisense RNA foci and dipeptide repeat protein accumulation in the C9orf72 mutation; SFPQ could be a therapeutic target in C9orf72 ALS and FTD.
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Affiliation(s)
- Mirjana Malnar
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia.,Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia .,Biomedical Research Institute, 1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Engineering, University of Ljubljana, 1000 Ljubljana, Slovenia
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31
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Liang S, Takahashi H, Hirose T, Kuramitsu Y, Hatakeyama S, Yoshiyama H, Wang R, Hamada JI, Iizasa H. NONO Is a Negative Regulator of SOX2 Promoter. Cancer Genomics Proteomics 2021; 17:359-367. [PMID: 32576581 DOI: 10.21873/cgp.20195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND/AIM Sex determining region Y (SRY)-box 2 (SOX2) is a transcription factor essential for the maintenance of proliferation and self-renewal of cancer stem cells and is associated with breast cancer initiation. Regulation of cancer stem cell plasticity by SOX2 requires both positive and negative SOX2 transcription factors, but the negative regulator is still largely unknown. MATERIALS AND METHODS SOX2 promoter-binding proteins were identified by liquid chromatography-mass spectrometry/mass spectrometry, luciferase assay, and chromatin immunoprecipitation. The effects of one such transcription factor on SOX2 expression was investigated by knockdown and overexpression experiments. RESULTS Non-POU domain-containing octamer-binding protein (NONO) (also known as 54-kDa nuclear RNA-binding protein, P54NRB) was identified as a SOX2 promoter-binding protein and a negative regulator of SOX2 expression. Its activity was controlled by its coiled-coil domain and the C-terminal domain. CONCLUSION These results suggest that NONO acts as a key regulator of SOX2 transcription through the repression of SOX2 promoter activity in breast cancer cells.
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Affiliation(s)
- Shanshan Liang
- The Key Laboratory of Biomarker High-throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Oncology Department, Affiliated Zhongshan Hospital of Dalian University, Dalian, P.R. China.,Department of Microbiology, Faculty of Medicine, Shimane University, Shimane, Japan.,Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Hidehisa Takahashi
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Japan.,Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama City University Graduate School of Medical Science, Yokohama, Japan
| | - Tetsuro Hirose
- Division of RNA Bio-function, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yasuhiro Kuramitsu
- Health Science University of Hokkaido School of Nursing & Social Services, Hokkaido, Japan
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hironori Yoshiyama
- Department of Microbiology, Faculty of Medicine, Shimane University, Shimane, Japan
| | - Ruoyu Wang
- The Key Laboratory of Biomarker High-throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Oncology Department, Affiliated Zhongshan Hospital of Dalian University, Dalian, P.R. China
| | - Jun-Ichi Hamada
- Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan .,Health Science University of Hokkaido School of Nursing & Social Services, Hokkaido, Japan
| | - Hisashi Iizasa
- Department of Microbiology, Faculty of Medicine, Shimane University, Shimane, Japan .,Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
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32
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Sun H, Han L, Zhang X, Hao X, Zhou X, Pan R, Zhang H, He Y. Case Report: Characterization of a Novel NONO Intronic Mutation in a Fetus With X-Linked Syndromic Mental Retardation-34. Front Genet 2020; 11:593688. [PMID: 33304389 PMCID: PMC7701169 DOI: 10.3389/fgene.2020.593688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/28/2020] [Indexed: 11/13/2022] Open
Abstract
Background The NONO gene is located on chromosome Xq13.1 and encodes a nuclear protein involved in RNA synthesis, transcriptional regulation, and DNA repair. Hemizygous variants in NONO have been reported to cause mental retardation, X-linked, syndromic 34 (MRXS34) in males. Due to the scarcity of clinical reports, the clinical characteristics and mutation spectrum of NONO-related disorder have not been entirely determined. Methods We reported a fetus with hypoplastic left heart syndrome, performed a comprehensive genotyping examination, including copy-number variation sequencing and whole-exome sequencing, and screened for the genetic abnormality. We also conducted an in vitro mini-gene splicing assay to demonstrate the predicted deleterious effects of an intronic variant of NONO. Results Exome sequencing identified a novel intronic variant (c.154 + 9A > G) in intron 4 of the NONO gene (NM_001145408.1). It was predicted to insert 4 bp of intron 4 into the mature mRNA. Minigene assay revealed that the c.154 + 9A > G variant caused the activation of the intronic cryptic splice site and 4 bp insertion (c.154_155ins GTGT) in mature mRNA. Literature review shows that cardiac phenotype, including left ventricular non-compaction cardiomyopathy and congenital heart disease, are consistent features of MRXS34. Conclusion This study enlarges the mutation spectrum of NONO, further expands hypoplastic left heart syndrome to the phenotype of MRXS34 and points out the importance of intronic sequence analysis and the need for integrative functional studies in the interpretation of sequence variants.
