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Tilliole P, Fix S, Godin JD. hnRNPs: roles in neurodevelopment and implication for brain disorders. Front Mol Neurosci 2024; 17:1411639. [PMID: 39086926 PMCID: PMC11288931 DOI: 10.3389/fnmol.2024.1411639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) constitute a family of multifunctional RNA-binding proteins able to process nuclear pre-mRNAs into mature mRNAs and regulate gene expression in multiple ways. They comprise at least 20 different members in mammals, named from A (HNRNP A1) to U (HNRNP U). Many of these proteins are components of the spliceosome complex and can modulate alternative splicing in a tissue-specific manner. Notably, while genes encoding hnRNPs exhibit ubiquitous expression, increasing evidence associate these proteins to various neurodevelopmental and neurodegenerative disorders, such as intellectual disability, epilepsy, microcephaly, amyotrophic lateral sclerosis, or dementias, highlighting their crucial role in the central nervous system. This review explores the evolution of the hnRNPs family, highlighting the emergence of numerous new members within this family, and sheds light on their implications for brain development.
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Affiliation(s)
- Pierre Tilliole
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Simon Fix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Juliette D. Godin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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2
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Kwanten B, Deconick T, Walker C, Wang F, Landesman Y, Daelemans D. E3 ubiquitin ligase ASB8 promotes selinexor-induced proteasomal degradation of XPO1. Biomed Pharmacother 2023; 160:114305. [PMID: 36731340 DOI: 10.1016/j.biopha.2023.114305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
Selinexor (KPT-330), a small-molecule inhibitor of exportin-1 (XPO1, CRM1) with potent anticancer activity, has recently been granted FDA approval for treatment of relapsed/refractory multiple myeloma and diffuse large B-cell lymphoma (DLBCL), with a number of additional indications currently under clinical investigation. Since selinexor has often demonstrated synergy when used in combination with other drugs, notably bortezomib and dexamethasone, a more comprehensive approach to uncover new beneficial interactions would be of great value. Moreover, stratifying patients, personalizing therapeutics and improving clinical outcomes requires a better understanding of the genetic vulnerabilities and resistance mechanisms underlying drug response. Here, we used CRISPR-Cas9 loss-of-function chemogenetic screening to identify drug-gene interactions with selinexor in chronic myeloid leukemia, multiple myeloma and DLBCL cell lines. We identified the TGFβ-SMAD4 pathway as an important mediator of resistance to selinexor in multiple myeloma cells. Moreover, higher activity of this pathway correlated with prolonged progression-free survival in multiple myeloma patients treated with selinexor, indicating that the TGFβ-SMAD4 pathway is a potential biomarker predictive of therapeutic outcome. In addition, we identified ASB8 (ankyrin repeat and SOCS box containing 8) as a shared modulator of selinexor sensitivity across all tested cancer types, with both ASB8 knockout and overexpression resulting in selinexor hypersensitivity. Mechanistically, we showed that ASB8 promotes selinexor-induced proteasomal degradation of XPO1. This study provides insight into the genetic factors that influence response to selinexor treatment and could support both the development of predictive biomarkers as well as new drug combinations.
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Affiliation(s)
- Bert Kwanten
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy (Rega Institute), Leuven, Belgium
| | - Tine Deconick
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy (Rega Institute), Leuven, Belgium
| | | | - Feng Wang
- Karyopharm Therapeutics, Newton, MA 02459, USA
| | | | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy (Rega Institute), Leuven, Belgium.
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3
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Reviewing the Potential Links between Viral Infections and TDP-43 Proteinopathies. Int J Mol Sci 2023; 24:ijms24021581. [PMID: 36675095 PMCID: PMC9867397 DOI: 10.3390/ijms24021581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Transactive response DNA binding protein 43 kDa (TDP-43) was discovered in 2001 as a cellular factor capable to inhibit HIV-1 gene expression. Successively, it was brought to new life as the most prevalent RNA-binding protein involved in several neurological disorders, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Despite the fact that these two research areas could be considered very distant from each other, in recent years an increasing number of publications pointed out the existence of a potentially important connection. Indeed, the ability of TDP-43 to act as an important regulator of all aspects of RNA metabolism makes this protein also a critical factor during expression of viral RNAs. Here, we summarize all recent observations regarding the involvement of TDP-43 in viral entry, replication and latency in several viruses that include enteroviruses (EVs), Theiler's murine encephalomyelitis virus (TMEV), human immunodeficiency virus (HIV), human endogenous retroviruses (HERVs), hepatitis B virus (HBV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), West Nile virus (WNV), and herpes simplex virus-2 (HSV). In particular, in this work, we aimed to highlight the presence of similarities with the most commonly studied TDP-43 related neuronal dysfunctions.
