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Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science 2024; 384:eadh7688. [PMID: 38781356 DOI: 10.1126/science.adh7688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders; yet, the role of cell type-specific splicing and transcript-isoform diversity during human brain development has not been systematically investigated. In this work, we leveraged single-molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone and cortical plate regions of the developing human neocortex at tissue and single-cell resolution. We identified 214,516 distinct isoforms, of which 72.6% were novel (not previously annotated in Gencode version 33), and uncovered a substantial contribution of transcript-isoform diversity-regulated by RNA binding proteins-in defining cellular identity in the developing neocortex. We leveraged this comprehensive isoform-centric gene annotation to reprioritize thousands of rare de novo risk variants and elucidate genetic risk mechanisms for neuropsychiatric disorders.
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Affiliation(s)
- Ashok Patowary
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Connor Jops
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Celine K Vuong
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xinzhou Ge
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Minsoo Kim
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Naihua Gong
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Margolis
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Vo
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jingyi Jessica Li
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Luis de la Torre-Ubieta
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
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2
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Cesari E, Farini D, Medici V, Ehrmann I, Guerra M, Testa E, Naro C, Geloso MC, Pagliarini V, La Barbera L, D’Amelio M, Orsini T, Vecchioli SF, Tamagnone L, Fort P, Viscomi MT, Elliott DJ, Sette C. Differential expression of paralog RNA binding proteins establishes a dynamic splicing program required for normal cerebral cortex development. Nucleic Acids Res 2024; 52:4167-4184. [PMID: 38324473 PMCID: PMC11077083 DOI: 10.1093/nar/gkae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
Sam68 and SLM2 are paralog RNA binding proteins (RBPs) expressed in the cerebral cortex and display similar splicing activities. However, their relative functions during cortical development are unknown. We found that these RBPs exhibit an opposite expression pattern during development. Sam68 expression declines postnatally while SLM2 increases after birth, and this developmental pattern is reinforced by hierarchical control of Sam68 expression by SLM2. Analysis of Sam68:Slm2 double knockout (Sam68:Slm2dko) mice revealed hundreds of exons that respond to joint depletion of these proteins. Moreover, parallel analysis of single and double knockout cortices indicated that exons regulated mainly by SLM2 are characterized by a dynamic splicing pattern during development, whereas Sam68-dependent exons are spliced at relatively constant rates. Dynamic splicing of SLM2-sensitive exons is completely suppressed in the Sam68:Slm2dko developing cortex. Sam68:Slm2dko mice die perinatally with defects in neurogenesis and in neuronal differentiation, and develop a hydrocephalus, consistent with splicing alterations in genes related to these biological processes. Thus, our study reveals that developmental control of separate Sam68 and Slm2 paralog genes encoding homologous RBPs enables the orchestration of a dynamic splicing program needed for brain development and viability, while ensuring a robust redundant mechanism that supports proper cortical development.
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Affiliation(s)
- Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Donatella Farini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Vanessa Medici
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Ingrid Ehrmann
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle NE1 3BZ, UK
| | - Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Erika Testa
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Maria Concetta Geloso
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
| | - Livia La Barbera
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Marcello D’Amelio
- Fondazione Santa Lucia IRCCS, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
- Università Campus Bio-Medico di Roma, Via Álvaro del Portillo, 21, 00128 Rome, Italy
| | - Tiziana Orsini
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC/CNR), Monterotondo, 00015 Rome, Italy
| | - Stefano Farioli Vecchioli
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC/CNR), Monterotondo, 00015 Rome, Italy
| | - Luca Tamagnone
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - Philippe Fort
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 05, France
| | - Maria Teresa Viscomi
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
- Department of Life Science and Public Health, Section of Histology and Embryology, Catholic University of the Sacred Heart, Rome
| | - David J Elliott
- Newcastle University Centre for Cancer, Newcastle University Institute of Biosciences, Newcastle NE1 3BZ, UK
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Agostino Gemelli IRCCS, Largo Agostino Gemelli, 00168 Rome, Italy
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3
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Fan R, Liu F, Gong Q, Liu D, Tang S, Shen D. KHDRBS1 as a novel prognostic signaling biomarker influencing hepatocellular carcinoma cell proliferation, migration, immune microenvironment, and drug sensitivity. Front Immunol 2024; 15:1393801. [PMID: 38660302 PMCID: PMC11041018 DOI: 10.3389/fimmu.2024.1393801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
Background Human tumors pose significant challenges, with targeted therapy against specific molecular targets or signaling pathways being a mainstay alongside surgical resection. Previous studies have implicated KHDRBS1 in the oncogenesis of certain human tumors such as colorectal and prostate cancers, underscoring its potential as a therapeutic target. However, the comprehensive expression pattern of KHDRBS1 in hepatocellular carcinoma (HCC) warrants further exploration. Methods Integrating and analyzing multi-omics, multi-cohort data from public databases, coupled with clinical samples and molecular biology validation, we elucidate the oncogenic role of KHDRBS1 in HCC progression. Additionally, leveraging HCC single-cell sequencing data, we segregate malignant cells into KHDRBS1-positive and negative subsets, uncovering significant differences in their expression profiles and functional roles. Results Our study identifies KHDRBS1 as a tumor-promoting factor in HCC, with its positivity correlating with tumor progression. Furthermore, we highlight the clinical significance of KHDRBS1-positive malignant cells, aiming to further propel its clinical utility. Conclusion KHDRBS1 plays a key role in HCC development. This study provides crucial insights for further investigation into KHDRBS1 as a therapeutic target in HCC.