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Affiliation(s)
- Hairui Sun
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Key Laboratory of Medical Engineering for Cardiovascular Disease, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Maternal-Fetal Medicine and Fetal Heart Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Lu Han
- Key Laboratory of Medical Engineering for Cardiovascular Disease, Ministry of Education, Beijing, China.,Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xiaoshan Zhang
- Affiliated Hospital of Innermongolia Medical University, Hohhot, China
| | - Xiaoyan Hao
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Maternal-Fetal Medicine and Fetal Heart Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Xiaoxue Zhou
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Maternal-Fetal Medicine and Fetal Heart Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | | | - Hongjia Zhang
- Key Laboratory of Medical Engineering for Cardiovascular Disease, Ministry of Education, Beijing, China.,Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yihua He
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Key Laboratory of Medical Engineering for Cardiovascular Disease, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Maternal-Fetal Medicine and Fetal Heart Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
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33
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NEAT1 and Paraspeckles in Cancer Development and Chemoresistance. Noncoding RNA 2020; 6:ncrna6040043. [PMID: 33143162 PMCID: PMC7712271 DOI: 10.3390/ncrna6040043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNA were previously thought to be biologically useless molecules arising from simple transcriptional noise. These are now known to be an integral part of cellular biology and pathology. The wide range of RNA molecules have a diverse range of structures, functions, and mechanisms of action. However, structural long non-coding RNAs (lncRNAs) are a particular class of ncRNA that are proving themselves more and more important in cellular biology, as the exact structures that such RNAs form and stabilise become more understood. Nuclear Enriched Abundant Transcript 1 (NEAT1) is a specific structural RNA emerging as a critical component in the progress and development of cancer. NEAT1 forms part of multiple biological pathways, acting through a diverse group of mechanisms. The most important of these is the formation of the paraspeckle, through which it can influence the stability of a tumour to develop resistance to drugs. This review will thus cover the range of effects by which NEAT1 interacts with cancer progression in order to describe the various roles of NEAT1 in chemoresistance, as well as to identify drug targets that protein research alone could not provide.
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34
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Guo R, Chen Y, Borgard H, Jijiwa M, Nasu M, He M, Deng Y. The Function and Mechanism of Lipid Molecules and Their Roles in The Diagnosis and Prognosis of Breast Cancer. Molecules 2020; 25:E4864. [PMID: 33096860 PMCID: PMC7588012 DOI: 10.3390/molecules25204864] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Lipids are essential components of cell structure and play important roles in signal transduction between cells and body metabolism. With the continuous development and innovation of lipidomics technology, many studies have shown that the relationship between lipids and cancer is steadily increasing, involving cancer occurrence, proliferation, migration, and apoptosis. Breast cancer has seriously affected the safety and quality of life of human beings worldwide and has become a significant public health problem in modern society, with an especially high incidence among women. Therefore, the issue has inspired scientific researchers to study the link between lipids and breast cancer. This article reviews the research progress of lipidomics, the biological characteristics of lipid molecules, and the relationship between some lipids and cancer drug resistance. Furthermore, this work summarizes the lipid molecules related to breast cancer diagnosis and prognosis, and then it clarifies their impact on the occurrence and development of breast cancer The discussion revolves around the current research hotspot long-chain non-coding RNAs (lncRNAs), summarizes and explains their impact on tumor lipid metabolism, and provides more scientific basis for future cancer research studies.
