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Forcella P, Ifflander N, Rolando C, Balta EA, Lampada A, Giachino C, Mukhtar T, Bock T, Taylor V. SAFB regulates hippocampal stem cell fate by targeting Drosha to destabilize Nfib mRNA. eLife 2024; 13:e74940. [PMID: 38722021 PMCID: PMC11149935 DOI: 10.7554/elife.74940] [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: 10/22/2021] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
Neural stem cells (NSCs) are multipotent and correct fate determination is crucial to guarantee brain formation and homeostasis. How NSCs are instructed to generate neuronal or glial progeny is not well understood. Here, we addressed how murine adult hippocampal NSC fate is regulated and described how scaffold attachment factor B (SAFB) blocks oligodendrocyte production to enable neuron generation. We found that SAFB prevents NSC expression of the transcription factor nuclear factor I/B (NFIB) by binding to sequences in the Nfib mRNA and enhancing Drosha-dependent cleavage of the transcripts. We show that increasing SAFB expression prevents oligodendrocyte production by multipotent adult NSCs, and conditional deletion of Safb increases NFIB expression and oligodendrocyte formation in the adult hippocampus. Our results provide novel insights into a mechanism that controls Drosha functions for selective regulation of NSC fate by modulating the post-transcriptional destabilization of Nfib mRNA in a lineage-specific manner.
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Affiliation(s)
- Pascal Forcella
- Department of Biomedicine, University of BaselBaselSwitzerland
| | | | - Chiara Rolando
- Department of Biomedicine, University of BaselBaselSwitzerland
- Department of Biosciences, University of MilanMilanItaly
| | - Elli-Anna Balta
- Department of Biomedicine, University of BaselBaselSwitzerland
| | | | | | - Tanzila Mukhtar
- Department of Biomedicine, University of BaselBaselSwitzerland
| | - Thomas Bock
- Proteomics Core Facility, Biozentrum, University of BaselBaselSwitzerland
| | - Verdon Taylor
- Department of Biomedicine, University of BaselBaselSwitzerland
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2
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Sudhakar SRN, Khan SN, Clark A, Hendrickson-Rebizant T, Patel S, Lakowski TM, Davie JR. Protein arginine methyltransferase 1, a major regulator of biological processes. Biochem Cell Biol 2024; 102:106-126. [PMID: 37922507 DOI: 10.1139/bcb-2023-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) is a major type I arginine methyltransferase that catalyzes the formation of monomethyl and asymmetric dimethylarginine in protein substrates. It was first identified to asymmetrically methylate histone H4 at the third arginine residue forming the H4R3me2a active histone mark. However, several protein substrates are now identified as being methylated by PRMT1. As a result of its association with diverse classes of substrates, PRMT1 regulates several biological processes like chromatin dynamics, transcription, RNA processing, and signal transduction. The review provides an overview of PRMT1 structure, biochemical features, specificity, regulation, and role in cellular functions. We discuss the genomic distribution of PRMT1 and its association with tRNA genes. Further, we explore the different substrates of PRMT1 involved in splicing. In the end, we discuss the proteins that interact with PRMT1 and their downstream effects in diseased states.
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Affiliation(s)
- Sadhana R N Sudhakar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Shahper N Khan
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ariel Clark
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | | | - Shrinal Patel
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ted M Lakowski
- College of Pharmacy Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
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3
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da Silva AM, Yevdokimova V, Benoit YD. Sam68 is a druggable vulnerability point in cancer stem cells. Cancer Metastasis Rev 2024; 43:441-456. [PMID: 37792222 PMCID: PMC11016129 DOI: 10.1007/s10555-023-10145-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023]
Abstract
Sam68 (Src associated in mitosis of 68 kDa) is an RNA-binding and multifunctional protein extensively characterized in numerous cellular functions, such as RNA processing, cell cycle regulation, kinase- and growth factor signaling. Recent investigations highlighted Sam68 as a primary target of a class of reverse-turn peptidomimetic drugs, initially developed as inhibitors of Wnt/β-catenin mediated transcription. Further investigations on such compounds revealed their capacity to selectively eliminate cancer stem cell (CSC) activity upon engaging Sam68. This work highlighted previously unappreciated roles for Sam68 in the maintenance of neoplastic self-renewal and tumor-initiating functions. Here, we discuss the implication of Sam68 in tumorigenesis, where central findings support its contribution to chromatin regulation processes essential to CSCs. We also review advances in CSC-targeting drug discovery aiming to modulate Sam68 cellular distribution and protein-protein interactions. Ultimately, Sam68 constitutes a vulnerability point of CSCs and an attractive therapeutic target to impede neoplastic stemness in human tumors.
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Affiliation(s)
- Amanda Mendes da Silva
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Veronika Yevdokimova
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Yannick D Benoit
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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4
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Verdile V, Palombo R, Ferrante G, Ferri A, Amadio S, Volonté C, Paronetto MP. Dysregulation of alternative splicing underlies synaptic defects in familial amyotrophic lateral sclerosis. Prog Neurobiol 2023; 231:102529. [PMID: 37739207 DOI: 10.1016/j.pneurobio.2023.102529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease characterized by the degeneration of upper and lower motor neurons, progressive wasting and paralysis of voluntary muscles. A hallmark of ALS is the frequent nuclear loss and cytoplasmic accumulation of RNA binding proteins (RBPs) in motor neurons (MN), which leads to aberrant alternative splicing regulation. However, whether altered splicing patterns are also present in familial models of ALS without mutations in RBP-encoding genes has not been investigated yet. Herein, we found that altered splicing of synaptic genes is a common trait of familial ALS MNs. Similar deregulation was also observed in hSOD1G93A MN-like cells. In silico analysis identified the potential regulators of these pre-mRNAs, including the RBP Sam68. Immunofluorescence analysis and biochemical fractionation experiments revealed that Sam68 accumulates in the cytoplasmic insoluble ribonucleoprotein fraction of MN. Remarkably, the synaptic splicing events deregulated in ALS MNs were also affected in Sam68-/- spinal cords. Recombinant expression of Sam68 protein was sufficient to rescue these splicing changes in ALS hSOD1G93A MN-like cells. Hence, our study highlights an aberrant function of Sam68, which leads to splicing changes in synaptic genes and may contribute to the MN phenotype that characterizes ALS.
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Affiliation(s)
- Veronica Verdile
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135 Rome, Italy; Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy
| | - Ramona Palombo
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135 Rome, Italy
| | - Gabriele Ferrante
- Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy
| | - Alberto Ferri
- Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy; National Research Council (CNR), Institute of Translational Pharmacology (IFT), Rome, Italy
| | - Susanna Amadio
- Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy
| | - Cinzia Volonté
- Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy; National Research Council (CNR), Institute for Systems Analysis and Computer Science (IASI), Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135 Rome, Italy; Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy.
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5
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Naing YT, Sun L. The Role of Splicing Factors in Adipogenesis and Thermogenesis. Mol Cells 2023; 46:268-277. [PMID: 37170770 PMCID: PMC10183792 DOI: 10.14348/molcells.2023.2195] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 05/13/2023] Open
Abstract
Obesity is a significant global health risk that can cause a range of serious metabolic problems, such as type 2 diabetes and cardiovascular diseases. Adipose tissue plays a pivotal role in regulating energy and lipid storage. New research has underlined the crucial role of splicing factors in the physiological and functional regulation of adipose tissue. By generating multiple transcripts from a single gene, alternative splicing allows for a greater diversity of the proteome and transcriptome, which subsequently influence adipocyte development and metabolism. In this review, we provide an outlook on the part of splicing factors in adipogenesis and thermogenesis, and investigate how the different spliced isoforms can affect the development and function of adipose tissue.
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Affiliation(s)
- Yadanar Than Naing
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore 169857
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore 169857
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Adinolfi A, Di Sante G, Rivignani Vaccari L, Tredicine M, Ria F, Bonvissuto D, Corvino V, Sette C, Geloso MC. Regionally restricted modulation of Sam68 expression and Arhgef9 alternative splicing in the hippocampus of a murine model of multiple sclerosis. Front Mol Neurosci 2023; 15:1073627. [PMID: 36710925 PMCID: PMC9878567 DOI: 10.3389/fnmol.2022.1073627] [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: 10/18/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Multiple sclerosis (MS) and its preclinical models are characterized by marked changes in neuroplasticity, including excitatory/inhibitory imbalance and synaptic dysfunction that are believed to underlie the progressive cognitive impairment (CI), which represents a significant clinical hallmark of the disease. In this study, we investigated several parameters of neuroplasticity in the hippocampus of the experimental autoimmune encephalomyelitis (EAE) SJL/J mouse model, characterized by rostral inflammatory and demyelinating lesions similar to Relapsing-Remitting MS. By combining morphological and molecular analyses, we found that the hippocampus undergoes extensive inflammation in EAE-mice, more pronounced in the CA3 and dentate gyrus (DG) subfields than in the CA1, associated with changes in GABAergic circuitry, as indicated by the increased expression of the interneuron marker Parvalbumin selectively in CA3. By laser-microdissection, we investigated the impact of EAE on the alternative splicing of Arhgef9, a gene encoding a post-synaptic protein playing an essential role in GABAergic synapses and whose mutations have been related to CI and epilepsy. Our results indicate that EAE induces a specific increase in inclusion of the alternative exon 11a only in the CA3 and DG subfields, in line with the higher local levels of inflammation. Consistently, we found a region-specific downregulation of Sam68, a splicing-factor that represses this splicing event. Collectively, our findings confirm a regionalized distribution of inflammation in the hippocampus of EAE-mice. Moreover, since neuronal circuit rearrangement and dynamic remodeling of structural components of the synapse are key processes that contribute to neuroplasticity, our study suggests potential new molecular players involved in EAE-induced hippocampal dysfunction.
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Affiliation(s)
- Annalisa Adinolfi
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gabriele Di Sante
- Section of Human, Clinic and Forensic Anatomy, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luca Rivignani Vaccari
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maria Tredicine
- Section of General Pathology, Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Ria
- Section of General Pathology, Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Davide Bonvissuto
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Valentina Corvino
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Claudio Sette
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy,*Correspondence: Claudio Sette, ✉
| | - Maria Concetta Geloso
- Section of Human Anatomy, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy,Maria Concetta Geloso, ✉
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Boxer EE, Aoto J. Neurexins and their ligands at inhibitory synapses. Front Synaptic Neurosci 2022; 14:1087238. [PMID: 36618530 PMCID: PMC9812575 DOI: 10.3389/fnsyn.2022.1087238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
Since the discovery of neurexins (Nrxns) as essential and evolutionarily conserved synaptic adhesion molecules, focus has largely centered on their functional contributions to glutamatergic synapses. Recently, significant advances to our understanding of neurexin function at GABAergic synapses have revealed that neurexins can play pleiotropic roles in regulating inhibitory synapse maintenance and function in a brain-region and synapse-specific manner. GABAergic neurons are incredibly diverse, exhibiting distinct synaptic properties, sites of innervation, neuromodulation, and plasticity. Different classes of GABAergic neurons often express distinct repertoires of Nrxn isoforms that exhibit differential alternative exon usage. Further, Nrxn ligands can be differentially expressed and can display synapse-specific localization patterns, which may contribute to the formation of a complex trans-synaptic molecular code that establishes the properties of inhibitory synapse function and properties of local circuitry. In this review, we will discuss how Nrxns and their ligands sculpt synaptic inhibition in a brain-region, cell-type and synapse-specific manner.