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MESH Headings
- Humans
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/metabolism
- Liver Neoplasms/immunology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Tumor Microenvironment/immunology
- Cell Proliferation
- Biomarkers, Tumor
- Cell Movement
- Prognosis
- Signal Transduction
- Cell Line, Tumor
- Gene Expression Regulation, Neoplastic
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Drug Resistance, Neoplasm/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/genetics
- Male
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Affiliation(s)
- Rui Fan
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Fahui Liu
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Qiming Gong
- Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Metabolic Diseases (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Donghua Liu
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Shihang Tang
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Dongyan Shen
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
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4
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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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5
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Darwish M, Ito M, Iijima Y, Takase A, Ayukawa N, Suzuki S, Tanaka M, Komori K, Kaida D, Iijima T. Neuronal SAM68 differentially regulates alternative last exon splicing and ensures proper synapse development and function. J Biol Chem 2023; 299:105168. [PMID: 37595869 PMCID: PMC10562862 DOI: 10.1016/j.jbc.2023.105168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023] Open
Abstract
Alternative splicing in the 3'UTR of mammalian genes plays a crucial role in diverse biological processes, including cell differentiation and development. SAM68 is a key splicing regulator that controls the diversity of 3'UTR isoforms through alternative last exon (ALE) selection. However, the tissue/cell type-specific mechanisms underlying the splicing control at the 3' end and its functional significance remain unclear. Here, we show that SAM68 regulates ALE splicing in a dose-dependent manner and the neuronal splicing is differentially regulated depending on the characteristics of the target transcript. Specifically, we found that SAM68 regulates interleukin-1 receptor-associated protein splicing through the interaction with U1 small nuclear ribonucleoprotein. In contrast, the ALE splicing of protocadherin-15 (Pcdh15), a gene implicated in several neuropsychiatric disorders, is independent of U1 small nuclear ribonucleoprotein but modulated by the calcium/calmodulin-dependent protein kinase signaling pathway. We found that the aberrant ALE selection of Pcdh15 led to a conversion from a membrane-bound to a soluble isoform and consequently disrupted its localization into excitatory and inhibitory synapses. Notably, the neuronal expression of the soluble form of PCDH15 preferentially affected the number of inhibitory synapses. Moreover, the soluble form of PCDH15 interacted physically with α-neurexins and further disrupted neuroligin-2-induced inhibitory synapses in artificial synapse formation assays. Our findings provide novel insights into the role of neuron-specific alternative 3'UTR isoform selections in synapse development.
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Affiliation(s)
- Mohamed Darwish
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, School of Medicine, Tokai University, Kanagawa, Japan; Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Masatoshi Ito
- The Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Yoko Iijima
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, School of Medicine, Tokai University, Kanagawa, Japan; Tokai University Institute of Innovative Science and Technology, Isehara, Kanagawa, Japan
| | - Akinori Takase
- The Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Noriko Ayukawa
- Tokai University Institute of Innovative Science and Technology, Isehara, Kanagawa, Japan
| | - Satoko Suzuki
- Tokai University Institute of Innovative Science and Technology, Isehara, Kanagawa, Japan
| | - Masami Tanaka
- Tokai University Institute of Innovative Science and Technology, Isehara, Kanagawa, Japan
| | - Kanae Komori
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Daisuke Kaida
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Takatoshi Iijima
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, School of Medicine, Tokai University, Kanagawa, Japan; Tokai University Institute of Innovative Science and Technology, Isehara, Kanagawa, Japan.
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6
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Khudhair MK, Mohammed NI, Zabibah RS. Validating Sam68 expression and protein level in breast cancer. J Med Life 2023; 16:1136-1139. [PMID: 37900073 PMCID: PMC10600683 DOI: 10.25122/jml-2022-0229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 05/29/2023] [Indexed: 10/31/2023] Open
Abstract
Breast carcinoma ranks as the second most common cancer among women worldwide. Despite significant therapeutic advancements, approximately 25% of breast carcinoma cases have resistance to current treatment modalities, posing a significant challenge for patient management. This study aimed to investigate the role of Sam68 mRNA and its protein in promoting oncogenesis and breast cancer progression. Sam68 protein levels were assessed in tissue samples using an Enzyme-Linked Immunosorbent Assay kit from Sun Long Biotech. Whole RNA was isolated from malignant breast tissue samples obtained from patients. The RNA concentration was determined using an Eppendorf photometer, yielding an average concentration of 62.1±10.07 ng/µl. The purity of the isolated RNA was evaluated by measuring the A260/A280 ratio (1.9±0.07) and the A260/A230 ratio (1.7±0.3). The results indicated a significant upregulation of Sam68 mRNA expression in breast cancer tissues, supporting the findings from previous studies and indicating the correlation between altered Sam68 expression and the development of breast carcinoma, highlighting the potential significance of Sam68 in the pathogenesis of the disease. Estimating Sam68 in the blood may serve as a potential biomarker for assessing the malignant grade and metastatic spread of breast carcinoma cells.
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Affiliation(s)
- Muneer Kadhum Khudhair
- Department of Laboratory Investigation, Faculty of Science, University of Kufa, Kufa, Iraq
| | - Noaman Ibadi Mohammed
- Department of Physiology, Faculty of Veterinary Medicine, University of Kufa, Kufa, Iraq
| | - Rahman Sahib Zabibah
- Medical Laboratory Technology Department, College of Medicine, Islamic University, Najaf, Iraq
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7
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Pieraccioli M, Caggiano C, Mignini L, Zhong C, Babini G, Lattanzio R, Di Stasi S, Tian B, Sette C, Bielli P. The transcriptional terminator XRN2 and the RNA-binding protein Sam68 link alternative polyadenylation to cell cycle progression in prostate cancer. Nat Struct Mol Biol 2022; 29:1101-1112. [PMID: 36344846 PMCID: PMC9872553 DOI: 10.1038/s41594-022-00853-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Alternative polyadenylation (APA) yields transcripts differing in their 3'-end, and its regulation is altered in cancer, including prostate cancer. Here we have uncovered a mechanism of APA regulation impinging on the interaction between the exonuclease XRN2 and the RNA-binding protein Sam68, whose increased expression in prostate cancer is promoted by the transcription factor MYC. Genome-wide transcriptome profiling revealed a widespread impact of the Sam68/XRN2 complex on APA. XRN2 promotes recruitment of Sam68 to its target transcripts, where it competes with the cleavage and polyadenylation specificity factor for binding to strong polyadenylation signals at distal ends of genes, thus promoting usage of suboptimal proximal polyadenylation signals. This mechanism leads to 3' untranslated region shortening and translation of transcripts encoding proteins involved in G1/S progression and proliferation. Thus, our findings indicate that the APA program driven by Sam68/XRN2 promotes cell cycle progression and may represent an actionable target for therapeutic intervention.