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Affiliation(s)
- Rui Guo
- School of Public Health, Guangxi Medical University, 22 Shuangyong Rd, Qingxiu District, Nanning 530021, China;
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
| | - Yu Chen
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa,1955 East West Road, Agricultural Sciences, Honolulu, HI 96822, USA
| | - Heather Borgard
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
| | - Mayumi Jijiwa
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
| | - Min He
- School of Public Health, Guangxi Medical University, 22 Shuangyong Rd, Qingxiu District, Nanning 530021, China;
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, 651 Ilalo Street, Honolulu, HI 96813, USA; (Y.C.); (H.B.); (M.J.); (M.N.)
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The Emerging Role of the RNA-Binding Protein SFPQ in Neuronal Function and Neurodegeneration. Int J Mol Sci 2020; 21:ijms21197151. [PMID: 32998269 PMCID: PMC7582472 DOI: 10.3390/ijms21197151] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are a class of proteins known for their diverse roles in RNA biogenesis, from regulating transcriptional processes in the nucleus to facilitating translation in the cytoplasm. With higher demand for RNA metabolism in the nervous system, RBP misregulation has been linked to a wide range of neurological and neurodegenerative diseases. One of the emerging RBPs implicated in neuronal function and neurodegeneration is splicing factor proline- and glutamine-rich (SFPQ). SFPQ is a ubiquitous and abundant RBP that plays multiple regulatory roles in the nucleus such as paraspeckle formation, DNA damage repair, and various transcriptional regulation processes. An increasing number of studies have demonstrated the nuclear and also cytoplasmic roles of SFPQ in neurons, particularly in post-transcriptional regulation and RNA granule formation. Not surprisingly, the misregulation of SFPQ has been linked to pathological features shown by other neurodegenerative disease-associated RBPs such as aberrant RNA splicing, cytoplasmic mislocalization, and aggregation. In this review, we discuss recent findings on the roles of SFPQ with a particular focus on those in neuronal development and homeostasis as well as its implications in neurodegenerative diseases.
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Girbes Minguez M, Wolters-Eisfeld G, Lutz D, Buck F, Schachner M, Kleene R. The cell adhesion molecule L1 interacts with nuclear proteins via its intracellular domain. FASEB J 2020; 34:9869-9883. [PMID: 32533745 DOI: 10.1096/fj.201902242r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 02/05/2023]
Abstract
Proteolytic cleavage of the cell adhesion molecule L1 (L1) in brain tissue and in cultured cerebellar neurons results in the generation and nuclear import of a 30 kDa fragment comprising most of L1's C-terminal, intracellular domain. In search of molecules that interact with this domain, we performed affinity chromatography with the recombinant intracellular L1 domain and a nuclear extract from mouse brains, and identified potential nuclear L1 binding partners involved in transcriptional regulation, RNA processing and transport, DNA repair, chromatin remodeling, and nucleocytoplasmic transport. By co-immunoprecipitation and enzyme-linked immunosorbent assay using recombinant proteins, we verified the direct interaction between L1 and the nuclear binding partners non-POU domain containing octamer-binding protein and splicing factor proline/glutamine-rich. The proximity ligation assay confirmed this close interaction in cultures of cerebellar granule cells. Our findings suggest that L1 fragments regulate multiple nuclear functions in the nervous system. We discuss possible physiological and pathological roles of these interactions in regulation of chromatin structure, gene expression, RNA processing, and DNA repair.
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Affiliation(s)
- Maria Girbes Minguez
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gerrit Wolters-Eisfeld
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - David Lutz
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Buck
- Zentrum für Diagnostik, Institut für Klinische Chemie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Melitta Schachner
- Center for Neuroscience, Shantou University Medical College, Shantou, China
- Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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Emerging Contribution of PancRNAs in Cancer. Cancers (Basel) 2020; 12:cancers12082035. [PMID: 32722129 PMCID: PMC7464463 DOI: 10.3390/cancers12082035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
“Cancer” includes a heterogeneous group of diseases characterized by abnormal growth beyond natural boundaries. Neoplastic transformation of cells is orchestrated by multiple molecular players, including oncogenic transcription factors, epigenetic modifiers, RNA binding proteins, and coding and noncoding transcripts. The use of computational methods for global and quantitative analysis of RNA processing regulation provides new insights into the genomic and epigenomic features of the cancer transcriptome. In particular, noncoding RNAs are emerging as key molecular players in oncogenesis. Among them, the promoter-associated noncoding RNAs (pancRNAs) are noncoding transcripts acting in cis to regulate their host genes, including tumor suppressors and oncogenes. In this review, we will illustrate the role played by pancRNAs in cancer biology and will discuss the latest findings that connect pancRNAs with cancer risk and progression. The molecular mechanisms involved in the function of pancRNAs may open the path to novel therapeutic opportunities, thus expanding the repertoire of targets to be tested as anticancer agents in the near future.