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Affiliation(s)
| | - Jason Aoto
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Denver, CO, United States
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8
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Fisher E, Feng J. RNA splicing regulators play critical roles in neurogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1728. [PMID: 35388651 DOI: 10.1002/wrna.1728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
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9
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Chan JNM, Sánchez-Vidaña DI, Anoopkumar-Dukie S, Li Y, Benson Wui-Man L. RNA-binding protein signaling in adult neurogenesis. Front Cell Dev Biol 2022; 10:982549. [PMID: 36187492 PMCID: PMC9523427 DOI: 10.3389/fcell.2022.982549] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
The process of neurogenesis in the brain, including cell proliferation, differentiation, survival, and maturation, results in the formation of new functional neurons. During embryonic development, neurogenesis is crucial to produce neurons to establish the nervous system, but the process persists in certain brain regions during adulthood. In adult neurogenesis, the production of new neurons in the hippocampus is accomplished via the division of neural stem cells. Neurogenesis is regulated by multiple factors, including gene expression at a temporal scale and post-transcriptional modifications. RNA-binding Proteins (RBPs) are known as proteins that bind to either double- or single-stranded RNA in cells and form ribonucleoprotein complexes. The involvement of RBPs in neurogenesis is crucial for modulating gene expression changes and posttranscriptional processes. Since neurogenesis affects learning and memory, RBPs are closely associated with cognitive functions and emotions. However, the pathways of each RBP in adult neurogenesis remain elusive and not clear. In this review, we specifically summarize the involvement of several RBPs in adult neurogenesis, including CPEB3, FXR2, FMRP, HuR, HuD, Lin28, Msi1, Sam68, Stau1, Smaug2, and SOX2. To understand the role of these RBPs in neurogenesis, including cell proliferation, differentiation, survival, and maturation as well as posttranscriptional gene expression, we discussed the protein family, structure, expression, functional domain, and region of action. Therefore, this narrative review aims to provide a comprehensive overview of the RBPs, their function, and their role in the process of adult neurogenesis as well as to identify possible research directions on RBPs and neurogenesis.
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Affiliation(s)
- Jackie Ngai-Man Chan
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - Dalinda Isabel Sánchez-Vidaña
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- Mental Health Research Centre, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | | | - Yue Li
- State Key Laboratory of Component-Based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lau Benson Wui-Man
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- Mental Health Research Centre, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- *Correspondence: Lau Benson Wui-Man,
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Yamanaka Y, Ishizuka T, Fujita KI, Fujiwara N, Kurata M, Masuda S. CHERP Regulates the Alternative Splicing of pre-mRNAs in the Nucleus. Int J Mol Sci 2022; 23:ijms23052555. [PMID: 35269695 PMCID: PMC8910253 DOI: 10.3390/ijms23052555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 12/17/2022] Open
Abstract
Calcium homeostasis endoplasmic reticulum protein (CHERP) is colocalized with the inositol 1,4,5-trisphosphate receptor (IP3R) in the endoplasmic reticulum or perinuclear region, and has been involved in intracellular calcium signaling. Structurally, CHERP carries the nuclear localization signal and arginine/serine-dipeptide repeats, like domain, and interacts with the spliceosome. However, the exact function of CHERP in the nucleus remains unknown. Here, we showed that poly(A)+ RNAs accumulated in the nucleus of CHERP-depleted U2OS cells. Our global analysis revealed that CHERP regulated alternative mRNA splicing events by interaction with U2 small nuclear ribonucleoproteins (U2 snRNPs) and U2 snRNP-related proteins. Among the five alternative splicing patterns analyzed, intron retention was the most frequently observed event. This was in accordance with the accumulation of poly(A)+ RNAs in the nucleus. Furthermore, intron retention and cassette exon choices were influenced by the strength of the 5′ or 3′ splice site, the branch point site, GC content, and intron length. In addition, CHERP depletion induced anomalies in the cell cycle progression into the M phase, and abnormal cell division. These results suggested that CHERP is involved in the regulation of alternative splicing.
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Affiliation(s)
- Yasutaka Yamanaka
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; (Y.Y.); (T.I.); (K.-i.F.); (N.F.); (M.K.)
| | - Takaki Ishizuka
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; (Y.Y.); (T.I.); (K.-i.F.); (N.F.); (M.K.)
| | - Ken-ichi Fujita
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; (Y.Y.); (T.I.); (K.-i.F.); (N.F.); (M.K.)
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Naoko Fujiwara
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; (Y.Y.); (T.I.); (K.-i.F.); (N.F.); (M.K.)
| | - Masashi Kurata
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; (Y.Y.); (T.I.); (K.-i.F.); (N.F.); (M.K.)
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; (Y.Y.); (T.I.); (K.-i.F.); (N.F.); (M.K.)
- Department of Food Science and Nutrition, Faculty of Agriculture, Kindai University, Nara 631-8505, Japan
- Correspondence: ; Tel.: +81-742-43-1713
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11
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Zhang W, Liu L, Zhao S, Chen L, Wei Y, Chen W, Ge F. Research progress on RNA‑binding proteins in breast cancer (Review). Oncol Lett 2022; 23:121. [PMID: 35261635 PMCID: PMC8867207 DOI: 10.3892/ol.2022.13241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/03/2022] [Indexed: 11/28/2022] Open
Abstract
Breast cancer is the most common malignancy among women, and the abnormal regulation of gene expression serves an important role in its occurrence and development. However, the molecular mechanisms underlying gene expression are highly complex and heterogeneous, and RNA-binding proteins (RBPs) are among the key regulatory factors. RBPs bind targets in an environment-dependent or environment-independent manner to influence mRNA stability and the translation of genes involved in the formation, progression, metastasis and treatment of breast cancer. Due to the growing interest in these regulators, the present review summarizes the most influential studies concerning RBPs associated with breast cancer to elucidate the role of RBPs in breast cancer and to assess how they interact with other key pathways to provide new molecular targets for the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Wenzhu Zhang
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Shengdi Zhao
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Liang Chen
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Yuxian Wei
- Department of Endocrine Breast Surgery, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wenlin Chen
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Fei Ge
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
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12
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Jaswal S, Anand V, Ali SA, Jena MK, Kumar S, Kaushik JK, Mohanty AK. TMT based deep proteome analysis of buffalo mammary epithelial cells and identification of novel protein signatures during lactogenic differentiation. FASEB J 2021; 35:e21621. [PMID: 33977573 DOI: 10.1096/fj.202002476rr] [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: 11/26/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/04/2023]
Abstract
The lactating mammary gland harbours numerous matured alveoli with their lumen surrounded by differentiated mammary epithelial cells (MECs), which are exclusively involved in milk synthesis and secretion. Buffalo (Bubalus bubalis) is the second major milk-producing animal, and its physiology is different from cattle. The complete protein machinery involved in MECs differentiation is still not defined in ruminants, in particular, buffalo. Therefore, we have studied the differential expression of regulated proteins in the in vitro grown buffalo MECs (BuMECs) at different time points (on 3, 6, 12, and 15 days) of their differentiation in the presence of lactogenic hormones. TMT-based MS analysis identified 4,934 proteins; of them, 681 were differentially expressed proteins (DEPs). The principal component analysis suggested a highly heterogeneous expression of DEPs at the four-time points of hormone treatment, with most of them (307) attained the highest expression on 12 days. Bioinformatics analysis revealed the association of DEPs with 24 KEGG pathways. We observed few new proteins, namely ABCA13, IVL, VPS37, CZIB, RFX7, Rab5, TTLL12, SMEK1, GDI2, and TMEM131 in BuMECs. The function of one of the highly upregulated proteins, namely involucrin in the differentiation of BuMECs was confirmed based on biochemical inhibition assay. The results further conclude that the proteins with higher abundance can be considered as the potential biomarkers for differentiation, and they may have a significant association with the lactation process in buffalo too. The proteome dataset obtained can be used to understand the species-specific variations among other lactating animals.
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Affiliation(s)
- Shalini Jaswal
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| | - Vijay Anand
- Department of Veterinary Physiology and Biochemistry, Veterinary College and Research Institute (TANUVAS), Orathanadu, India
| | - Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| | - Manoj K Jena
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Sudarshan Kumar
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| | - Jai K Kaushik
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| | - Ashok K Mohanty
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
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13
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Cazurro-Gutiérrez A, Marcé-Grau A, Correa-Vela M, Salazar A, Vanegas MI, Macaya A, Bayés À, Pérez-Dueñas B. ε-Sarcoglycan: Unraveling the Myoclonus-Dystonia Gene. Mol Neurobiol 2021; 58:3938-3952. [PMID: 33886091 DOI: 10.1007/s12035-021-02391-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/08/2021] [Indexed: 01/23/2023]
Abstract
Myoclonus-dystonia (MD) is a rare childhood-onset movement disorder, with an estimated prevalence of about 2 per 1,000,.000 in Europe, characterized by myoclonic jerks in combination with focal or segmental dystonia. Pathogenic variants in the gene encoding ε-sarcoglycan (SGCE), a maternally imprinted gene, are the most frequent genetic cause of MD. To date, the exact role of ε-sarcoglycan and the pathogenic mechanisms that lead to MD are still unknown. However, there are more than 40 reported isoforms of human ε-sarcoglycan, pointing to a complex biology of this protein. Additionally, some of these are brain-specific isoforms, which may suggest an important role within the central nervous system. In the present review, we aim to provide an overview of the current state of knowledge of ε-sarcoglycan. We will focus on the genetic landscape of SGCE and the presence and plausible role of ε-sarcoglycan in the brain. Finally, we discuss the importance of the brain-specific isoforms and hypothesize that SGCE may play essential roles in normal synaptic functioning and their alteration will be strongly related to MD.
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Affiliation(s)
- Ana Cazurro-Gutiérrez
- Paediatric Neurology Research Group, Hospital Vall d'Hebrón, Universitat Autònoma de Barcelona, Vall d'Hebrón Research Institute, Barcelona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Marcé-Grau
- Paediatric Neurology Research Group, Hospital Vall d'Hebrón, Universitat Autònoma de Barcelona, Vall d'Hebrón Research Institute, Barcelona, Spain
| | - Marta Correa-Vela
- Paediatric Neurology Research Group, Hospital Vall d'Hebrón, Universitat Autònoma de Barcelona, Vall d'Hebrón Research Institute, Barcelona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ainara Salazar
- Paediatric Neurology Research Group, Hospital Vall d'Hebrón, Universitat Autònoma de Barcelona, Vall d'Hebrón Research Institute, Barcelona, Spain
- Paediatric Neurology Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - María I Vanegas
- Paediatric Neurology Research Group, Hospital Vall d'Hebrón, Universitat Autònoma de Barcelona, Vall d'Hebrón Research Institute, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Alfons Macaya
- Paediatric Neurology Research Group, Hospital Vall d'Hebrón, Universitat Autònoma de Barcelona, Vall d'Hebrón Research Institute, Barcelona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Paediatric Neurology Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - Àlex Bayés
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain
| | - Belén Pérez-Dueñas
- Paediatric Neurology Research Group, Hospital Vall d'Hebrón, Universitat Autònoma de Barcelona, Vall d'Hebrón Research Institute, Barcelona, Spain.