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Affiliation(s)
- Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy.,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy.,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Luca Mignini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Chuwei Zhong
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Gabriele Babini
- GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Rossano Lattanzio
- Department of Innovative Technologies in Medicine & Dentistry, G. d’Annunzio University, Chieti, Italy.,Center for Advanced Studies and Technology (CAST), G. d’Annunzio University, Chieti, Italy
| | - Savino Di Stasi
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Bin Tian
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy. .,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy.
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy. .,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome, Italy.
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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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Qiao A, Ma W, Jiang Y, Han C, Yan B, Zhou J, Qin G. Hepatic Sam68 Regulates Systemic Glucose Homeostasis and Insulin Sensitivity. Int J Mol Sci 2022; 23:ijms231911469. [PMID: 36232770 PMCID: PMC9569775 DOI: 10.3390/ijms231911469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Hepatic glucose production (HGP) is an important component of glucose homeostasis, and deregulated HGP, particularly through gluconeogenesis, contributes to hyperglycemia and pathology of type-2 diabetes (T2D). It has been shown that the gluconeogenic gene expression is governed primarily by the transcription factor cAMP-response element (CRE)-binding protein (CREB) and its coactivator, CREB-regulated transcriptional coactivator 2 (CRTC2). Recently, we have discovered that Sam68, an adaptor protein and Src kinase substrate, potently promotes hepatic gluconeogenesis by promoting CRTC2 stability; however, the detailed mechanisms remain unclear. Here we show that in response to glucagon, Sam68 increases CREB/CRTC2 transactivity by interacting with CRTC2 in the CREB/CRTC2 complex and occupying the CRE motif of promoters, leading to gluconeogenic gene expression and glucose production. In hepatocytes, glucagon promotes Sam68 nuclear import, whereas insulin elicits its nuclear export. Furthermore, ablation of Sam68 in hepatocytes protects mice from high-fat diet (HFD)-induced hyperglycemia and significantly increased hepatic and peripheral insulin sensitivities. Thus, hepatic Sam68 potentiates CREB/CRTC2-mediated glucose production, contributes to the pathogenesis of insulin resistance, and may serve as a therapeutic target for T2D.
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Affiliation(s)
- Aijun Qiao
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- Correspondence: (A.Q.); (G.Q.); Tel.: +205-934-6690 (G.Q.); Fax: +205-934-9101 (G.Q.)
| | - Wenxia Ma
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ying Jiang
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chaoshan Han
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Baolong Yan
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Junlan Zhou
- Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Gangjian Qin
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Correspondence: (A.Q.); (G.Q.); Tel.: +205-934-6690 (G.Q.); Fax: +205-934-9101 (G.Q.)
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10
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DNA Damage Regulates the Functions of the RNA Binding Protein Sam68 through ATM-Dependent Phosphorylation. Cancers (Basel) 2022; 14:cancers14163847. [PMID: 36010841 PMCID: PMC9405969 DOI: 10.3390/cancers14163847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/26/2022] [Accepted: 08/05/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Alterations of the complex network of interactions between the DNA damage response pathway and RNA metabolism have been described in several tumors, and increasing efforts are devoted to the elucidation of the molecular mechanisms involved in this network. Previous large-scale proteomic studies identified the RNA binding protein Sam68 as a putative target of the ATM kinase. Herein, we demonstrate that ATM phosphorylates Sam68 upon DNA damage induction, and this post-translational modification regulates both the signaling function of Sam68 in the initial phase of the DNA damage response and its RNA processing activity. Thus, our study uncovers anew crosstalk between ATM and Sam68, which may represent a paradigm for the functional interaction between the DDR pathway and RNA binding proteins, and a possible actionabletarget in human cancers. Abstract Cancer cells frequently exhibit dysregulation of the DNA damage response (DDR), genomic instability, and altered RNA metabolism. Recent genome-wide studies have strongly suggested an interaction between the pathways involved in the cellular response to DDR and in the regulation of RNA metabolism, but the molecular mechanism(s) involved in this crosstalk are largely unknown. Herein, we found that activation of the DDR kinase ATM promotes its interaction with Sam68, leading to phosphorylation of this multifunctional RNA binding protein (RBP) on three residues: threonine 61, serine 388 and serine 390. Moreover, we demonstrate that ATM-dependent phosphorylation of threonine 61 promotes the function of Sam68 in the DDR pathway and enhances its RNA processing activity. Importantly, ATM-mediated phosphorylation of Sam68 in prostate cancer cells modulates alternative polyadenylation of transcripts that are targets of Sam68, supporting the notion that the ATM–Sam68 axis exerts a multifaceted role in the response to DNA damage. Thus, our work validates Sam68 as an ATM kinase substrate and uncovers an unexpected bidirectional interplay between ATM and Sam68, which couples the DDR pathway to modulation of RNA metabolism in response to genotoxic stress.