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Cappelli S, Spalloni A, Feiguin F, Visani G, Šušnjar U, Brown AL, De Bardi M, Borsellino G, Secrier M, Phatnani H, Romano M, Fratta P, Longone P, Buratti E. NOS1AP is a novel molecular target and critical factor in TDP-43 pathology. Brain Commun 2022; 4:fcac242. [PMID: 36267332 PMCID: PMC9576154 DOI: 10.1093/braincomms/fcac242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/05/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Many lines of evidence have highlighted the role played by heterogeneous nuclear ribonucleoproteins in amyotrophic lateral sclerosis. In this study, we have aimed to identify transcripts co-regulated by TAR DNA-binding protein 43 kDa and highly conserved heterogeneous nuclear ribonucleoproteins which have been previously shown to regulate TAR DNA-binding protein 43 kDa toxicity (deleted in azoospermia-associated protein 1, heterogeneous nuclear ribonucleoprotein -Q, -D, -K and -U). Using the transcriptome analyses, we have uncovered that Nitric Oxide Synthase 1 Adaptor Protein mRNA is a direct TAR DNA-binding protein 43 kDa target, and in flies, its modulation alone can rescue TAR DNA-binding protein 43 kDa pathology. In primary mouse cortical neurons, we show that TAR DNA-binding protein 43 kDa mediated downregulation of Nitric Oxide Synthase 1 Adaptor Protein expression strongly affects the NMDA-receptor signalling pathway. In human patients, the downregulation of Nitric Oxide Synthase 1 Adaptor Protein mRNA strongly correlates with TAR DNA-binding protein 43 kDa proteinopathy as measured by cryptic Stathmin-2 and Unc-13 homolog A cryptic exon inclusion. Overall, our results demonstrate that Nitric Oxide Synthase 1 Adaptor Protein may represent a novel disease-relevant gene, potentially suitable for the development of new therapeutic strategies.
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Affiliation(s)
- Sara Cappelli
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Alida Spalloni
- Molecular Neurobiology, Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy
| | - Fabian Feiguin
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Giulia Visani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Urša Šušnjar
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Marco De Bardi
- Neuroimmunology Unit, Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy
| | - Giovanna Borsellino
- Neuroimmunology Unit, Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Patrizia Longone
- Molecular Neurobiology, Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Padriciano 99, 34149 Trieste, Italy
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Šušnjar U, Škrabar N, Brown AL, Abbassi Y, Phatnani H, Cortese A, Cereda C, Bugiardini E, Cardani R, Meola G, Ripolone M, Moggio M, Romano M, Secrier M, Fratta P, Buratti E. Cell environment shapes TDP-43 function with implications in neuronal and muscle disease. Commun Biol 2022; 5:314. [PMID: 35383280 PMCID: PMC8983780 DOI: 10.1038/s42003-022-03253-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/11/2022] [Indexed: 12/26/2022] Open
Abstract
TDP-43 (TAR DNA-binding protein 43) aggregation and redistribution are recognised as a hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. As TDP-43 inclusions have recently been described in the muscle of inclusion body myositis patients, this highlights the need to understand the role of TDP-43 beyond the central nervous system. Using RNA-seq, we directly compare TDP-43-mediated RNA processing in muscle (C2C12) and neuronal (NSC34) mouse cells. TDP-43 displays a cell-type-characteristic behaviour targeting unique transcripts in each cell-type, which is due to characteristic expression of RNA-binding proteins, that influence TDP-43's performance and define cell-type specific splicing. Among splicing events commonly dysregulated in both cell lines, we identify some that are TDP-43-dependent also in human cells. Inclusion levels of these alternative exons are altered in tissues of patients suffering from FTLD and IBM. We therefore propose that TDP-43 dysfunction contributes to disease development either in a common or a tissue-specific manner.
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Affiliation(s)
- Urša Šušnjar
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Neva Škrabar
- Tumour Virology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Generatio GmbH, Center for Animal, Genetics, Tübingen, Germany
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Yasmine Abbassi
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, USA
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- Department of Brain and Behaviour Sciences, University of Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Rosanna Cardani
- BioCor Biobank, UOC SMEL-1 of Clinical Pathology, IRCCS-Policlinico San Donato, San Donato Milanese, Italy
| | - Giovanni Meola
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
- Department of Neurorehabilitation Sciences, Casa di Cura del Policlinico, Milan, Italy
| | - Michela Ripolone
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maurizio Moggio
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Emanuele Buratti
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.