- Universitat Autònoma de Barcelona, Barcelona, Spain.
- Paediatric Neurology Department, Hospital Vall d'Hebron, Barcelona, Spain.
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14
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Naro C, Cesari E, Sette C. Splicing regulation in brain and testis: common themes for highly specialized organs. Cell Cycle 2021; 20:480-489. [PMID: 33632061 PMCID: PMC8018374 DOI: 10.1080/15384101.2021.1889187] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/17/2021] [Accepted: 02/07/2021] [Indexed: 12/26/2022] Open
Abstract
Expansion of the coding and regulatory capabilities of eukaryotic transcriptomes by alternative splicing represents one of the evolutionary forces underlying the increased structural complexity of metazoans. Brain and testes stand out as the organs that mostly exploit the potential of alternative splicing, thereby expressing the largest repertoire of splice variants. Herein, we will review organ-specific as well as common mechanisms underlying the high transcriptome complexity of these organs and discuss the impact exerted by this widespread alternative splicing regulation on the functionality and differentiation of brain and testicular cells.
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Affiliation(s)
- Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome, Italy
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15
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Klein ME, Younts TJ, Cobo CF, Buxbaum AR, Aow J, Erdjument-Bromage H, Richard S, Malinow R, Neubert TA, Singer RH, Castillo PE, Jordan BA. Sam68 Enables Metabotropic Glutamate Receptor-Dependent LTD in Distal Dendritic Regions of CA1 Hippocampal Neurons. Cell Rep 2020; 29:1789-1799.e6. [PMID: 31722197 PMCID: PMC6871770 DOI: 10.1016/j.celrep.2019.10.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/15/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
The transport and translation of dendritic mRNAs by RNA-binding proteins (RBPs) allows for spatially restricted gene expression in neuronal processes. Although local translation in neuronal dendrites is now well documented, there is little evidence for corresponding effects on local synaptic function. Here, we report that the RBP Sam68 promotes the localization and translation of Arc mRNA preferentially in distal dendrites of rodent hippocampal CA1 pyramidal neurons. Consistent with Arc function in translation-dependent synaptic plasticity, we find that Sam68 knockout (KO) mice display impaired metabotropic glutamate-receptor-dependent long-term depression (mGluR-LTD) and impaired structural plasticity exclusively at distal Schaffer-collateral synapses. Moreover, by using quantitative proteomics, we find that the Sam68 interactome contains numerous regulators of mRNA translation and synaptic function. This work identifies an important player in Arc expression, provides a general framework for Sam68 regulation of protein synthesis, and uncovers a mechanism that enables the precise spatiotemporal expression of long-term plasticity throughout neurons.
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Affiliation(s)
- Matthew E Klein
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Thomas J Younts
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Carmen Freire Cobo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Jonathan Aow
- Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montréal, QC H3T 1E2, Canada
| | - Roberto Malinow
- Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Thomas A Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Robert H Singer
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
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16
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De Paola E, Forcina L, Pelosi L, Pisu S, La Rosa P, Cesari E, Nicoletti C, Madaro L, Mercatelli N, Biamonte F, Nobili A, D'Amelio M, De Bardi M, Volpe E, Caporossi D, Sette C, Musarò A, Paronetto MP. Sam68 splicing regulation contributes to motor unit establishment in the postnatal skeletal muscle. Life Sci Alliance 2020; 3:3/10/e201900637. [PMID: 32753528 PMCID: PMC7409371 DOI: 10.26508/lsa.201900637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 01/08/2023] Open
Abstract
Sam68 ensures the establishment of neuromuscular junctions (NMJs) and motor unit integrity by orchestrating a neuronal splicing program. RNA-binding proteins orchestrate the composite life of RNA molecules and impact most physiological processes, thus underlying complex phenotypes. The RNA-binding protein Sam68 regulates differentiation processes by modulating splicing, polyadenylation, and stability of select transcripts. Herein, we found that Sam68−/− mice display altered regulation of alternative splicing in the spinal cord of key target genes involved in synaptic functions. Analysis of the motor units revealed that Sam68 ablation impairs the establishment of neuromuscular junctions and causes progressive loss of motor neurons in the spinal cord. Importantly, alterations of neuromuscular junction morphology and properties in Sam68−/− mice correlate with defects in muscle and motor unit integrity. Sam68−/− muscles display defects in postnatal development, with manifest signs of atrophy. Furthermore, fast-twitch muscles in Sam68−/− mice show structural features typical of slow-twitch muscles, suggesting alterations in the metabolic and functional properties of myofibers. Collectively, our data identify a key role for Sam68 in muscle development and suggest that proper establishment of motor units requires timely expression of synaptic splice variants.
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Affiliation(s)
- Elisa De Paola
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico," Rome, Italy.,IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy
| | - Laura Forcina
- Laboratory Affiliated to Istituto Pasteur-Fondazione Cenci Bolognetti, DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Laura Pelosi
- Laboratory Affiliated to Istituto Pasteur-Fondazione Cenci Bolognetti, DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Simona Pisu
- Laboratory Affiliated to Istituto Pasteur-Fondazione Cenci Bolognetti, DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Piergiorgio La Rosa
- IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy
| | - Eleonora Cesari
- IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy.,Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Heart, Rome, Italy
| | - Carmine Nicoletti
- Laboratory Affiliated to Istituto Pasteur-Fondazione Cenci Bolognetti, DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Luca Madaro
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Heart, Rome, Italy
| | - Neri Mercatelli
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico," Rome, Italy.,IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy
| | - Filippo Biamonte
- Institute of Biochemistry and Clinical Biochemistry, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Annalisa Nobili
- IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy.,Department of Medicine, University Campus-Biomedico, Rome, Italy
| | - Marcello D'Amelio
- IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy.,Department of Medicine, University Campus-Biomedico, Rome, Italy
| | - Marco De Bardi
- IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy
| | - Elisabetta Volpe
- IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy
| | - Daniela Caporossi
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico," Rome, Italy
| | - Claudio Sette
- IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy .,Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Heart, Rome, Italy
| | - Antonio Musarò
- Laboratory Affiliated to Istituto Pasteur-Fondazione Cenci Bolognetti, DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico," Rome, Italy .,IRCCS (Institute for Treatment and Research) Fondazione Santa Lucia, Rome, Italy
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17
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Subramania S, Gagné LM, Campagne S, Fort V, O'Sullivan J, Mocaer K, Feldmüller M, Masson JY, Allain FHT, Hussein SM, Huot MÉ. SAM68 interaction with U1A modulates U1 snRNP recruitment and regulates mTor pre-mRNA splicing. Nucleic Acids Res 2019; 47:4181-4197. [PMID: 30767021 PMCID: PMC6486544 DOI: 10.1093/nar/gkz099] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Abstract
Src associated in mitosis (SAM68) plays major roles in regulating RNA processing events, such as alternative splicing and mRNA translation, implicated in several developmental processes. It was previously shown that SAM68 regulates the alternative splicing of the mechanistic target of rapamycin (mTor), but the mechanism regulating this process remains elusive. Here, we report that SAM68 interacts with U1 small nuclear ribonucleoprotein (U1 snRNP) to promote splicing at the 5′ splice site in intron 5 of mTor. We also show that this direct interaction is mediated through U1A, a core-component of U1snRNP. SAM68 was found to bind the RRM1 domain of U1A through its C-terminal tyrosine rich region (YY domain). Deletion of the U1A-SAM68 interaction domain or mutation in SAM68-binding sites in intron 5 of mTor abrogates U1A recruitment and 5′ splice site recognition by the U1 snRNP, leading to premature intron 5 termination and polyadenylation. Taken together, our results provide the first mechanistic study by which SAM68 modulates alternative splicing decision, by affecting U1 snRNP recruitment at 5′ splice sites.
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Affiliation(s)
- Suryasree Subramania
- Centre de recherche du CHU de Québec-Université Laval (axe Oncologie), Québec, QC G1R 3S3, Canada.,CRCHU de Québec - Axe Oncologie, Québec, QC G1R 3S3, Canada
| | - Laurence M Gagné
- Centre de recherche du CHU de Québec-Université Laval (axe Oncologie), Québec, QC G1R 3S3, Canada.,CRCHU de Québec - Axe Oncologie, Québec, QC G1R 3S3, Canada
| | - Sébastien Campagne
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Victoire Fort
- Centre de recherche du CHU de Québec-Université Laval (axe Oncologie), Québec, QC G1R 3S3, Canada.,CRCHU de Québec - Axe Oncologie, Québec, QC G1R 3S3, Canada
| | - Julia O'Sullivan
- Centre de recherche du CHU de Québec-Université Laval (axe Oncologie), Québec, QC G1R 3S3, Canada.,CRCHU de Québec - Axe Oncologie, Québec, QC G1R 3S3, Canada
| | - Karel Mocaer
- Centre de recherche du CHU de Québec-Université Laval (axe Oncologie), Québec, QC G1R 3S3, Canada
| | - Miki Feldmüller
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jean-Yves Masson
- Centre de recherche du CHU de Québec-Université Laval (axe Oncologie), Québec, QC G1R 3S3, Canada.,CRCHU de Québec - Axe Oncologie, Québec, QC G1R 3S3, Canada
| | - Frédéric H T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Samer M Hussein
- Centre de recherche du CHU de Québec-Université Laval (axe Oncologie), Québec, QC G1R 3S3, Canada.,CRCHU de Québec - Axe Oncologie, Québec, QC G1R 3S3, Canada
| | - Marc-Étienne Huot
- Centre de recherche du CHU de Québec-Université Laval (axe Oncologie), Québec, QC G1R 3S3, Canada.,CRCHU de Québec - Axe Oncologie, Québec, QC G1R 3S3, Canada
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18
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Iijima Y, Tanaka M, Suzuki S, Hauser D, Tanaka M, Okada C, Ito M, Ayukawa N, Sato Y, Ohtsuka M, Scheiffele P, Iijima T. SAM68-Specific Splicing Is Required for Proper Selection of Alternative 3' UTR Isoforms in the Nervous System. iScience 2019; 22:318-335. [PMID: 31805436 PMCID: PMC6909182 DOI: 10.1016/j.isci.2019.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/09/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022] Open
Abstract
Neuronal alternative splicing is a core mechanism for functional diversification. We previously found that STAR family proteins (SAM68, SLM1, SLM2) regulate spatiotemporal alternative splicing in the nervous system. However, the whole aspect of alternative splicing programs by STARs remains unclear. Here, we performed a transcriptomic analysis using SAM68 knockout and SAM68/SLM1 double-knockout midbrains. We revealed different alternative splicing activity between SAM68 and SLM1; SAM68 preferentially targets alternative 3′ UTR exons. SAM68 knockout causes a long-to-short isoform switch of a number of neuronal targets through the alteration in alternative last exon (ALE) selection or alternative polyadenylation. The altered ALE usage of a novel target, interleukin 1 receptor accessory protein (Il1rap), results in remarkable conversion from a membrane-bound type to a secreted type in Sam68KO brains. Proper ALE selection is necessary for IL1RAP neuronal function. Thus the SAM68-specific splicing program provides a mechanism for neuronal selection of alternative 3′ UTR isoforms. SAM68 and the related protein SLM1 exhibit distinct alternative splicing activity SAM68 specifically controls 3′ UTR selection of multiple neuronal genes Proper 3′ UTR selection is necessary for IL1RAP neuronal function Neuronal expression of SAM68 requires proper 3′ UTR selection in the nervous system
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Affiliation(s)
- Yoko Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Masami Tanaka
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Satoko Suzuki
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - David Hauser
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel 4056, Switzerland
| | - Masayuki Tanaka
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Chisa Okada
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Masatoshi Ito
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Noriko Ayukawa
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Yuji Sato
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Peter Scheiffele
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel 4056, Switzerland
| | - Takatoshi Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
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19
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Witte H, Schreiner D, Scheiffele P. A Sam68-dependent alternative splicing program shapes postsynaptic protein complexes. Eur J Neurosci 2019; 49:1436-1453. [PMID: 30589479 DOI: 10.1111/ejn.14332] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 12/30/2022]
Abstract
Alternative splicing is one of the key mechanisms to increase the diversity of cellular transcriptomes, thereby expanding the coding capacity of the genome. This diversity is of particular importance in the nervous system with its elaborated cellular networks. Sam68, a member of the Signal Transduction Associated RNA-binding (STAR) family of RNA-binding proteins, is expressed in the developing and mature nervous system but its neuronal functions are poorly understood. Here, we perform genome-wide mapping of the Sam68-dependent alternative splicing program in mice. We find that Sam68 is required for the regulation of a set of alternative splicing events in pre-mRNAs encoding several postsynaptic scaffolding molecules that are central to the function of GABAergic and glutamatergic synapses. These components include Collybistin (Arhgef9), Gephyrin (Gphn), and Densin-180 (Lrrc7). Sam68-regulated Lrrc7 variants engage in differential protein interactions with signalling proteins, thus, highlighting a contribution of the Sam68 splicing program to shaping synaptic complexes. These findings suggest an important role for Sam68-dependent alternative splicing in the regulation of synapses in the central nervous system.