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Qin H, Ni H, Liu Y, Yuan Y, Xi T, Li X, Zheng L. RNA-binding proteins in tumor progression. J Hematol Oncol 2020; 13:90. [PMID: 32653017 PMCID: PMC7353687 DOI: 10.1186/s13045-020-00927-w] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/25/2020] [Indexed: 02/08/2023] Open
Abstract
RNA-binding protein (RBP) has a highly dynamic spatiotemporal regulation process and important biological functions. They are critical to maintain the transcriptome through post-transcriptionally controlling the processing and transportation of RNA, including regulating RNA splicing, polyadenylation, mRNA stability, mRNA localization, and translation. Alteration of each process will affect the RNA life cycle, produce abnormal protein phenotypes, and thus lead to the occurrence and development of tumors. Here, we summarize RBPs involved in tumor progression and the underlying molecular mechanisms whereby they are regulated and exert their effects. This analysis is an important step towards the comprehensive characterization of post-transcriptional gene regulation involved in tumor progression.
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Affiliation(s)
- Hai Qin
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Haiwei Ni
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yichen Liu
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yaqin Yuan
- Guizhou Medical Device Testing Center, Guiyang, 550004, Guizhou, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China.
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
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Taiana E, Ronchetti D, Todoerti K, Nobili L, Tassone P, Amodio N, Neri A. LncRNA NEAT1 in Paraspeckles: A Structural Scaffold for Cellular DNA Damage Response Systems? Noncoding RNA 2020; 6:ncrna6030026. [PMID: 32630183 PMCID: PMC7549348 DOI: 10.3390/ncrna6030026] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/25/2020] [Accepted: 06/28/2020] [Indexed: 12/13/2022] Open
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect different cellular functions, including stress response. Furthermore, increasing evidence supports the crucial role of NEAT1 and essential structural proteins of PSs (PSPs) in the regulation of the DNA damage repair (DDR) system. This review aims to provide an overview of the current knowledge on the involvement of NEAT1 and PSPs in DDR, which might strengthen the rationale underlying future NEAT1-based therapeutic options in tumor and neurodegenerative diseases.
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Affiliation(s)
- Elisa Taiana
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
- Correspondence: (E.T.); (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.)
| | - Domenica Ronchetti
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
| | - Katia Todoerti
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
| | - Lucia Nobili
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (P.T.); (N.A.)
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (P.T.); (N.A.)
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
- Correspondence: (E.T.); (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.)
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Crooke ST, Vickers TA, Liang XH. Phosphorothioate modified oligonucleotide-protein interactions. Nucleic Acids Res 2020; 48:5235-5253. [PMID: 32356888 PMCID: PMC7261153 DOI: 10.1093/nar/gkaa299] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antisense oligonucleotides (ASOs) interact with target RNAs via hybridization to modulate gene expression through different mechanisms. ASO therapeutics are chemically modified and include phosphorothioate (PS) backbone modifications and different ribose and base modifications to improve pharmacological properties. Modified PS ASOs display better binding affinity to the target RNAs and increased binding to proteins. Moreover, PS ASO protein interactions can affect many aspects of their performance, including distribution and tissue delivery, cellular uptake, intracellular trafficking, potency and toxicity. In this review, we summarize recent progress in understanding PS ASO protein interactions, highlighting the proteins with which PS ASOs interact, the influence of PS ASO protein interactions on ASO performance, and the structure activity relationships of PS ASO modification and protein interactions. A detailed understanding of these interactions can aid in the design of safer and more potent ASO drugs, as illustrated by recent findings that altering ASO chemical modifications dramatically improves therapeutic index.