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11
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Naro C, Barbagallo F, Caggiano C, De Musso M, Panzeri V, Di Agostino S, Paronetto MP, Sette C. Functional Interaction Between the Oncogenic Kinase NEK2 and Sam68 Promotes a Splicing Program Involved in Migration and Invasion in Triple-Negative Breast Cancer. Front Oncol 2022; 12:880654. [PMID: 35530315 PMCID: PMC9068942 DOI: 10.3389/fonc.2022.880654] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/16/2022] [Indexed: 12/01/2022] Open
Abstract
Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype. Poor prognosis in TNBC is partly due to lack of efficacious targeted therapy and high propensity to metastasize. Dysregulation of alternative splicing has recently emerged as a trait of TNBC, suggesting that unveiling the molecular mechanisms underlying its regulation could uncover new druggable cancer vulnerabilities. The oncogenic kinase NEK2 is significantly upregulated in TNBC and contributes to shaping their unique splicing profile. Herein, we found that NEK2 interacts with the RNA binding protein Sam68 in TNBC cells and that NEK2-mediated phosphorylation of Sam68 enhances its splicing activity. Genome-wide transcriptome analyses identified the splicing targets of Sam68 in TNBC cells and revealed a common set of exons that are co-regulated by NEK2. Functional annotation of splicing-regulated genes highlighted cell migration and spreading as biological processes regulated by Sam68. Accordingly, Sam68 depletion reduces TNBC cell migration and invasion, and these effects are potentiated by the concomitant inhibition of NEK2 activity. Our findings indicate that Sam68 and NEK2 functionally cooperate in the regulation of a splicing program that sustains the pro-metastatic features of TNBC cells.
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Affiliation(s)
- Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy.,Gemelli SCIENCE and TECHNOLOGY PARK (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Federica Barbagallo
- Department of Experimental Medicine, University of Rome Sapienza, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy.,Gemelli SCIENCE and TECHNOLOGY PARK (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Monica De Musso
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy
| | - Valentina Panzeri
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy.,Gemelli SCIENCE and TECHNOLOGY PARK (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Silvia Di Agostino
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy.,Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy.,Gemelli SCIENCE and TECHNOLOGY PARK (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
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12
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Jobbins AM, Haberman N, Artigas N, Amourda C, Paterson HAB, Yu S, Blackford SJI, Montoya A, Dore M, Wang YF, Sardini A, Cebola I, Zuber J, Rashid ST, Lenhard B, Vernia S. Dysregulated RNA polyadenylation contributes to metabolic impairment in non-alcoholic fatty liver disease. Nucleic Acids Res 2022; 50:3379-3393. [PMID: 35293570 PMCID: PMC8989518 DOI: 10.1093/nar/gkac165] [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: 10/20/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
Pre-mRNA processing is an essential mechanism for the generation of mature mRNA and the regulation of gene expression in eukaryotic cells. While defects in pre-mRNA processing have been implicated in a number of diseases their involvement in metabolic pathologies is still unclear. Here, we show that both alternative splicing and alternative polyadenylation, two major steps in pre-mRNA processing, are significantly altered in non-alcoholic fatty liver disease (NAFLD). Moreover, we find that Serine and Arginine Rich Splicing Factor 10 (SRSF10) binding is enriched adjacent to consensus polyadenylation motifs and its expression is significantly decreased in NAFLD, suggesting a role mediating pre-mRNA dysregulation in this condition. Consistently, inactivation of SRSF10 in mouse and human hepatocytes in vitro, and in mouse liver in vivo, was found to dysregulate polyadenylation of key metabolic genes such as peroxisome proliferator-activated receptor alpha (PPARA) and exacerbate diet-induced metabolic dysfunction. Collectively our work implicates dysregulated pre-mRNA polyadenylation in obesity-induced liver disease and uncovers a novel role for SRSF10 in this process.
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Affiliation(s)
- Andrew M Jobbins
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Nejc Haberman
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Natalia Artigas
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Christopher Amourda
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Helen A B Paterson
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Sijia Yu
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Samuel J I Blackford
- Department of Metabolism, Digestion & Reproduction, Imperial College London, London W12 0NN, UK
| | - Alex Montoya
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Marian Dore
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alessandro Sardini
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion & Reproduction, Imperial College London, London W12 0NN, UK
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Sheikh Tamir Rashid
- Department of Metabolism, Digestion & Reproduction, Imperial College London, London W12 0NN, UK
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Santiago Vernia
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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13
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Verdile V, Svetoni F, La Rosa P, Ferrante G, Cesari E, Sette C, Paronetto M. EWS splicing regulation contributes to balancing Foxp1 isoforms required for neuronal differentiation. Nucleic Acids Res 2022; 50:3362-3378. [PMID: 35253879 PMCID: PMC8989529 DOI: 10.1093/nar/gkac154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/27/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is a key regulatory process underlying the amplification of genomic information and the expansion of proteomic diversity, particularly in brain. Here, we identify the Ewing sarcoma protein (EWS) as a new player of alternative splicing regulation during neuronal differentiation. Knockdown of EWS in neuronal progenitor cells leads to premature differentiation. Transcriptome profiling of EWS-depleted cells revealed global changes in splicing regulation. Bioinformatic analyses and biochemical experiments demonstrated that EWS regulates alternative exons in a position-dependent fashion. Notably, several EWS-regulated splicing events are physiologically modulated during neuronal differentiation and EWS depletion in neuronal precursors anticipates the splicing-pattern of mature neurons. Among other targets, we found that EWS controls the alternative splicing of the forkhead family transcription factor FOXP1, a pivotal transcriptional regulator of neuronal differentiation, possibly contributing to the switch of gene expression underlying the neuronal differentiation program.