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Affiliation(s)
- Harald Witte
- Biozentrum of the University of Basel, Basel, Switzerland
| | - Dietmar Schreiner
- Biozentrum of the University of Basel, Basel, Switzerland.,Institute of Neuroanatomy and Cell Biology, Hannover, Germany
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20
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Südhof TC. Synaptic Neurexin Complexes: A Molecular Code for the Logic of Neural Circuits. Cell 2017; 171:745-769. [PMID: 29100073 DOI: 10.1016/j.cell.2017.10.024] [Citation(s) in RCA: 478] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/04/2017] [Accepted: 10/15/2017] [Indexed: 10/18/2022]
Abstract
Synapses are specialized junctions between neurons in brain that transmit and compute information, thereby connecting neurons into millions of overlapping and interdigitated neural circuits. Here, we posit that the establishment, properties, and dynamics of synapses are governed by a molecular logic that is controlled by diverse trans-synaptic signaling molecules. Neurexins, expressed in thousands of alternatively spliced isoforms, are central components of this dynamic code. Presynaptic neurexins regulate synapse properties via differential binding to multifarious postsynaptic ligands, such as neuroligins, cerebellin/GluD complexes, and latrophilins, thereby shaping the input/output relations of their resident neural circuits. Mutations in genes encoding neurexins and their ligands are associated with diverse neuropsychiatric disorders, especially schizophrenia, autism, and Tourette syndrome. Thus, neurexins nucleate an overall trans-synaptic signaling network that controls synapse properties, which thereby determines the precise responses of synapses to spike patterns in a neuron and circuit and which is vulnerable to impairments in neuropsychiatric disorders.
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Affiliation(s)
- Thomas C Südhof
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University Medical School, 265 Campus Drive, CA 94305-5453, USA.
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21
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Popovitchenko T, Rasin MR. Transcriptional and Post-Transcriptional Mechanisms of the Development of Neocortical Lamination. Front Neuroanat 2017; 11:102. [PMID: 29170632 PMCID: PMC5684109 DOI: 10.3389/fnana.2017.00102] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/25/2017] [Indexed: 12/31/2022] Open
Abstract
The neocortex is a laminated brain structure that is the seat of higher cognitive capacity and responses, long-term memory, sensory and emotional functions, and voluntary motor behavior. Proper lamination requires that progenitor cells give rise to a neuron, that the immature neuron can migrate away from its mother cell and past other cells, and finally that the immature neuron can take its place and adopt a mature identity characterized by connectivity and gene expression; thus lamination proceeds through three steps: genesis, migration, and maturation. Each neocortical layer contains pyramidal neurons that share specific morphological and molecular characteristics that stem from their prenatal birth date. Transcription factors are dynamic proteins because of the cohort of downstream factors that they regulate. RNA-binding proteins are no less dynamic, and play important roles in every step of mRNA processing. Indeed, recent screens have uncovered post-transcriptional mechanisms as being integral regulatory mechanisms to neocortical development. Here, we summarize major aspects of neocortical laminar development, emphasizing transcriptional and post-transcriptional mechanisms, with the aim of spurring increased understanding and study of its intricacies.
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Affiliation(s)
- Tatiana Popovitchenko
- Neuroscience and Cell Biology, Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Mladen-Roko Rasin
- Neuroscience and Cell Biology, Robert Wood Johnson Medical School, New Brunswick, NJ, United States
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22
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Wen H, Li P, Ma H, Zheng J, Yu Y, Lv G. High expression of Sam68 in sacral chordomas is associated with worse clinical outcomes. Onco Targets Ther 2017; 10:4691-4700. [PMID: 29026317 PMCID: PMC5626414 DOI: 10.2147/ott.s147446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Src-associated in mitosis of 68 kDa (Sam68), also known as KHDRBS1 (KH domain-containing, RNA-binding, signal transduction-associated 1), is a member of the signal transduction and activation of RNA family. Previous studies have demonstrated that the aberrant expression of Sam68 is associated with the progression and prognosis of a variety of cancers, but little is known about its expression and role in chordomas, which are rare and aggressive bone neoplasms. In this study, we analyzed 40 tumor tissues and 20 distant normal tissues obtained from 40 patients with sacral chordoma using immunohistochemistry, and observed the expression of Sam68 was significantly upregulated in sacral chordomas compared with normal tissues (P=0.001). A positive correlation between the expression of Sam68 and the cell proliferation index Ki-67 was determined using Spearman’s rank correlation test (γ =0.599, P<0.001). In addition, high expression of Sam68 was significantly associated with surrounding muscle invasion (P<0.001). Moreover, Kaplan–Meier curves showed that patients with overexpressed Sam68 had shorter local recurrence-free survival time (P<0.001). Lastly, multivariate analysis indicated that Sam68 is an independent prognostic factor for the local recurrence-free survival of sacral chordomas (hazard ratio =5.929, 95% CI: 1.092–32.188, P=0.039). Our findings suggest the use of Sam68 as a predictor for the recurrence of sacral chordomas.
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Affiliation(s)
- Hai Wen
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Pengzhi Li
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hong Ma
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiaoyun Zheng
- Department of Pathology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yipin Yu
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Guohua Lv
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Danilenko M, Dalgliesh C, Pagliarini V, Naro C, Ehrmann I, Feracci M, Kheirollahi-Chadegani M, Tyson-Capper A, Clowry GJ, Fort P, Dominguez C, Sette C, Elliott DJ. Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control. Nucleic Acids Res 2017; 45:4120-4130. [PMID: 27994030 PMCID: PMC5397175 DOI: 10.1093/nar/gkw1277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 12/08/2016] [Indexed: 01/09/2023] Open
Abstract
SLM2 and Sam68 are splicing regulator paralogs that usually overlap in function, yet only SLM2 and not Sam68 controls the Neurexin2 AS4 exon important for brain function. Herein we find that SLM2 and Sam68 similarly bind to Neurexin2 pre-mRNA, both within the mouse cortex and in vitro. Protein domain-swap experiments identify a region including the STAR domain that differentiates SLM2 and Sam68 activity in splicing target selection, and confirm that this is not established via the variant amino acids involved in RNA contact. However, far fewer SLM2 and Sam68 RNA binding sites flank the Neurexin2 AS4 exon, compared with those flanking the Neurexin1 and Neurexin3 AS4 exons under joint control by both Sam68 and SLM2. Doubling binding site numbers switched paralog sensitivity, by placing the Neurexin2 AS4 exon under joint splicing control by both Sam68 and SLM2. Our data support a model where the density of shared RNA binding sites around a target exon, rather than different paralog-specific protein-RNA binding sites, controls functional target specificity between SLM2 and Sam68 on the Neurexin2 AS4 exon. Similar models might explain differential control by other splicing regulators within families of paralogs with indistinguishable RNA binding sites.
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Affiliation(s)
- Marina Danilenko
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Caroline Dalgliesh
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Vittoria Pagliarini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy.,Laboratory of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Chiara Naro
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy.,Laboratory of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Ingrid Ehrmann
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Mikael Feracci
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | | | - Alison Tyson-Capper
- Institute for Cellular Medicine, Newcastle University, Framlington Place, Newcastle NE2 4HH, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle, UK
| | - Philippe Fort
- Université Montpellier, UMR 5237, Centre de Recherche de Biologie cellulaire de Montpellier, CNRS, 34293 Montpellier, France
| | - Cyril Dominguez
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Claudio Sette
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy.,Laboratory of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - David J Elliott
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
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Mannen T, Yamashita S, Tomita K, Goshima N, Hirose T. The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL. J Cell Biol 2017; 214:45-59. [PMID: 27377249 PMCID: PMC4932371 DOI: 10.1083/jcb.201601024] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/14/2016] [Indexed: 01/21/2023] Open
Abstract
The mammalian cell nucleus contains membraneless suborganelles referred to as nuclear bodies (NBs). Some NBs are formed with an architectural RNA (arcRNA) as the structural core. Here, we searched for new NBs that are built on unidentified arcRNAs by screening for ribonuclease (RNase)-sensitive NBs using 32,651 fluorescently tagged human cDNA clones. We identified 32 tagged proteins that required RNA for their localization in distinct nuclear foci. Among them, seven RNA-binding proteins commonly localized in the Sam68 nuclear body (SNB), which was disrupted by RNase treatment. Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures.
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Affiliation(s)
- Taro Mannen
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Seisuke Yamashita
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Kozo Tomita
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koutou 135-0064, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
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25
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Faus-Garriga J, Novoa I, Ozaita A. mTOR signaling in proteostasis and its relevance to autism spectrum disorders. AIMS BIOPHYSICS 2017. [DOI: 10.3934/biophy.2017.1.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Abstract
During pre-mRNA splicing events, introns are removed from the pre-mRNA, and the remaining exons are connected together to form a single continuous molecule. Alternative splicing is a common mechanism for the regulation of gene expression in eukaryotes. More than 90% of human genes are known to undergo alternative splicing. The most common type of alternative splicing is exon skipping, which is also known as cassette exon. Other known alternative splicing events include alternative 5' splice sites, alternative 3' splice sites, intron retention, and mutually exclusive exons. Alternative splicing events are controlled by regulatory proteins responsible for both positive and negative regulation. In this review, we focus on neuronal splicing regulators and discuss several notable regulators in depth. In addition, we have also included an example of splicing regulation mediated by the RBFox protein family. Lastly, as previous studies have shown that a number of splicing factors are associated with neuronal diseases such as Alzheime's disease (AD) and Autism spectrum disorder (ASD), here we consider their importance in neuronal diseases wherein the underlying mechanisms have yet to be elucidated.