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41
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Zhang H, Brown RD, Stenmark KR, Hu CJ. RNA-Binding Proteins in Pulmonary Hypertension. Int J Mol Sci 2020; 21:ijms21113757. [PMID: 32466553 PMCID: PMC7312837 DOI: 10.3390/ijms21113757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
Pulmonary hypertension (PH) is a life-threatening disease characterized by significant vascular remodeling and aberrant expression of genes involved in inflammation, apoptosis resistance, proliferation, and metabolism. Effective therapeutic strategies are limited, as mechanisms underlying PH pathophysiology, especially abnormal expression of genes, remain unclear. Most PH studies on gene expression have focused on gene transcription. However, post-transcriptional alterations have been shown to play a critical role in inflammation and metabolic changes in diseases such as cancer and systemic cardiovascular diseases. In these diseases, RNA-binding proteins (RBPs) have been recognized as important regulators of aberrant gene expression via post-transcriptional regulation; however, their role in PH is less clear. Identifying RBPs in PH is of great importance to better understand PH pathophysiology and to identify new targets for PH treatment. In this manuscript, we review the current knowledge on the role of dysregulated RBPs in abnormal mRNA gene expression as well as aberrant non-coding RNA processing and expression (e.g., miRNAs) in PH.
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Affiliation(s)
- Hui Zhang
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - R. Dale Brown
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - Kurt R. Stenmark
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - Cheng-Jun Hu
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
- Department of Craniofacial Biology School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence: ; Tel.: +1-303-724-4576; Fax: +1-303-724-4580
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Zamani-Ahmadmahmudi M, Nassiri SM, Soltaninezhad F. Development of an RNA sequencing-based prognostic gene signature in multiple myeloma. Br J Haematol 2020; 192:310-321. [PMID: 32410217 DOI: 10.1111/bjh.16744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 01/08/2023]
Abstract
Several prognostic gene signatures have been developed to predict the clinical outcome in patients with multiple myeloma (MM). The most salient disadvantage of the previous signatures is their non-reproducibility in external datasets. Given the disadvantages and the superiority of RNA sequencing over microarrays in transcriptome profiling to produce more reliable outputs, we sought to develop a reproducible RNA sequencing-based prognostic gene signature for MM. Genes significantly associated with survival were detected in The Cancer Genome Atlas (TCGA) MM RNA sequencing dataset (MMRF-CoMMpass) (n = 412) through a strict pipeline containing four rigid filters. The reproducibility of the selected genes was checked in an independent dataset (GSE24080), containing 559 newly diagnosed patients with MM. The RNA sequencing-based prognostic signature was reconstructed based on the final genes in the training dataset (MMRF-CoMMpass) and externally validated in five independent datasets (i.e. GSE2658, GSE13624, GSE9782, GSE6477 and GSE57317), containing 1461 MM cases. The RNA sequencing-based signature was reconstructed using finally five reproducible genes: CCT2, CKS1B, PRKDC, NONO and UBE2A. This signature was able to robustly discriminate between low- and high-risk patients in both training and validation datasets (Ps ≤ 0·001). Our signature was also independent of and more powerful than the routine MM prognostic factors (i.e. β2-microglobulin, albumin, age and sex) (Ps ≤ 0·01). Treatment regimens had no effect on RNA sequencing-based signature insofar as this signature succeeded in predicting the clinical outcome in various treatment groups (Ps ≤ 0·001).