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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
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Francesca Svetoni
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Piergiorgio La Rosa
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Gabriele Ferrante
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Eleonora Cesari
- GSTEP-Organoids Core Facility, IRCCS Fondazione Policlinico Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- GSTEP-Organoids Core Facility, IRCCS Fondazione Policlinico Agostino Gemelli, 00168 Rome, Italy
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, 00168 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
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
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14
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Schiavi S, La Rosa P, Petrillo S, Carbone E, D'Amico J, Piemonte F, Trezza V. N-Acetylcysteine Mitigates Social Dysfunction in a Rat Model of Autism Normalizing Glutathione Imbalance and the Altered Expression of Genes Related to Synaptic Function in Specific Brain Areas. Front Psychiatry 2022; 13:851679. [PMID: 35280167 PMCID: PMC8916240 DOI: 10.3389/fpsyt.2022.851679] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
Prenatal exposure to valproic acid (VPA) is a risk factor for autism spectrum disorder (ASD) in humans and it induces autistic-like behaviors in rodents. Imbalances between GABAergic and glutamatergic neurotransmission and increased oxidative stress together with altered glutathione (GSH) metabolism have been hypothesized to play a role in both VPA-induced embriotoxicity and in human ASD. N-acetylcysteine (NAC) is an antioxidant precursor of glutathione and a modulator of glutamatergic neurotransmission that has been tested in ASD, although the clinical studies currently available provided controversial results. Here, we explored the effects of repeated NAC (150 mg/kg) administration on core autistic-like features and altered brain GSH metabolism in the VPA (500 mg/kg) rat model of ASD. Furthermore, we measured the mRNA expression of genes encoding for scaffolding and transcription regulation proteins, as well as the subunits of NMDA and AMPA receptors and metabotropic glutamate receptors mGLUR1 and mGLUR5 in brain areas that are relevant to ASD. NAC administration ameliorated the social deficit displayed by VPA-exposed rats in the three-chamber test, but not their stereotypic behavior in the hole board test. Furthermore, NAC normalized the altered GSH levels displayed by these animals in the hippocampus and nucleus accumbens, and it partially rescued the altered expression of post-synaptic terminal network genes found in VPA-exposed rats, such as NR2a, MGLUR5, GLUR1, and GLUR2 in nucleus accumbens, and CAMK2, NR1, and GLUR2 in cerebellum. These data indicate that NAC treatment selectively mitigates the social dysfunction displayed by VPA-exposed rats normalizing GSH imbalance and reestablishing the expression of genes related to synaptic function in a brain region-specific manner. Taken together, these data contribute to clarify the behavioral impact of NAC in ASD and the molecular mechanisms that underlie its effects.
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Affiliation(s)
- Sara Schiavi
- Department of Science, University "Roma Tre", Rome, Italy
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University, Rome, Italy
| | - Sara Petrillo
- Neuromuscular and Neurodegenerative Diseases Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Emilia Carbone
- Department of Science, University "Roma Tre", Rome, Italy
| | - Jessica D'Amico
- Neuromuscular and Neurodegenerative Diseases Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fiorella Piemonte
- Neuromuscular and Neurodegenerative Diseases Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Viviana Trezza
- Department of Science, University "Roma Tre", Rome, Italy
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15
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Domínguez-Bajo A, Rosa JM, González-Mayorga A, Rodilla BL, Arché-Núñez A, Benayas E, Ocón P, Pérez L, Camarero J, Miranda R, González MT, Aguilar J, López-Dolado E, Serrano MC. Nanostructured gold electrodes promote neural maturation and network connectivity. Biomaterials 2021; 279:121186. [PMID: 34700221 DOI: 10.1016/j.biomaterials.2021.121186] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/22/2022]
Abstract
Progress in the clinical application of recording and stimulation devices for neural diseases is still limited, mainly because of suboptimal material engineering and unfavorable interactions with biological entities. Nanotechnology is providing upgraded designs of materials to better mimic the native extracellular environment and attain more intimate contacts with individual neurons, besides allowing for the miniaturization of the electrodes. However, little progress has been done to date on the understanding of the biological impact that such neural interfaces have on neural network maturation and functionality. In this work, we elucidate the effect of a gold (Au) highly ordered nanostructure on the morphological and functional interactions with neural cells and tissues. Alumina-templated Au nanostructured electrodes composed of parallel nanowires of 160 nm in diameter and 1.2 μm in length (Au-NWs), with 320 nm of pitch, are designed and characterized. Equivalent non-structured Au electrodes (Au-Flat) are used for comparison. By using diverse techniques in in vitro cell cultures including live calcium imaging, we found that Au-NWs interfaced with primary neural cortical cells for up to 14 days allow neural networks growth and increase spontaneous activity and ability of neuronal synchronization, thus indicating that nanostructured features favor neuronal network. The enhancement in the number of glial cells found is hypothesized to be behind these beneficial functional effects. The in vivo effect of the implantation of these nanostructured electrodes and its potential relevance for future clinical applicability has been explored in an experimental model of rat spinal cord injury. Subacute responses to implanted Au-NWs show no overt reactive or toxic biological reactions besides those triggered by the injury itself. These results highlight the translational potential of Au-NWs electrodes for in vivo applications as neural interfaces in contact with central nervous tissues including the injured spinal cord.