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Affiliation(s)
- Nor Hakimah Ab Hakim
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia
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27
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Wang Y, Zhang W, Wang X, Wang D, Xie J, Tang C, Xi Q, Zhong J, Deng Y. Expression of Sam68 Correlates With Cell Proliferation and Survival in Epithelial Ovarian Cancer. Reprod Sci 2016; 24:97-108. [PMID: 27222230 DOI: 10.1177/1933719116650757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Src associated in mitosis, 68 kDa (Sam68) is a KH domain RNA-binding protein that belongs to the signal transduction and activation of RNA family. It is a multifunctional protein known to regulate cellular signal transduction, transcription, RNA metabolism, proliferation, and apoptosis, thus implicated in tumor growth. Herein, we investigated the clinical significance of Sam68 in human epithelial ovarian cancer (EOC). Western blot and immunohistochemical staining demonstrated that Sam68 expression was upregulated in EOC tissues and cell lines. Statistical analysis showed that high expression of Sam68 correlated with poor prognosis of patients with EOC. In vitro, serum starvation-refeeding experiment was primarily performed to confirm that Sam68 participated in the cell cycle progression of EOC cell lines. Then knocking down Sam68 level with small interfering RNA, cell cycle was arrested at G1 phase and cell proliferation impaired. Furthermore, we demonstrated that the antiproliferative effect of silencing Sam68 in EOC cells was associated with the upregulation of cyclin-dependent kinase inhibitors p21Cip1 and p27Kip1, along with the downregulation of p-FOXO3a, p-Akt, and p-GSK-3β. Taken together, our findings uncovered that Sam68 played an important role in promoting the proliferation of human ovarian cancer, thereby might be a novel therapeutic target for EOC.
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Affiliation(s)
- Yingying Wang
- 1 Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Department of Pathogen Biology, Medical College, Nantong University, Nantong, People's Republic of China
| | - Weiwei Zhang
- 2 Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Xia Wang
- 3 Center for Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Di Wang
- 3 Center for Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Juan Xie
- 3 Center for Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Chunhui Tang
- 2 Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Qinghua Xi
- 2 Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Jianxin Zhong
- 2 Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Yan Deng
- 2 Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
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28
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Yang WY, He F, Strack RL, Oh SY, Frazer M, Jaffrey SR, Todd PK, Disney MD. Small Molecule Recognition and Tools to Study Modulation of r(CGG)(exp) in Fragile X-Associated Tremor Ataxia Syndrome. ACS Chem Biol 2016; 11:2456-65. [PMID: 27276216 DOI: 10.1021/acschembio.6b00147] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA transcripts containing expanded nucleotide repeats cause many incurable diseases via various mechanisms. One such disorder, fragile X-associated tremor ataxia syndrome (FXTAS), is caused by a noncoding r(CGG) repeat expansion (r(CGG)(exp)) that (i) sequesters proteins involved in RNA metabolism in nuclear foci, causing dysregulation of alternative pre-mRNA splicing, and (ii) undergoes repeat associated non-ATG translation (RANT), which produces toxic homopolymeric proteins without using a start codon. Here, we describe the design of two small molecules that inhibit both modes of toxicity and the implementation of various tools to study perturbation of these cellular events. Competitive Chemical Cross Linking and Isolation by Pull Down (C-Chem-CLIP) established that compounds bind r(CGG)(exp) and defined small molecule occupancy of r(CGG)(exp) in cells, the first approach to do so. Using an RNA GFP mimic, r(CGG)(exp)-Spinach2, we observe that our optimal designed compound binds r(CGG)(exp) and affects RNA localization by disrupting preformed RNA foci. These events correlate with an improvement of pre-mRNA splicing defects caused by RNA gain of function. In addition, the compounds reduced levels of toxic homopolymeric proteins formed via RANT. Polysome profiling studies showed that small molecules decreased loading of polysomes onto r(CGG)(exp), explaining decreased translation.
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Affiliation(s)
- Wang-Yong Yang
- Departments
of Chemistry and Neuroscience, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Fang He
- Department
of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, United States
| | - Rita L. Strack
- Department
of Pharmacology, Weill Medical College of Cornell University, 1300
York Avenue, Box 70, New York, New York 10065, United States
| | - Seok Yoon Oh
- Department
of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, United States
| | - Michelle Frazer
- Department
of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, United States
| | - Samie R. Jaffrey
- Department
of Pharmacology, Weill Medical College of Cornell University, 1300
York Avenue, Box 70, New York, New York 10065, United States
| | - Peter K. Todd
- Department
of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, United States
| | - Matthew D. Disney
- Departments
of Chemistry and Neuroscience, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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29
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Dong L, Che H, Li M, Li X. Sam68 is Overexpressed in Epithelial Ovarian Cancer and Promotes Tumor Cell Proliferation. Med Sci Monit 2016; 22:3248-56. [PMID: 27623016 PMCID: PMC5031168 DOI: 10.12659/msm.899980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Epithelial ovarian cancer (EOC) is the deadliest gynecological malignancy, and evidence is accumulating on how molecular markers may be associated with the origin and process of EOC. Sam68 (Src-associated in mitosis, of 68 kD), is a K homology domain RNA-binding protein that has been investigated as a risk factor in multiple types of tumors. The aim of the present study was to investigate the contribution of the Sam68 gene in the pathogenesis of EOC. MATERIAL AND METHODS Western blot assay and real-time quantitative PCR methods were performed to examine Sam68 expression in EOC tissue specimens. The association of Sam68 expression with clinic-pathologic variables of EOC was evaluated. Then gain-of-function and loss-of-function strategies were adopted to examine the regulation of Sam68 on the proliferation of EOC OVCAR-3 cells using CCK-8 and colony forming assays. RESULTS Sam68 was overexpressed in both mRNA and protein levels in EOC tumor tissue (n=152) in an association with malignant factors of EOC such as International Federation of Gynecology and Obstetrics (FIGO) stage, residual tumor size (cm), histological grade, and lymph node metastasis. In vitro results demonstrated that Sam68 overexpression was upregulated while Sam68 knockdown downregulated the proliferation of EOC OVCAR-3 cells via regulation of cell growth and colony formation. CONCLUSIONS Sam68 was overexpressed in EOC tissue in association with such cancer malignant factors of FIGO stage, histological grade, and lymph node metastasis, and also positively regulated the proliferation of EOC cells. Our research suggests that Sam68 might accelerate cell cycle progression, and present as a prognostic marker for EOC.
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Affiliation(s)
- Lijuan Dong
- Department of Obstetrics and Gynecology, Zaozhuang Municipal Hospital, Zaozhuang, Shandong, China (mainland)
| | - Hailuo Che
- Department of Obstetrics and Gynecology, Zaozhuang Municipal Hospital, Zaozhuang, Shandong, China (mainland)
| | - Mingmei Li
- , Health and Family Planning Bureau in Shanting District, Zaozhuang, Shandong, China (mainland)
| | - Xuepeng Li
- Department of Obstetrics and Gynecology, Zaozhuang Municipal Hospital, Zaozhuang, Shandong, China (mainland)
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30
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Sam68 Mediates the Activation of Insulin and Leptin Signalling in Breast Cancer Cells. PLoS One 2016; 11:e0158218. [PMID: 27415018 PMCID: PMC4944952 DOI: 10.1371/journal.pone.0158218] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 06/13/2016] [Indexed: 12/23/2022] Open
Abstract
Obesity is a well-known risk factor for breast cancer development in postmenopausal women. High insulin and leptin levels seem to have a role modulating the growth of these tumours. Sam68 is an RNA-binding protein with signalling functions that has been found to be overexpressed in breast cancer. Moreover, Sam68 may be recruited to insulin and leptin signalling pathways, mediating its effects on survival, growth and proliferation in different cellular types. We aimed to study the expression of Sam68 and its phosphorylation level upon insulin and leptin stimulation, and the role of Sam68 in the proliferative effect and signalling pathways that are activated by insulin or leptin in human breast adenocarcinoma cells. In the human breast adenocarcinoma cell lines MCF7, MDA-MB-231 and BT-474, Sam68 protein quantity and gene expression were increased upon leptin or insulin stimulation, as it was checked by qPCR and immunoblot. Moreover, both insulin and leptin stimulation promoted an increase in Sam68 tyrosine phosphorylation and negatively regulated its RNA binding capacity. siRNA was used to downregulate Sam68 expression, which resulted in lower proliferative effects of both insulin and leptin, as well as a lower activation of MAPK and PI3K pathways promoted by both hormones. These effects may be partly explained by the decrease in IRS-1 expression by down-regulation of Sam68. These results suggest the participation of Sam68 in both leptin and insulin receptor signaling in human breast cancer cells, mediating the trophic effects of these hormones in proliferation and cellular growth.
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31
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Wang Q, Li Y, Cheng J, Chen L, Xu H, Li Q, Pang T. Sam68 affects cell proliferation and apoptosis of human adult T-acute lymphoblastic leukemia cells via AKT/mTOR signal pathway. Leuk Res 2016; 46:1-9. [DOI: 10.1016/j.leukres.2016.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 01/02/2023]
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32
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Iijima T, Hidaka C, Iijima Y. Spatio-temporal regulations and functions of neuronal alternative RNA splicing in developing and adult brains. Neurosci Res 2016; 109:1-8. [PMID: 26853282 DOI: 10.1016/j.neures.2016.01.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 10/25/2022]
Abstract
Alternative pre-mRNA splicing is a fundamental mechanism that generates molecular diversity from a single gene. In the central nervous system (CNS), key neural developmental steps are thought to be controlled by alternative splicing decisions, including the molecular diversity underlying synaptic wiring, plasticity, and remodeling. Significant progress has been made in understanding the molecular mechanisms and functions of alternative pre-mRNA splicing in neurons through studies in invertebrate systems; however, recent studies have begun to uncover the potential role of neuronal alternative splicing in the mammalian CNS. This article provides an overview of recent findings regarding the regulation and function of neuronal alternative splicing. In particular, we focus on the spatio-temporal regulation of neurexin, a synaptic adhesion molecule, by neuronal cell type-specific factors and neuronal activity, which are thought to be especially important for characterizing neural development and function within the mammalian CNS. Notably, there is increasing evidence that implicates the dysregulation of neuronal splicing events in several neurological disorders. Therefore, understanding the detailed mechanisms of neuronal alternative splicing in the mammalian CNS may provide plausible treatment strategies for these diseases.