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6
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Semino F, Schröter J, Willemsen MH, Bast T, Biskup S, Beck-Woedl S, Brennenstuhl H, Schaaf CP, Kölker S, Hoffmann GF, Haack TB, Syrbe S. Further evidence for de novo variants in SYNCRIP as the cause of a neurodevelopmental disorder. Hum Mutat 2021; 42:1094-1100. [PMID: 34157790 DOI: 10.1002/humu.24245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/10/2021] [Accepted: 06/19/2021] [Indexed: 11/06/2022]
Abstract
SYNCRIP encodes for the Synaptotagmin-binding cytoplasmic RNA-interacting protein, involved in RNA-binding and regulation of multiple cellular pathways. It has been proposed as a candidate gene for neurodevelopmental disorders (NDDs) with autism spectrum disorder (ASD), intellectual disability (ID), and epilepsy. We ascertained genetic, clinical, and neuroradiological data of three additional individuals with novel de novo SYNCRIP variants. All individuals had ID. Autistic features were observed in two. One individual showed myoclonic-atonic epilepsy. Neuroradiological features comprised periventricular nodular heterotopia and widening of subarachnoid spaces. Two frameshift variants in the more severely affected individuals, likely result in haploinsufficiency. The third missense variant lies in the conserved RNA recognition motif (RRM) 2 domain likely affecting RNA-binding. Our findings support the importance of RRM domains for SYNCRIP functionality and suggest genotype-phenotype correlations. Our study provides further evidence for a SYNCRIP-associated NDD characterized by ID and ASD sporadically accompanied by malformations of cortical development and myoclonic-atonic epilepsy.
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Affiliation(s)
- Francesca Semino
- Division of Pediatric Epileptology, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany.,Institute for Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Julian Schröter
- Division of Pediatric Epileptology, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Bast
- Epilepsy Center Kork, Kehl, Germany.,Medical Faculty of the University of Freiburg, Kehl, Germany
| | - Saskia Biskup
- Praxis für Humangenetik Tübingen, Tuebingen, Germany.,CEGAT GmbH, Tuebingen, Germany
| | - Stefanie Beck-Woedl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Heiko Brennenstuhl
- Division of Neuropediatrics and Inherited Metabolic Diseases, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Stefan Kölker
- Division of Neuropediatrics and Inherited Metabolic Diseases, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Division of Neuropediatrics and Inherited Metabolic Diseases, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Steffen Syrbe
- Division of Pediatric Epileptology, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
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The role of hnRNPs in frontotemporal dementia and amyotrophic lateral sclerosis. Acta Neuropathol 2020; 140:599-623. [PMID: 32748079 PMCID: PMC7547044 DOI: 10.1007/s00401-020-02203-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022]
Abstract
Dysregulated RNA metabolism is emerging as a crucially important mechanism underpinning the pathogenesis of frontotemporal dementia (FTD) and the clinically, genetically and pathologically overlapping disorder of amyotrophic lateral sclerosis (ALS). Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins with diverse, multi-functional roles across all aspects of mRNA processing. The role of these proteins in neurodegeneration is far from understood. Here, we review some of the unifying mechanisms by which hnRNPs have been directly or indirectly linked with FTD/ALS pathogenesis, including their incorporation into pathological inclusions and their best-known roles in pre-mRNA splicing regulation. We also discuss the broader functionalities of hnRNPs including their roles in cryptic exon repression, stress granule assembly and in co-ordinating the DNA damage response, which are all emerging pathogenic themes in both diseases. We then present an integrated model that depicts how a broad-ranging network of pathogenic events can arise from declining levels of functional hnRNPs that are inadequately compensated for by autoregulatory means. Finally, we provide a comprehensive overview of the most functionally relevant cellular roles, in the context of FTD/ALS pathogenesis, for hnRNPs A1-U.