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Affiliation(s)
- Ana Domínguez-Bajo
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, Calle Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain
| | - Juliana M Rosa
- Hospital Nacional de Parapléjicos, SESCAM, Finca La Peraleda s/n, 45071, Toledo, Spain
| | | | - Beatriz L Rodilla
- Instituto Madrileño de Estudios Avanzados (IMDEA Nanociencia), Calle Faraday 9, 28049, Madrid, Spain; Departamento de Física de Materiales, Universidad Complutense de Madrid, Plaza de las Ciencias s/n, 28040, Madrid, Spain
| | - Ana Arché-Núñez
- Instituto Madrileño de Estudios Avanzados (IMDEA Nanociencia), Calle Faraday 9, 28049, Madrid, Spain
| | - Esther Benayas
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, Calle Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain
| | - Pilar Ocón
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Lucas Pérez
- Instituto Madrileño de Estudios Avanzados (IMDEA Nanociencia), Calle Faraday 9, 28049, Madrid, Spain; Departamento de Física de Materiales, Universidad Complutense de Madrid, Plaza de las Ciencias s/n, 28040, Madrid, Spain
| | - Julio Camarero
- Instituto Madrileño de Estudios Avanzados (IMDEA Nanociencia), Calle Faraday 9, 28049, Madrid, Spain; Instituto "Nicolás Cabrera" and Condensed Matter Physics Center (IFIMAC), Departamento de Física de la Materia Condensada, Universidad Autonoma de Madrid, Madrid, 28049, Spain
| | - Rodolfo Miranda
- Instituto Madrileño de Estudios Avanzados (IMDEA Nanociencia), Calle Faraday 9, 28049, Madrid, Spain; Instituto "Nicolás Cabrera" and Condensed Matter Physics Center (IFIMAC), Departamento de Física de la Materia Condensada, Universidad Autonoma de Madrid, Madrid, 28049, Spain
| | - M Teresa González
- Instituto Madrileño de Estudios Avanzados (IMDEA Nanociencia), Calle Faraday 9, 28049, Madrid, Spain
| | - Juan Aguilar
- Hospital Nacional de Parapléjicos, SESCAM, Finca La Peraleda s/n, 45071, Toledo, Spain; Research Unit of "Design and development of biomaterials for neural regeneration", Hospital Nacional de Parapléjicos, Joint Research Unit with CSIC, Finca La Peraleda s/n, 45071, Toledo, Spain
| | - Elisa López-Dolado
- Hospital Nacional de Parapléjicos, SESCAM, Finca La Peraleda s/n, 45071, Toledo, Spain; Research Unit of "Design and development of biomaterials for neural regeneration", Hospital Nacional de Parapléjicos, Joint Research Unit with CSIC, Finca La Peraleda s/n, 45071, Toledo, Spain
| | - María C Serrano
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, Calle Sor Juana Inés de la Cruz 3, 28049, Madrid, Spain.
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16
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Ruta V, Pagliarini V, Sette C. Coordination of RNA Processing Regulation by Signal Transduction Pathways. Biomolecules 2021; 11:biom11101475. [PMID: 34680108 PMCID: PMC8533259 DOI: 10.3390/biom11101475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.
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Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Correspondence:
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17
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Brunetti D, Dykstra W, Le S, Zink A, Prigione A. Mitochondria in neurogenesis: Implications for mitochondrial diseases. Stem Cells 2021; 39:1289-1297. [PMID: 34089537 DOI: 10.1002/stem.3425] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Mitochondria are organelles with recognized key roles in cellular homeostasis, including bioenergetics, redox, calcium signaling, and cell death. Mitochondria are essential for neuronal function, given the high energy demands of the human brain. Consequently, mitochondrial diseases affecting oxidative phosphorylation (OXPHOS) commonly exhibit neurological impairment. Emerging evidence suggests that mitochondria are important not only for mature postmitotic neurons but also for the regulation of neural progenitor cells (NPCs) during the process of neurogenesis. These recent findings put mitochondria as central regulator of cell fate decisions during brain development. OXPHOS mutations may disrupt the function of NPCs and thereby impair the metabolic programming required for neural fate commitment. Promoting the mitochondrial function of NPCs could therefore represent a novel interventional approach against incurable mitochondrial diseases.
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Affiliation(s)
- Dario Brunetti
- Mitochondrial Medicine Laboratory, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico "C. Besta", Milan, Italy
| | - Werner Dykstra
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Stephanie Le
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Annika Zink
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Alessandro Prigione
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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18
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A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. Blood Adv 2021; 5:1310-1323. [PMID: 33656539 DOI: 10.1182/bloodadvances.2020002090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 01/19/2021] [Indexed: 11/20/2022] Open
Abstract
The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and is disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined central role, and mutations promote malignant transformation. More recently, studies have illuminated the importance of posttranscriptional regulation by RNA-binding proteins (RBPs) in hematopoiesis and leukemia development. However, the RBPs involved and the breadth of regulation are only beginning to be elucidated. Furthermore, the intersection between posttranscriptional regulation and hematopoietic transcription factor function is poorly understood. Here, we studied the posttranscriptional regulation of RUNX1, a key hematopoietic transcription factor. Alternative polyadenylation (APA) of RUNX1 produces functionally antagonistic protein isoforms (RUNX1a vs RUNX1b/c) that mediate HSC self-renewal vs differentiation, an RNA-processing event that is dysregulated in malignancy. Consequently, RBPs that regulate this event directly contribute to healthy and aberrant hematopoiesis. We modeled RUNX1 APA using a split GFP minigene reporter and confirmed the sensitivity of our model to detect changes in RNA processing. We used this reporter in a clustered regularly interspaced short palindromic repeats (CRISPR) screen consisting of single guide RNAs exclusively targeting RBPs and uncovered HNRNPA1 and KHDRBS1 as antagonistic regulators of RUNX1a isoform generation. Overall, our study provides mechanistic insight into the posttranscriptional regulation of a key hematopoietic transcription factor and identifies RBPs that may have widespread and important functions in hematopoiesis.