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Affiliation(s)
- Takatoshi Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Tokai University Institute of Innovative Science and Technology, 4-1-1 Kitakaname, Hiratsuka City, Kanagawa 259-1292, Japan; School of Medicine, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan.
| | - Chiharu Hidaka
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Tokai University Institute of Innovative Science and Technology, 4-1-1 Kitakaname, Hiratsuka City, Kanagawa 259-1292, Japan; School of Medicine, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Yoko Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Tokai University Institute of Innovative Science and Technology, 4-1-1 Kitakaname, Hiratsuka City, Kanagawa 259-1292, Japan; School of Medicine, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
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Feracci M, Foot JN, Grellscheid SN, Danilenko M, Stehle R, Gonchar O, Kang HS, Dalgliesh C, Meyer NH, Liu Y, Lahat A, Sattler M, Eperon IC, Elliott DJ, Dominguez C. Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68. Nat Commun 2016; 7:10355. [PMID: 26758068 PMCID: PMC4735526 DOI: 10.1038/ncomms10355] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 12/01/2015] [Indexed: 11/13/2022] Open
Abstract
Sam68 and T-STAR are members of the STAR family of proteins that directly link signal transduction with post-transcriptional gene regulation. Sam68 controls the alternative splicing of many oncogenic proteins. T-STAR is a tissue-specific paralogue that regulates the alternative splicing of neuronal pre-mRNAs. STAR proteins differ from most splicing factors, in that they contain a single RNA-binding domain. Their specificity of RNA recognition is thought to arise from their property to homodimerize, but how dimerization influences their function remains unknown. Here, we establish at atomic resolution how T-STAR and Sam68 bind to RNA, revealing an unexpected mode of dimerization different from other members of the STAR family. We further demonstrate that this unique dimerization interface is crucial for their biological activity in splicing regulation, and suggest that the increased RNA affinity through dimer formation is a crucial parameter enabling these proteins to select their functional targets within the transcriptome. Sam68 and T-STAR are members of the STAR family of proteins, which regulate various aspects of RNA metabolism. Here, the authors reveal structural features required for alternative splicing regulation by these proteins.
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Affiliation(s)
- Mikael Feracci
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Jaelle N Foot
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Sushma N Grellscheid
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Marina Danilenko
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Ralf Stehle
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, DE-85747 Garching, Germany
| | - Oksana Gonchar
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Hyun-Seo Kang
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, DE-85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, DE-85764 Oberschleißheim, Germany
| | - Caroline Dalgliesh
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - N Helge Meyer
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, DE-85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, DE-85764 Oberschleißheim, Germany
| | - Yilei Liu
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Albert Lahat
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK
| | - Michael Sattler
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, DE-85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, DE-85764 Oberschleißheim, Germany
| | - Ian C Eperon
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
| | - David J Elliott
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Cyril Dominguez
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
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Proteostasis and RNA Binding Proteins in Synaptic Plasticity and in the Pathogenesis of Neuropsychiatric Disorders. Neural Plast 2016; 2016:3857934. [PMID: 26904297 PMCID: PMC4745388 DOI: 10.1155/2016/3857934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/30/2015] [Indexed: 12/30/2022] Open
Abstract
Decades of research have demonstrated that rapid alterations in protein abundance are required for synaptic plasticity, a cellular correlate for learning and memory. Control of protein abundance, known as proteostasis, is achieved across a complex neuronal morphology that includes a tortuous axon as well as an extensive dendritic arbor supporting thousands of individual synaptic compartments. To regulate the spatiotemporal synthesis of proteins, neurons must efficiently coordinate the transport and metabolism of mRNAs. Among multiple levels of regulation, transacting RNA binding proteins (RBPs) control proteostasis by binding to mRNAs and mediating their transport and translation in response to synaptic activity. In addition to synthesis, protein degradation must be carefully balanced for optimal proteostasis, as deviations resulting in excess or insufficient abundance of key synaptic factors produce pathologies. As such, mutations in components of the proteasomal or translational machinery, including RBPs, have been linked to the pathogenesis of neurological disorders such as Fragile X Syndrome (FXS), Fragile X Tremor Ataxia Syndrome (FXTAS), and Autism Spectrum Disorders (ASD). In this review, we summarize recent scientific findings, highlight ongoing questions, and link basic molecular mechanisms to the pathogenesis of common neuropsychiatric disorders.
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The RNA-binding protein Sam68 regulates tumor cell viability and hepatic carcinogenesis by inhibiting the transcriptional activity of FOXOs. J Mol Histol 2015; 46:485-97. [PMID: 26438629 DOI: 10.1007/s10735-015-9639-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 09/30/2015] [Indexed: 12/31/2022]
Abstract
Src associated in mitosis (Sam68; 68 kDa) is a KH domain RNA-binding protein that belongs to the signal transduction and activation of RNA family, and has been implicated in the oncogenesis and progression of several human cancers. Our study aimed to investigated the clinicopathologic significance of Sam68 expression and its role in cell proliferation and the underlying molecular mechanism in hepatocellular carcinoma (HCC). We demonstrated that Sam68 expression was significantly increased in HCC and high expression of Sam68 was significantly associated with Edmondson grade, tumor size, tumor nodule number, HBsAg status and Ki-67 expression. The Kaplan-Meier survival curves showed that increased expression of Sam68 was correlated with poor prognosis in HCC patients and served as an independent prognostic marker of overall survival in a multivariable analysis. In addition, through serum starvation and refeeding assay, we demonstrated that Sam68 was lowly expressed in serum-starved HCC cells, and was progressively increased after serum-additioning. Furthermore, siRNA knockdown of endogenous Sam68 inhibited cell proliferation and tumourigenicity of HCC cells in vitro, through blocking the G1 to S phase transition. Moreover, we reported that the anti-proliferative effect of silencing Sam68 was accompanied with up-regulated expression of cyclin-dependent kinase inhibitors, p21(Cip1) and p27(Kip1), enhanced transactivation of FOXO factors (FOXO4), and dysreuglation of Akt/GSK-3β signaling. Taken together, these findings provide a rational framework for the progression of HCC and thereby indicated that Sam68 might be a novel and useful prognostic marker and a potential target for human HCC treatment.
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Crisci A, Raleff F, Bagdiul I, Raabe M, Urlaub H, Rain JC, Krämer A. Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins. Nucleic Acids Res 2015; 43:10456-73. [PMID: 26420826 PMCID: PMC4666396 DOI: 10.1093/nar/gkv952] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 09/10/2015] [Indexed: 02/03/2023] Open
Abstract
Splicing factor 1 (SF1) recognizes the branch point sequence (BPS) at the 3′ splice site during the formation of early complex E, thereby pre-bulging the BPS adenosine, thought to facilitate subsequent base-pairing of the U2 snRNA with the BPS. The 65-kDa subunit of U2 snRNP auxiliary factor (U2AF65) interacts with SF1 and was shown to recruit the U2 snRNP to the spliceosome. Co-immunoprecipitation experiments of SF1-interacting proteins from HeLa cell extracts shown here are consistent with the presence of SF1 in early splicing complexes. Surprisingly almost all U2 snRNP proteins were found associated with SF1. Yeast two-hybrid screens identified two SURP domain-containing U2 snRNP proteins as partners of SF1. A short, evolutionarily conserved region of SF1 interacts with the SURP domains, stressing their role in protein–protein interactions. A reduction of A complex formation in SF1-depleted extracts could be rescued with recombinant SF1 containing the SURP-interaction domain, but only partial rescue was observed with SF1 lacking this sequence. Thus, SF1 can initially recruit the U2 snRNP to the spliceosome during E complex formation, whereas U2AF65 may stabilize the association of the U2 snRNP with the spliceosome at later times. In addition, these findings may have implications for alternative splicing decisions.
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Affiliation(s)
- Angela Crisci
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Flore Raleff
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Ivona Bagdiul
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Monika Raabe
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | | | - Angela Krämer
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
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Wang Y, Liang L, Zhang J, Li M, Zhu J, Gong C, Yang L, Zhu J, Chen L, Ni R. Sam68 promotes cellular proliferation and predicts poor prognosis in esophageal squamous cell carcinoma. Tumour Biol 2015; 36:8735-45. [PMID: 26050229 DOI: 10.1007/s13277-015-3631-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/31/2015] [Indexed: 12/14/2022] Open
Abstract
Sam68 (Src-associated in mitosis of 68 kD) is a KH domain RNA-binding protein. The expression of Sam68 was correlated with kinds of tumors. Yet, the expression mechanisms and physiological significance of Sam68 in ESCC remains unclear. In this study, we clarified a potential role of Sam68 in the treatment of ESCC. Western blot and immunohistochemistry (IHC) analysis revealed that the protein level of Sam68 was higher in ESCC tumor tissues and cell lines. In addition, IHC stain revealed that Sam68 was positively correlated with clinical pathologic variables such as tumor grade and tumor invasion. In addition, Sam68 could be an independent prognostic indicator for patients' overall survival. In vitro studies such as starvation and refeeding assay along with Sam68-shRNA transfection assay demonstrated that Sam68 expression promoted proliferation of ESCC cells. And Sam68 downregulation caused decreased rate of cell growth and colony formation. Reasons are associated with growth arrest of cell cycle at G1/S phase. Moreover, our results clarified that Sam68 could promote ESCC cell proliferation via the activation of Akt/GSK-3β pathway. This research indicated that Sam68 might accelerate the cell cycle progression and be considered as a new therapy target in ESCC.
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Affiliation(s)
- Yayun Wang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Li Liang
- Department of Medical Oncology, Affiliated Hospital of Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Jianguo Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Mei Li
- Department of Medical Oncology, Affiliated Hospital of Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Junya Zhu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Chen Gong
- Department of Gastroenterology, Affiliated Hospital of Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Linlin Yang
- Department of Oncology, Affiliated Cancer Hospital of Nantong University, Nantong, 226361, Jiangsu, China
| | - Jia Zhu
- Department of Oncology, Affiliated Cancer Hospital of Nantong University, Nantong, 226361, Jiangsu, China
| | - Lingling Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Runzhou Ni
- Department of Gastroenterology, Affiliated Hospital of Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China.
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Sam68 Regulates S6K1 Alternative Splicing during Adipogenesis. Mol Cell Biol 2015; 35:1926-39. [PMID: 25776557 DOI: 10.1128/mcb.01488-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/11/2015] [Indexed: 01/13/2023] Open
Abstract
The requirement for alternative splicing during adipogenesis is poorly understood. The Sam68 RNA binding protein is a known regulator of alternative splicing, and mice deficient for Sam68 exhibit adipogenesis defects due to defective mTOR signaling. Sam68 null preadipocytes were monitored for alternative splicing imbalances in components of the mTOR signaling pathway. Herein, we report that Sam68 regulates isoform expression of the ribosomal S6 kinase gene (Rps6kb1). Sam68-deficient adipocytes express Rps6kb1-002 and its encoded p31S6K1 protein, in contrast to wild-type adipocytes that do not express this isoform. Sam68 binds an RNA sequence encoded by Rps6kb1 intron 6 and prevents serine/arginine-rich splicing factor 1 (SRSF1)-mediated alternative splicing of Rps6kb1-002, as assessed by cross-linking and immunoprecipitation (CLIP) and minigene assays. Depletion of p31S6K1 with small interfering RNAs (siRNAs) partially restored adipogenesis of Sam68-deficient preadipocytes. The ectopic expression of p31S6K1 in wild-type 3T3-L1 cells resulted in adipogenesis differentiation defects, showing that p31S6K1 is an inhibitor of adipogenesis. Our findings indicate that Sam68 is required to prevent the expression of p31S6K1 in adipocytes for adipogenesis to occur.