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Affiliation(s)
- Mohamad Zamani-Ahmadmahmudi
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Seyed Mahdi Nassiri
- Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Soltaninezhad
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
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Sebbag-Sznajder N, Brody Y, Hochberg-Laufer H, Shav-Tal Y, Sperling J, Sperling R. Dynamic Supraspliceosomes Are Assembled on Different Transcripts Regardless of Their Intron Number and Splicing State. Front Genet 2020; 11:409. [PMID: 32499811 PMCID: PMC7243799 DOI: 10.3389/fgene.2020.00409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Splicing and alternative splicing of pre-mRNA are key sources in the formation of diversity in the human proteome. These processes have a central role in the regulation of the gene expression pathway. Yet, how spliceosomes are assembled on a multi-intronic pre-mRNA is at present not well understood. To study the spliceosomes assembled in vivo on transcripts with variable number of introns, we examined a series of three related transcripts derived from the β-globin gene, where two transcript types contained increasing number of introns, while one had only an exon. Each transcript had multiple MS2 sequence repeats that can be bound by the MS2 coat protein. Using our protocol for isolation of endogenous spliceosomes under native conditions from cell nuclei, we show that all three transcripts are found in supraspliceosomes – 21 MDa dynamic complexes, sedimenting at 200S in glycerol gradients, and composed of four native spliceosomes connected by the transcript. Affinity purification of complexes assembled on the transcript with most introns (termed E6), using the MS2 tag, confirmed the assembly of E6 in supraspliceosomes with components such as Sm proteins and PSF. Furthermore, splicing inhibition by spliceostatin A did not inhibit the assembly of supraspliceosomes on the E6 transcript, yet increased the percentage of E6 pre-mRNA supraspliceosomes. These findings were corroborated in intact cells, using RNA FISH to detect the MS2-tagged E6 mRNA, together with GFP-tagged splicing factors, showing the assembly of splicing factors SRSF2, U1-70K, and PRP8 onto the E6 transcripts under normal conditions and also when splicing was inhibited. This study shows that different transcripts with different number of introns, or lacking an intron, are assembled in supraspliceosomes even when splicing is inhibited. This assembly starts at the site of transcription and can continue during the life of the transcript in the nucleoplasm. This study further confirms the dynamic and universal nature of supraspliceosomes that package RNA polymerase II transcribed pre-mRNAs into complexes composed of four native spliceosomes connected by the transcript, independent of their length, number of introns, or splicing state.
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Affiliation(s)
| | - Yehuda Brody
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Hodaya Hochberg-Laufer
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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Vickers TA, Rahdar M, Prakash TP, Crooke ST. Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1. Nucleic Acids Res 2020; 47:10865-10880. [PMID: 31495875 PMCID: PMC6846478 DOI: 10.1093/nar/gkz771] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
The rapid RNase H1-dependent mislocalization of heterodimer proteins P54nrb and PSF to nucleoli is an early event in the pathway that explains the effects of most toxic phosphorothioate ASOs (PS-ASOs). Using a recently developed NanoLuciferace (NLuc)-based structural complementation reporter system which allows us to observe ASO/protein interactions in real time in live cells, we have determined that safe and toxic PS-ASOs associate with these proteins with kinetics and impact on subcellular localization that differ. Toxic PS-ASOs interact in a complex that includes RNase H1, P54nrb and PSF; but RNase H1/P54nrb complexes were observed in only the cells treated with toxic, but not safe PS-ASOs. In addition, experiments performed in vitro suggest that RNA is also a required component of the complex. The protein–protein interaction between P54nrb and RNase H1 requires the spacer region of RNAse H1, while the P54nrb core domains are required for association with RNase H1. In addition, we have determined that PS-ASOs bind P54nrb via RRM1 and RRM2, while they bind RNase H1 primarily via the hybrid binding domain, however catalytic domain interactions also contribute to overall affinity. These ASO–protein interactions are highly influenced by the chemistry of the PS-ASO binding environment, however little correlation between affinity for specific proteins and PS-ASO toxicity was observed.
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Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Meghdad Rahdar
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Thazha P Prakash
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
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Pellarin I, Dall'Acqua A, Gambelli A, Pellizzari I, D'Andrea S, Sonego M, Lorenzon I, Schiappacassi M, Belletti B, Baldassarre G. Splicing factor proline- and glutamine-rich (SFPQ) protein regulates platinum response in ovarian cancer-modulating SRSF2 activity. Oncogene 2020; 39:4390-4403. [PMID: 32332923 PMCID: PMC7253352 DOI: 10.1038/s41388-020-1292-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/23/2020] [Accepted: 03/31/2020] [Indexed: 11/09/2022]
Abstract
In epithelial ovarian cancer (EOC), response to platinum (PT)-based chemotherapy dictates subsequent treatments and predicts patients' prognosis. Alternative splicing is often deregulated in human cancers and can be altered by chemotherapy. Whether and how changes in alternative splicing regulation could impact on the response of EOC to PT-based chemotherapy is still not clarified. We identified the splicing factor proline and glutamine rich (SFPQ) as a critical mediator of response to PT in an unbiased functional genomic screening in EOC cells and, using a large cohort of primary and recurrent EOC samples, we observed that it is frequently overexpressed in recurrent PT-treated samples and that its overexpression correlates with PT resistance. At mechanistic level, we show that, under PT treatment, SFPQ, in complex with p54nrb, binds and regulates the activity of the splicing factor SRSF2. SFPQ/p54nrb complex decreases SRSF2 binding to caspase-9 RNA, favoring the expression of its alternative spliced antiapoptotic form. As a consequence, SFPQ/p54nrb protects cells from PT-induced death, eventually contributing to chemoresistance. Overall, our work unveils a previously unreported SFPQ/p54nrb/SRSF2 pathway that in EOC cells plays a central role in regulating alternative splicing and PT-induced apoptosis and that could result in the design of new possible ways of intervention to overcome PT resistance.