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19
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Napierala JS, Rajapakshe K, Clark A, Chen YY, Huang S, Mesaros C, Xu P, Blair IA, Hauser LA, Farmer J, Lynch DR, Edwards DP, Coarfa C, Napierala M. Reverse Phase Protein Array Reveals Correlation of Retinoic Acid Metabolism With Cardiomyopathy in Friedreich's Ataxia. Mol Cell Proteomics 2021; 20:100094. [PMID: 33991687 PMCID: PMC8214145 DOI: 10.1016/j.mcpro.2021.100094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022] Open
Abstract
Identifying biomarkers is important for assessment of disease progression, prediction of symptom development, and determination of treatment effectiveness. While unbiased analyses of differential gene expression using next-generation sequencing methods are now routinely conducted, proteomics studies are more challenging because of traditional methods predominantly being low throughput and offering a limited dynamic range for simultaneous detection of hundreds of proteins that drastically differ in their intracellular abundance. We utilized a sensitive and high-throughput proteomic technique, reverse phase protein array (RPPA), to attain protein expression profiles of primary fibroblasts obtained from patients with Friedreich's ataxia (FRDA) and unaffected controls (CTRLs). The RPPA was designed to detect 217 proteins or phosphorylated proteins by individual antibody, and the specificity of each antibody was validated prior to the experiment. Among 62 fibroblast samples (44 FRDA and 18 CTRLs) analyzed, 30 proteins/phosphoproteins were significantly changed in FRDA fibroblasts compared with CTRL cells (p < 0.05), mostly representing signaling molecules and metabolic enzymes. As expected, frataxin was significantly downregulated in FRDA samples, thus serving as an internal CTRL for assay integrity. Extensive bioinformatics analyses were conducted to correlate differentially expressed proteins with critical disease parameters (e.g., selected symptoms, age of onset, guanine-adenine-adenine sizes, frataxin levels, and Functional Assessment Rating Scale scores). Members of the integrin family of proteins specifically associated with hearing loss in FRDA. Also, RPPA data, combined with results of transcriptome profiling, uncovered defects in the retinoic acid metabolism pathway in FRDA samples. Moreover, expression of aldehyde dehydrogenase family 1 member A3 differed significantly between cardiomyopathy-positive and cardiomyopathy-negative FRDA cohorts, demonstrating that metabolites such as retinol, retinal, or retinoic acid could become potential predictive biomarkers of cardiac presentation in FRDA.
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Affiliation(s)
- Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Amanda Clark
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yu-Yun Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shixia Huang
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Clementina Mesaros
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Peining Xu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lauren A Hauser
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer Farmer
- Friedreich's Ataxia Research Alliance, Downingtown, Pennsylvania, USA
| | - David R Lynch
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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20
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Sommerkamp P, Cabezas-Wallscheid N, Trumpp A. Alternative Polyadenylation in Stem Cell Self-Renewal and Differentiation. Trends Mol Med 2021; 27:660-672. [PMID: 33985920 DOI: 10.1016/j.molmed.2021.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is shaped by transcriptional and post-transcriptional mechanisms, including alternative polyadenylation (APA). By directly controlling 3'- untranslated region (UTR) length and the selection of the last exon, APA regulates up to 70% of all cellular transcripts influencing RNA stability, output, and protein isoform expression. Cell-state-dependent 3'-UTR shortening has been identified as a hallmark of cellular proliferation. Hence, quiescent/dormant stem cells are characterized by long 3'-UTRs, whereas proliferative stem/progenitor cells exhibit 3'-UTR shortening. Here, the latest studies analyzing the role of APA in regulating stem cell state, self-renewal, differentiation, and metabolism are reviewed. The new role of APA in controlling stem cell fate opens novel potential therapeutic avenues in the field of regenerative medicine.
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Affiliation(s)
- Pia Sommerkamp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | | | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
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21
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Farini D, Cesari E, Weatheritt RJ, La Sala G, Naro C, Pagliarini V, Bonvissuto D, Medici V, Guerra M, Di Pietro C, Rizzo FR, Musella A, Carola V, Centonze D, Blencowe BJ, Marazziti D, Sette C. A Dynamic Splicing Program Ensures Proper Synaptic Connections in the Developing Cerebellum. Cell Rep 2021; 31:107703. [PMID: 32492419 DOI: 10.1016/j.celrep.2020.107703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/13/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
Tight coordination of gene expression in the developing cerebellum is crucial for establishment of neuronal circuits governing motor and cognitive function. However, transcriptional changes alone do not explain all of the switches underlying neuronal differentiation. Here we unveiled a widespread and highly dynamic splicing program that affects synaptic genes in cerebellar neurons. The motifs enriched in modulated exons implicated the splicing factor Sam68 as a regulator of this program. Sam68 controls splicing of exons with weak branchpoints by directly binding near the 3' splice site and competing with U2AF recruitment. Ablation of Sam68 disrupts splicing regulation of synaptic genes associated with neurodevelopmental diseases and impairs synaptic connections and firing of Purkinje cells, resulting in motor coordination defects, ataxia, and abnormal social behavior. These findings uncover an unexpectedly dynamic splicing regulatory network that shapes the synapse in early life and establishes motor and cognitive circuitry in the developing cerebellum.
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Affiliation(s)
- Donatella Farini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy; Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Robert J Weatheritt
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Gina La Sala
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Rome, Italy
| | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Davide Bonvissuto
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
| | - Vanessa Medici
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy; Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Chiara Di Pietro
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Rome, Italy
| | - Francesca Romana Rizzo
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy; San Raffaele Pisana and University San Raffaele, IRCCS, Rome, Italy
| | | | - Valeria Carola
- Fondazione Santa Lucia, IRCCS, Rome, Italy; Department of Dynamic and Clinical Psychology, University of Rome Sapienza, Rome, Italy
| | - Diego Centonze
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy; Unit of Neurology, IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Daniela Marazziti
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Rome, Italy
| | - Claudio Sette
- Fondazione Santa Lucia, IRCCS, Rome, Italy; Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.
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22
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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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23
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Namba T, Nardelli J, Gressens P, Huttner WB. Metabolic Regulation of Neocortical Expansion in Development and Evolution. Neuron 2020; 109:408-419. [PMID: 33306962 DOI: 10.1016/j.neuron.2020.11.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2020] [Accepted: 11/13/2020] [Indexed: 12/18/2022]
Abstract
The neocortex, the seat of our higher cognitive abilities, has expanded in size during the evolution of certain mammals such as primates, including humans. This expansion occurs during development and is linked to the proliferative capacity of neural stem and progenitor cells (NPCs) in the neocortex. A number of cell-intrinsic and cell-extrinsic factors have been implicated in increasing NPC proliferative capacity. However, NPC metabolism has only recently emerged as major regulator of NPC proliferation. In this Perspective, we summarize recent insights into the role of NPC metabolism in neocortical development and neurodevelopmental disorders and its relevance for neocortex evolution. We discuss certain human-specific genes and microcephaly-implicated genes that operate in, or at, the mitochondria of NPCs and stimulate their proliferation by promoting glutaminolysis. We also discuss other metabolic pathways and develop a perspective on how metabolism mechanistically regulates NPC proliferation in neocortical development and how this contributed to neocortex evolution.