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Pedrotti S, Giudice J, Dagnino-Acosta A, Knoblauch M, Singh RK, Hanna A, Mo Q, Hicks J, Hamilton S, Cooper TA. The RNA-binding protein Rbfox1 regulates splicing required for skeletal muscle structure and function. Hum Mol Genet 2015; 24:2360-74. [PMID: 25575511 DOI: 10.1093/hmg/ddv003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Rbfox family of RNA-binding proteins is highly conserved with established roles in alternative splicing (AS) regulation. High-throughput studies aimed at understanding transcriptome remodeling have revealed skeletal muscle as displaying one of the largest number of AS events. This finding is consistent with requirements for tissue-specific protein isoforms needed to sustain muscle-specific functions. Rbfox1 is abundant in vertebrate brain, heart and skeletal muscle. Genome-wide genetic approaches have linked the Rbfox1 gene to autism, and a brain-specific knockout mouse revealed a critical role for this splicing regulator in neuronal function. Moreover, a Caenorhabditis elegans Rbfox1 homolog regulates muscle-specific splicing. To determine the role of Rbfox1 in muscle function, we developed a conditional knockout mouse model to specifically delete Rbfox1 in adult tissue. We show that Rbfox1 is required for muscle function but a >70% loss of Rbfox1 in satellite cells does not disrupt muscle regeneration. Deep sequencing identified aberrant splicing of multiple genes including those encoding myofibrillar and cytoskeletal proteins, and proteins that regulate calcium handling. Ultrastructure analysis of Rbfox1(-/-) muscle by electron microscopy revealed abundant tubular aggregates. Immunostaining showed mislocalization of the sarcoplasmic reticulum proteins Serca1 and Ryr1 in a pattern indicative of colocalization with the tubular aggregates. Consistent with mislocalization of Serca1 and Ryr1, calcium handling was drastically altered in Rbfox1(-/-) muscle. Moreover, muscle function was significantly impaired in Rbfox1(-/-) muscle as indicated by decreased force generation. These results demonstrate that Rbfox1 regulates a network of AS events required to maintain multiple aspects of muscle physiology.
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Affiliation(s)
| | | | | | | | | | - Amy Hanna
- Department of Molecular Physiology and Biophysics
| | - Qianxing Mo
- Dan L. Duncan Cancer Center, Department of Medicine
| | - John Hicks
- Department of Pathology and Immunology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA and Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Thomas A Cooper
- Department of Pathology and Immunology, Department of Molecular and Cellular Biology, Department of Molecular Physiology and Biophysics,
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Pretto DI, Eid JS, Yrigollen CM, Tang HT, Loomis EW, Raske C, Durbin-Johnson B, Hagerman PJ, Tassone F. Differential increases of specific FMR1 mRNA isoforms in premutation carriers. J Med Genet 2014; 52:42-52. [PMID: 25358671 DOI: 10.1136/jmedgenet-2014-102593] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Over 40% of male and ∼16% of female carriers of a premutation FMR1 allele (55-200 CGG repeats) will develop fragile X-associated tremor/ataxia syndrome, an adult onset neurodegenerative disorder, while about 20% of female carriers will develop fragile X-associated primary ovarian insufficiency. Marked elevation in FMR1 mRNA transcript levels has been observed with premutation alleles, and RNA toxicity due to increased mRNA levels is the leading molecular mechanism proposed for these disorders. However, although the FMR1 gene undergoes alternative splicing, it is unknown whether all or only some of the isoforms are overexpressed in premutation carriers and which isoforms may contribute to the premutation pathology. METHODS To address this question, we have applied a long-read sequencing approach using single-molecule real-time (SMRT) sequencing and qRT-PCR. RESULTS Our SMRT sequencing analysis performed on peripheral blood mononuclear cells, fibroblasts and brain tissue samples derived from premutation carriers and controls revealed the existence of 16 isoforms of 24 predicted variants. Although the relative abundance of all mRNA isoforms was significantly increased in the premutation group, as expected based on the bulk increase in mRNA levels, there was a disproportionate (fourfold to sixfold) increase, relative to the overall increase in mRNA, in the abundance of isoforms spliced at both exons 12 and 14, specifically Iso10 and Iso10b, containing the complete exon 15 and differing only in splicing in exon 17. CONCLUSIONS These findings suggest that RNA toxicity may arise from a relative increase of all FMR1 mRNA isoforms. Interestingly, the Iso10 and Iso10b mRNA isoforms, lacking the C-terminal functional sites for fragile X mental retardation protein function, are the most increased in premutation carriers relative to normal, suggesting a functional relevance in the pathology of FMR1-associated disorders.
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Affiliation(s)
- Dalyir I Pretto
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - John S Eid
- Pacific Biosciences, Menlo Park, California, USA
| | - Carolyn M Yrigollen
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Hiu-Tung Tang
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Erick W Loomis
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Chris Raske
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California Davis, School of Medicine, Davis, California, USA
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA MIND Institute, University of California Davis Medical Center, Sacramento, California, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA MIND Institute, University of California Davis Medical Center, Sacramento, California, USA
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Cappellari M, Bielli P, Paronetto MP, Ciccosanti F, Fimia GM, Saarikettu J, Silvennoinen O, Sette C. The transcriptional co-activator SND1 is a novel regulator of alternative splicing in prostate cancer cells. Oncogene 2014; 33:3794-802. [PMID: 23995791 DOI: 10.1038/onc.2013.360] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/03/2013] [Accepted: 07/05/2013] [Indexed: 01/12/2023]
Abstract
Splicing abnormalities have profound impact in human cancer. Several splicing factors, including SAM68, have pro-oncogenic functions, and their increased expression often correlates with human cancer development and progression. Herein, we have identified using mass spectrometry proteins that interact with endogenous SAM68 in prostate cancer (PCa) cells. Among other interesting proteins, we have characterized the interaction of SAM68 with SND1, a transcriptional co-activator that binds spliceosome components, thus coupling transcription and splicing. We found that both SAM68 and SND1 are upregulated in PCa cells with respect to benign prostate cells. Upregulation of SND1 exerts a synergic effect with SAM68 on exon v5 inclusion in the CD44 mRNA. The effect of SND1 on CD44 splicing required SAM68, as it was compromised after knockdown of this protein or mutation of the SAM68-binding sites in the CD44 pre-mRNA. More generally, we found that SND1 promotes the inclusion of CD44 variable exons by recruiting SAM68 and spliceosomal components on CD44 pre-mRNA. Inclusion of the variable exons in CD44 correlates with increased proliferation, motility and invasiveness of cancer cells. Strikingly, we found that knockdown of SND1, or SAM68, reduced proliferation and migration of PCa cells. Thus, our findings strongly suggest that SND1 is a novel regulator of alternative splicing that promotes PCa cell growth and survival.
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Affiliation(s)
- M Cappellari
- 1] Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy [2] Laboratory of Neuroembryology, Fondazione Santa Lucia, Rome, Italy
| | - P Bielli
- 1] Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy [2] Laboratory of Neuroembryology, Fondazione Santa Lucia, Rome, Italy
| | - M P Paronetto
- 1] Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy [2] Department of Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - F Ciccosanti
- Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases 'Lazzaro Spallanzani', Rome, Italy
| | - G M Fimia
- Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases 'Lazzaro Spallanzani', Rome, Italy
| | - J Saarikettu
- Laboratory of Molecular Immunology, School of Medicine and Institute of Biomedical Technology, Biomeditech, University of Tampere, Tampere, Finland
| | - O Silvennoinen
- 1] Laboratory of Molecular Immunology, School of Medicine and Institute of Biomedical Technology, Biomeditech, University of Tampere, Tampere, Finland [2] Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
| | - C Sette
- 1] Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy [2] Laboratory of Neuroembryology, Fondazione Santa Lucia, Rome, Italy
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High Sam68 expression predicts poor prognosis in non-small cell lung cancer. Clin Transl Oncol 2014; 16:886-91. [PMID: 24522888 DOI: 10.1007/s12094-014-1160-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/28/2014] [Indexed: 12/31/2022]
Abstract
BACKGROUND The nuclear protein Sam68 has been implicated in the oncogenesis and tumor growth. The aim of this study was to explore the clinical value of Sam68 in patients with non-small cell lung cancer (NSCLC). METHODS We examined Sam68 expression in 50 NSCLC tissues and matched adjacent noncancerous tissues by quantitative RT-PCR (qRT-PCR) and Western blotting. Furthermore, the Sam68 protein expression was analyzed by immunohistochemistry in 208 NSCLC samples. Kaplan-Meier method and multivariate Cox regression model were used to evaluate the prognostic value of nuclear Sam68 expression in NSCLC for disease survival. RESULTS The expression of Sam68 was significantly elevated in NSCLC tissues as compared with adjacent non-cancerous tissues (P < 0.01). The high expression of Sam68 in NSCLC was significantly correlated with lymph node metastasis and tumor TNM stage. Kaplan-Meier survival analysis revealed that high expression of Sam68 correlated with poor prognosis of NSCLC patients (P < 0.01). Multivariate analysis showed that Sam68 expression was an independent prognostic marker for overall survival of NSCLC patients (HR 2.73, 95 % CI 1.549-4.315, P = 0.002). CONCLUSION Our results suggest that high Sam68 expression predicts poor prognosis of NSCLC patients, and Sam68 may be potentially a prognostic biomarker for NSCLC.
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Foot JN, Feracci M, Dominguez C. Screening protein--single stranded RNA complexes by NMR spectroscopy for structure determination. Methods 2014; 65:288-301. [PMID: 24096002 PMCID: PMC3959648 DOI: 10.1016/j.ymeth.2013.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 12/23/2022] Open
Abstract
In the past few years, RNA molecules have been revealed to be at the center of numerous biological processes. Long considered as passive molecules transferring genetic information from DNA to proteins, it is now well established that RNA molecules play important regulatory roles. Associated with that, the number of identified RNA binding proteins (RBPs) has increased considerably and mutations in RNA molecules or RBP have been shown to cause various diseases, such as cancers. It is therefore crucial to understand at the molecular level how these proteins specifically recognise their RNA targets in order to design new generation drug therapies targeting protein-RNA complexes. Nuclear magnetic resonance (NMR) is a particularly well-suited technique to study such protein-RNA complexes at the atomic level and can provide valuable information for new drug discovery programs. In this article, we describe the NMR strategy that we and other laboratories use for screening optimal conditions necessary for structural studies of protein-single stranded RNA complexes, using two proteins, Sam68 and T-STAR, as examples.
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Affiliation(s)
- Jaelle N Foot
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, UK
| | - Mikael Feracci
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, UK
| | - Cyril Dominguez
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, UK.