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Affiliation(s)
- Ilenia Pellarin
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Alessandra Dall'Acqua
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Alice Gambelli
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Ilenia Pellizzari
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Sara D'Andrea
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Maura Sonego
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Ilaria Lorenzon
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Monica Schiappacassi
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy.
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Pinto-Díez C, Ferreras-Martín R, Carrión-Marchante R, González VM, Martín ME. Deeping in the Role of the MAP-Kinases Interacting Kinases (MNKs) in Cancer. Int J Mol Sci 2020; 21:ijms21082967. [PMID: 32340135 PMCID: PMC7215568 DOI: 10.3390/ijms21082967] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 02/05/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK)-interacting kinases (MNKs) are involved in oncogenic transformation and can promote metastasis and tumor progression. In human cells, there are four MNKs isoforms (MNK1a/b and MNK2a/b), derived from two genes by alternative splicing. These kinases play an important role controlling the expression of specific proteins involved in cell cycle, cell survival and cell motility via eukaryotic initiation factor 4E (eIF4E) regulation, but also through other substrates such as heterogeneous nuclear ribonucleoprotein A1, polypyrimidine tract-binding protein-associated splicing factor and Sprouty 2. In this review, we provide an overview of the role of MNK in human cancers, describing the studies conducted to date to elucidate the mechanism involved in the action of MNKs, as well as the development of MNK inhibitors in different hematological cancers and solid tumors.
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Feng P, Li L, Deng T, Liu Y, Ling N, Qiu S, Zhang L, Peng B, Xiong W, Cao L, Zhang L, Ye M. NONO and tumorigenesis: More than splicing. J Cell Mol Med 2020; 24:4368-4376. [PMID: 32168434 PMCID: PMC7176863 DOI: 10.1111/jcmm.15141] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/05/2020] [Accepted: 02/19/2020] [Indexed: 12/24/2022] Open
Abstract
The non-POU domain-containing octamer-binding protein NONO/p54nrb , which belongs to the Drosophila behaviour/human splicing (DBHS) family, is a multifunctional nuclear protein rarely functioning alone. Emerging solid evidences showed that NONO engages in almost every step of gene regulation, including but not limited to mRNA splicing, DNA unwinding, transcriptional regulation, nuclear retention of defective RNA and DNA repair. NONO is involved in many biological processes including cell proliferation, apoptosis, migration and DNA damage repair. Dysregulation of NONO has been found in many types of cancer. In this review, we summarize the current and fast-growing knowledge about the regulation of NONO, its biological function and implications in tumorigenesis and cancer progression. Overall, significant findings about the roles of NONO have been made, which might make NONO to be a new biomarker or/and a possible therapeutic target for cancers.