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8
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Oostdyk LT, Wang Z, Zang C, Li H, McConnell MJ, Paschal BM. An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding. Sci Rep 2020; 10:4844. [PMID: 32179771 PMCID: PMC7076015 DOI: 10.1038/s41598-020-61369-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022] Open
Abstract
KPNA7 is a member of the Importin-α family of nuclear import receptors. KPNA7 forms a complex with Importin-β and facilitates the translocation of signal-containing proteins from the cytoplasm to the nucleus. Exome sequencing of siblings with severe neurodevelopmental defects and clinical features of epilepsy identified two amino acid-altering mutations in KPNA7. Here, we show that the E344Q substitution reduces KPNA7 binding to nuclear localization signals, and that this limits KPNA7 nuclear import activity. The P339A substitution, by contrast, has little effect on KPNA7 binding to nuclear localization signals. Given the neuronal phenotype described in the two patients, we used SILAC labeling, affinity enrichment, and mass spectrometry to identify KPNA7-interacting proteins in human induced pluripotent stem cell-derived neurons. We identified heterogeneous nuclear ribonucleoproteins hnRNP R and hnRNP U as KPNA7-interacting proteins. The E344Q substitution reduced binding and KPNA7-mediated import of these cargoes. The c.1030G > C allele which generates E344Q is within a predicted CTCF binding site, and we found that it reduces CTCF binding by approximately 40-fold. Our data support a role for altered neuronal expression and activity of KPNA7 in a rare type of pediatric epilepsy.
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Affiliation(s)
- Luke T Oostdyk
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Zhenjia Wang
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Chongzhi Zang
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hui Li
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael J McConnell
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bryce M Paschal
- Department of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. .,Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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9
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Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM. Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA (NEW YORK, N.Y.) 2019; 25:1337-1352. [PMID: 31296583 PMCID: PMC6800478 DOI: 10.1261/rna.072157.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/27/2019] [Indexed: 05/10/2023]
Abstract
Proteins bind mRNA through their entire life cycle from transcription to degradation. We analyzed c-Myc mRNA protein interactors in vivo using the HyPR-MS method to capture the crosslinked mRNA by hybridization and then analyzed the bound proteins using mass spectrometry proteomics. Using HyPR-MS, 229 c-Myc mRNA-binding proteins were identified, confirming previously proposed interactors, suggesting new interactors, and providing information related to the roles and pathways known to involve c-Myc. We performed structural and functional analysis of these proteins and validated our findings with a combination of RIP-qPCR experiments, in vitro results released in past studies, publicly available RIP- and eCLIP-seq data, and results from software tools for predicting RNA-protein interactions.
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Affiliation(s)
- Michele Spiniello
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Medicine of Precision, University of Studi della Campania Luigi Vanvitelli, Naples 80138, Italy
- Division of Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, Naples 80131, Italy
| | - Maisie I Steinbrink
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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10
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Gittings LM, Foti SC, Benson BC, Gami-Patel P, Isaacs AM, Lashley T. Heterogeneous nuclear ribonucleoproteins R and Q accumulate in pathological inclusions in FTLD-FUS. Acta Neuropathol Commun 2019; 7:18. [PMID: 30755280 PMCID: PMC6371513 DOI: 10.1186/s40478-019-0673-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/03/2019] [Indexed: 12/14/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) is pathologically subdivided based on the presence of particular pathological proteins that are identified in inclusion bodies observed post-mortem. The FTLD-FUS subgroup is defined by the presence of the fused in sarcoma protein (FUS) in pathological inclusions. FUS is a heterogeneous nuclear ribonucleoprotein (hnRNP) protein and a member of the FET (FUS, EWS, TAF15) protein family. It shuttles between the nucleus and cytoplasm, and has been implicated in many cellular functions including translation, splicing, and RNA transport. EWS, TAF15 and the nuclear import receptor transportin have been shown to co-accumulate with FUS in neuronal inclusions specifically in FTLD-FUS, with transportin-positive inclusions most frequently observed. Here, we report the identification of hnRNP R and hnRNP Q in neuronal cytoplasmic and intranuclear inclusions in the frontal cortex and hippocampus of FTLD-FUS patients, as frequently as transportin. hnRNP R and hnRNP Q were not found in the characteristic pathological inclusions observed in FTLD-TDP (subtypes A-C). Additionally, we studied the expression of hnRNP R in the frontal and temporal cortices from patients with FTLD and found significantly increased expression of the heterogeneous nuclear ribonucleoprotein R in several FTLD disease groups. Our identification of the frequent presence of hnRNP R and hnRNP Q in FTLD-FUS inclusions suggests a potential role for these hnRNPs in FTLD-FUS pathogenesis and supports the role of dysfunctional RNA metabolism in FTLD.
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