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Zhao X, Li Z, He B, Liu J, Li S, Zhou L, Pan C, Yu Z, Xu Z. Sam68 is a novel marker for aggressive neuroblastoma. Onco Targets Ther 2013; 6:1751-60. [PMID: 24324342 PMCID: PMC3855102 DOI: 10.2147/ott.s52643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Neuroblastoma (NB) is the most common solid extracranial tumor in children. However, the molecular mechanism and progression of NB is largely unknown, and unfortunately, the prognosis is poor. Src-associated in mitosis with a molecular weight of 68 kDa (Sam68) is associated with carcinogenesis and neurogenesis. The present study aimed to investigate the clinical and prognostic significance of Sam68 in NB. Methods The expression of Sam68 in immortalized normal epithelial cells, NB cell lines, and in four cases of paired NB tissue and adjacent normal tissue from the same patient was examined using Western blotting, reverse transcription-polymerase chain reaction (PCR) and real-time reverse transcription-PCR. The proliferation of NB cells was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Furthermore, Sam68 protein expression was analyzed in 90 NB cases characterized as clinicopathological using immunohistochemistry. Statistical analyses were applied to evaluate the diagnostic value and associations of Sam68 with clinical parameters. Results Western blotting and reverse transcription-PCR showed that the expression level of Sam68 was markedly higher in NB cell lines than in the immortalized normal epithelial cells at both messenger RNA and protein levels. The MTT assay revealed that Sam68 expression supported proliferation of NB cells. Sam68 expression levels were significantly up-regulated in tumor tissues in comparison to the matched adjacent normal tissues from the same patient. Sam68 protein level was positively correlated with clinical stage (P<0.001), tumor histology (P<0.001), and distant metastasis (P=0.029). Patients with higher Sam68 expression had shorter overall survival time, whereas those with lower tumor Sam68 expression had longer survival time. Conclusion Our results suggest that Sam68 expression is associated with neuroblastoma progression and may represent a novel and valuable predictor for prognostic evaluation of neuroblastoma patients.
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Affiliation(s)
- Xiaohong Zhao
- Department of Pediatric Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
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Sánchez-Jiménez F, Sánchez-Margalet V. Role of Sam68 in post-transcriptional gene regulation. Int J Mol Sci 2013; 14:23402-19. [PMID: 24287914 PMCID: PMC3876053 DOI: 10.3390/ijms141223402] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/11/2013] [Accepted: 11/13/2013] [Indexed: 01/10/2023] Open
Abstract
The STAR family of proteins links signaling pathways to various aspects of post-transcriptional regulation and processing of RNAs. Sam68 belongs to this class of heteronuclear ribonucleoprotein particle K (hnRNP K) homology (KH) single domain-containing family of RNA-binding proteins that also contains some domains predicted to bind critical components in signal transduction pathways. In response to phosphorylation and other post-transcriptional modifications, Sam68 has been shown to have the ability to link signal transduction pathways to downstream effects regulating RNA metabolism, including transcription, alternative splicing or RNA transport. In addition to its function as a docking protein in some signaling pathways, this prototypic STAR protein has been identified to have a nuclear localization and to take part in the formation of both nuclear and cytosolic multi-molecular complexes such as Sam68 nuclear bodies and stress granules. Coupling with other proteins and RNA targets, Sam68 may play a role in the regulation of differential expression and mRNA processing and translation according to internal and external signals, thus mediating important physiological functions, such as cell death, proliferation or cell differentiation.
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Affiliation(s)
- Flora Sánchez-Jiménez
- Department of Medical Biochemistry and Molecular Biology and Immunology, UGC Clinical Biochemistry, Virgen Macarena University Hospital, Avenue. Sánchez Pizjuan 4, Medical School, University of Seville, Seville 41009, Spain.
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Liao WT, Liu JL, Wang ZG, Cui YM, Shi L, Li TT, Zhao XH, Chen XT, Ding YQ, Song LB. High expression level and nuclear localization of Sam68 are associated with progression and poor prognosis in colorectal cancer. BMC Gastroenterol 2013; 13:126. [PMID: 23937454 PMCID: PMC3751151 DOI: 10.1186/1471-230x-13-126] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 08/02/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Src-associated in mitosis (Sam68; 68 kDa) has been implicated in the oncogenesis and progression of several human cancers. The aim of this study was to investigate the clinicopathologic significance of Sam68 expression and its subcellular localization in colorectal cancer (CRC). METHODS Sam68 expression was examined in CRC cell lines, nine matched CRC tissues and adjacent noncancerous tissues using reverse transcription (RT)-PCR, quantitative RT-PCR and Western blotting. Sam68 protein expression and localization were determined in 224 paraffin-embedded archived CRC samples using immunohistochemistry. Statistical analyses were applied to evaluate the clinicopathologic significance. RESULTS Sam68 was upregulated in CRC cell lines and CRC, as compared with normal tissues; high Sam68 expression was detected in 120/224 (53.6%) of the CRC tissues. High Sam68 expression correlated significantly with poor differentiation (P = 0.033), advanced T stage (P < 0.001), N stage (P = 0.023) and distant metastasis (P = 0.033). Sam68 nuclear localization correlated significantly with poor differentiation (P = 0.002) and T stage (P =0.021). Patients with high Sam68 expression or Sam68 nuclear localization had poorer overall survival than patients with low Sam68 expression or Sam68 cytoplasmic localization. Patients with high Sam68 expression had a higher risk of recurrence than those with low Sam68 expression. CONCLUSIONS Overexpression of Sam68 correlated highly with cancer progression and poor differentiation in CRC. High Sam68 expression and Sam68 nuclear localization were associated with poorer overall survival.
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Lloyd-Burton S, Roskams AJ. SPARC-like 1 (SC1) is a diversely expressed and developmentally regulated matricellular protein that does not compensate for the absence of SPARC in the CNS. J Comp Neurol 2013; 520:2575-90. [PMID: 22173850 DOI: 10.1002/cne.23029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SPARC-like 1 (SC1) is a member of the SPARC family of matricellular proteins that has been implicated in the regulation of processes such as cell migration, proliferation, and differentiation. Here we show that SC1 exhibits remarkably diverse and dynamic expression in the developing and adult nervous system. During development, SC1 localizes to radial glia and pial-derived structures, including the vasculature, choroid plexus, and pial membranes. SC1 is not downregulated in postnatal development, but its expression shifts to distinct time windows in subtypes of glia and neurons, including astrocytes, large projection neurons, Bergmann glia, Schwann cells, and ganglionic satellite cells. In addition, SC1 expression levels and patterns are not altered in the SPARC null mouse, suggesting that SC1 does not compensate for the absence of SPARC. We conclude that SC1 and SPARC may share significant homology, but are likely to have distinct but complementary roles in nervous system development.
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Affiliation(s)
- Samantha Lloyd-Burton
- Department of Zoology, Life Sciences Institute and Brain Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
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Ehrmann I, Dalgliesh C, Liu Y, Danilenko M, Crosier M, Overman L, Arthur HM, Lindsay S, Clowry GJ, Venables JP, Fort P, Elliott DJ. The tissue-specific RNA binding protein T-STAR controls regional splicing patterns of neurexin pre-mRNAs in the brain. PLoS Genet 2013; 9:e1003474. [PMID: 23637638 PMCID: PMC3636136 DOI: 10.1371/journal.pgen.1003474] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 03/07/2013] [Indexed: 11/18/2022] Open
Abstract
The RNA binding protein T-STAR was created following a gene triplication 520-610 million years ago, which also produced its two parologs Sam68 and SLM-1. Here we have created a T-STAR null mouse to identify the endogenous functions of this RNA binding protein. Mice null for T-STAR developed normally and were fertile, surprisingly, given the high expression of T-STAR in the testis and the brain, and the known infertility and pleiotropic defects of Sam68 null mice. Using a transcriptome-wide search for splicing targets in the adult brain, we identified T-STAR protein as a potent splicing repressor of the alternatively spliced segment 4 (AS4) exons from each of the Neurexin1-3 genes, and exon 23 of the Stxbp5l gene. T-STAR protein was most highly concentrated in forebrain-derived structures like the hippocampus, which also showed maximal Neurexin1-3 AS4 splicing repression. In the absence of endogenous T-STAR protein, Nrxn1-3 AS4 splicing repression dramatically decreased, despite physiological co-expression of Sam68. In transfected cells Neurexin3 AS4 alternative splicing was regulated by either T-STAR or Sam68 proteins. In contrast, Neurexin2 AS4 splicing was only regulated by T-STAR, through a UWAA-rich response element immediately downstream of the regulated exon conserved since the radiation of bony vertebrates. The AS4 exons in the Nrxn1 and Nrxn3 genes were also associated with distinct patterns of conserved UWAA repeats. Consistent with an ancient mechanism of splicing control, human T-STAR protein was able to repress splicing inclusion of the zebrafish Nrxn3 AS4 exon. Although Neurexin1-3 and Stxbp5l encode critical synaptic proteins, T-STAR null mice had no detectable spatial memory deficits, despite an almost complete absence of AS4 splicing repression in the hippocampus. Our work identifies T-STAR as an ancient and potent tissue-specific splicing regulator that uses a concentration-dependent mechanism to co-ordinately regulate regional splicing patterns of the Neurexin1-3 AS4 exons in the mouse brain.
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Affiliation(s)
- Ingrid Ehrmann
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Caroline Dalgliesh
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yilei Liu
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina Danilenko
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Moira Crosier
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lynn Overman
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen M. Arthur
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gavin J. Clowry
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Julian P. Venables
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Philippe Fort
- Universités Montpellier 2 et 1, UMR 5237, Centre de Recherche de Biochimie Macromoléculaire, CNRS, Montpellier, France
| | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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RNA-binding protein Sam68 controls synapse number and local β-actin mRNA metabolism in dendrites. Proc Natl Acad Sci U S A 2013; 110:3125-30. [PMID: 23382180 DOI: 10.1073/pnas.1209811110] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Proper synaptic function requires the spatial and temporal compartmentalization of RNA metabolism via transacting RNA-binding proteins (RBPs). Loss of RBP activity leads to abnormal posttranscriptional regulation and results in diverse neurological disorders with underlying deficits in synaptic morphology and transmission. Functional loss of the 68-kDa RBP Src associated in mitosis (Sam68) is associated with the pathogenesis of the neurological disorder fragile X tremor/ataxia syndrome. Sam68 binds to the mRNA of β-actin (actb), an integral cytoskeletal component of dendritic spines. We show that Sam68 knockdown or disruption of the binding between Sam68 and its actb mRNA cargo in primary hippocampal cultures decreases the amount of actb mRNA in the synaptodendritic compartment and results in fewer dendritic spines. Consistent with these observations, we find that Sam68-KO mice have reduced levels of actb mRNA associated with synaptic polysomes and diminished levels of synaptic actb protein, suggesting that Sam68 promotes the translation of actb mRNA at synapses in vivo. Moreover, genetic knockout of Sam68 or acute knockdown in vivo results in fewer excitatory synapses in the hippocampal formation as assessed morphologically and functionally. Therefore, we propose that Sam68 regulates synapse number in a cell-autonomous manner through control of postsynaptic actb mRNA metabolism. Our research identifies a role for Sam68 in synaptodendritic posttranscriptional regulation of actb and may provide insight into the pathophysiology of fragile X tremor/ataxia syndrome.
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Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene 2013; 514:1-30. [PMID: 22909801 PMCID: PMC5632952 DOI: 10.1016/j.gene.2012.07.083] [Citation(s) in RCA: 509] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.
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Affiliation(s)
- Olga Kelemen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuan Wen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
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