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Affiliation(s)
- Peifu Feng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Ling Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Tanggang Deng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Yan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Neng Ling
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Siyuan Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Lin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Bo Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Wei Xiong
- Ophthalmology and Eye Research Center, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Lanqin Cao
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, China
| | - Lei Zhang
- Department of Nephrology, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
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Pisani G, Baron B. Nuclear paraspeckles function in mediating gene regulatory and apoptotic pathways. Noncoding RNA Res 2019; 4:128-134. [PMID: 32072080 PMCID: PMC7012776 DOI: 10.1016/j.ncrna.2019.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 12/26/2022] Open
Abstract
The nucleus is an essential hub for the regulation of gene expression in both spatial and temporal contexts. The complexity required to manage such a feat has resulted in the evolution of multiple sub-structures in the nucleus such as the nucleolus, small cajal bodies and nuclear stress bodies. The paraspeckle is another membraneless structure composed of RNA elements, primarily the long non-coding RNA (lncRNA) Nuclear Enriched Abundant Transcript 1 (NEAT1), associated with RNA binding proteins (RBPs). The paraspeckle is showing signs of being involved in various aspects of gene regulation and its role in many pathologies from cancer to viral infection is beginning to be addressed. Research into paraspeckle-directed gene regulation highlights the increase in the appreciation of the biological significance of non-coding RNA (ncRNA). This review will thus cover the basis of how a structure as large as a paraspeckle forms along with its functions. It will also explore how it effects pathological conditions and can be used in clinical intervention, with special emphasis on the multitude of methods utilised by paraspeckles for apoptotic regulation.
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Affiliation(s)
| | - Byron Baron
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, MSD2080, Malta
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Liu X, Zheng J, Qi S, Shen Q. NONO Regulates Cortical Neuronal Migration and Postnatal Neuronal Maturation. Neurosci Bull 2019; 35:1097-1101. [PMID: 31502212 DOI: 10.1007/s12264-019-00428-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/17/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Xiaoqing Liu
- Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tongji Hospital, Brain and Spinal Cord Innovative Research Center, School of Life Sciences and Technology, Frontier Science Research Center for Stem Cells, Ministry of Education, Tongji University, Shanghai, 200092, China
| | - Jiangli Zheng
- Tongji Hospital, Brain and Spinal Cord Innovative Research Center, School of Life Sciences and Technology, Frontier Science Research Center for Stem Cells, Ministry of Education, Tongji University, Shanghai, 200092, China.,Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - Shaojun Qi
- Tongji Hospital, Brain and Spinal Cord Innovative Research Center, School of Life Sciences and Technology, Frontier Science Research Center for Stem Cells, Ministry of Education, Tongji University, Shanghai, 200092, China.,Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - Qin Shen
- Tongji Hospital, Brain and Spinal Cord Innovative Research Center, School of Life Sciences and Technology, Frontier Science Research Center for Stem Cells, Ministry of Education, Tongji University, Shanghai, 200092, China.
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Knapp B, Roedig J, Boldt K, Krzysko J, Horn N, Ueffing M, Wolfrum U. Affinity proteomics identifies novel functional modules related to adhesion GPCRs. Ann N Y Acad Sci 2019; 1456:144-167. [PMID: 31441075 DOI: 10.1111/nyas.14220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/08/2019] [Accepted: 07/25/2019] [Indexed: 01/04/2023]
Abstract
Adhesion G protein-coupled receptors (ADGRs) have recently become a target of intense research. Their unique protein structure, which consists of a G protein-coupled receptor combined with long adhesive extracellular domains, suggests a dual role in cell signaling and adhesion. Despite considerable progress in the understanding of ADGR signaling over the past years, the knowledge about ADGR protein networks is still limited. For most receptors, only a few interaction partners are known thus far. We aimed to identify novel ADGR-interacting partners to shed light on cellular protein networks that rely on ADGR function. For this, we applied affinity proteomics, utilizing tandem affinity purifications combined with mass spectrometry. Analysis of the acquired proteomics data provides evidence that ADGRs not only have functional roles at synapses but also at intracellular membranes, namely at the endoplasmic reticulum, the Golgi apparatus, mitochondria, and mitochondria-associated membranes (MAMs). Specifically, we found an association of ADGRs with several scaffold proteins of the membrane-associated guanylate kinases family, elementary units of the γ-secretase complex, the outer/inner mitochondrial membrane, MAMs, and regulators of the Wnt signaling pathways. Furthermore, the nuclear localization of ADGR domains together with their physical interaction with nuclear proteins and several transcription factors suggests a role of ADGRs in gene regulation.
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Affiliation(s)
- Barbara Knapp
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Jens Roedig
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research and Medical Bioanalytics, Centre for Ophthalmology, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Jacek Krzysko
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Nicola Horn
- Institute for Ophthalmic Research and Medical Bioanalytics, Centre for Ophthalmology, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research and Medical Bioanalytics, Centre for Ophthalmology, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
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