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Affiliation(s)
- Takashi Namba
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Neuroscience Center, HiLIFE - Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Pierre Gressens
- Université de Paris, NeuroDiderot, Inserm, 75019 Paris, France.
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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24
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La Rosa P, Bartoli G, Farioli Vecchioli S, Cesari E, Pagliarini V, Sette C. Androgen Receptor signaling promotes the neural progenitor cell pool in the developing cortex. J Neurochem 2020; 157:1153-1166. [PMID: 32959393 DOI: 10.1111/jnc.15192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 01/16/2023]
Abstract
Neural Progenitor Cells (NPCs) are multipotent cells that are able to self-renew and differentiate into neurons. The size of the initial pool of NPCs during the brain development strongly affects the number of neurons that compose cortical multi-layer during development. Gonadal hormones can influence the balance between self-renewal and differentiation processes. Herein, we investigated the role of dihydrotestosterone (DHT), the active metabolite of testosterone, in the regulation of NPC stemness and differentiation. First, we evaluated the expression of the androgen receptor (AR), the transcription factor activated by DHT that mediates the physiological effects of androgens, in NPCs. Western blot analysis showed that DHT-mediated activation of AR induces mitogenic signaling pathways (PI3K/AKT and MAPK/ERK) in NPCs, whereas luciferase activity assays demonstrated the induction of AR transcriptional activity. AR activation mediated by DHT treatment strongly increased the proliferation of NPCs and reduced their propensity to differentiate into neurons. Furthermore, the effects of AR activation were mediated, at least in part, by increased expression of Aldehyde Dehydrogenase 1 Family Member A3 enzyme (ALDH1A3). Pharmacological inhibition of ALDH activity with N,N-diethylaminobenzaldehyde (DEAB) reduced the effect of DHT on NPC proliferation in vitro. Furthermore, inhibition of AR activity by Enzalutamide reduced the NPC pool in the developing cortex of male C57/BL6 mouse embryos. These findings indicate that androgens engage an AR-dependent signaling pathway that impact on neurogenesis by increasing the NPC pool in the developing mouse cortex.
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Affiliation(s)
- Piergiorgio La Rosa
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Giulia Bartoli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | | | - Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Claudio Sette
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome, Italy.,Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
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25
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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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26
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La Rosa P, Petrillo S, Bertini ES, Piemonte F. Oxidative Stress in DNA Repeat Expansion Disorders: A Focus on NRF2 Signaling Involvement. Biomolecules 2020; 10:biom10050702. [PMID: 32369911 PMCID: PMC7277112 DOI: 10.3390/biom10050702] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
DNA repeat expansion disorders are a group of neuromuscular and neurodegenerative diseases that arise from the inheritance of long tracts of nucleotide repetitions, located in the regulatory region, introns, or inside the coding sequence of a gene. Although loss of protein expression and/or the gain of function of its transcribed mRNA or translated product represent the major pathogenic effect of these pathologies, mitochondrial dysfunction and imbalance in redox homeostasis are reported as common features in these disorders, deeply affecting their severity and progression. In this review, we examine the role that the redox imbalance plays in the pathological mechanisms of DNA expansion disorders and the recent advances on antioxidant treatments, particularly focusing on the expression and the activity of the transcription factor NRF2, the main cellular regulator of the antioxidant response.
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27
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Pagliarini V, Jolly A, Bielli P, Di Rosa V, De la Grange P, Sette C. Sam68 binds Alu-rich introns in SMN and promotes pre-mRNA circularization. Nucleic Acids Res 2020; 48:633-645. [PMID: 31777926 PMCID: PMC6954450 DOI: 10.1093/nar/gkz1117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 11/12/2019] [Accepted: 11/22/2019] [Indexed: 01/01/2023] Open
Abstract
The Spinal Muscular Atrophy (SMA) gene SMN was recently duplicated (SMN1 and SMN2) in higher primates. Furthermore, invasion of the locus by repetitive elements almost doubled its size with respect to mouse Smn, in spite of an almost identical protein-coding sequence. Herein, we found that SMN ranks among the human genes with highest density of Alus, which are evolutionary conserved in primates and often occur in inverted orientation. Inverted repeat Alus (IRAlus) negatively regulate splicing of long introns within SMN, while promoting widespread alternative circular RNA (circRNA) biogenesis. Bioinformatics analyses revealed the presence of ultra-conserved Sam68 binding sites in SMN IRAlus. Cross-link-immunoprecipitation (CLIP), mutagenesis and silencing experiments showed that Sam68 binds in proximity of intronic Alus in the SMN pre-mRNA, thus favouring circRNA biogenesis in vitro and in vivo. These findings highlight a novel layer of regulation in SMN expression, uncover the crucial impact exerted by IRAlus and reveal a role for Sam68 in SMN circRNA biogenesis.
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Affiliation(s)
- Vittoria Pagliarini
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Heart, Rome 00168, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome 00168, Italy
| | - Ariane Jolly
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, Paris 75013, France
| | - Pamela Bielli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome 00143, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Valentina Di Rosa
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome 00143, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Pierre De la Grange
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, Paris 75013, France
| | - Claudio Sette
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Heart, Rome 00168, Italy.,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome 00143, Italy
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28
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Caggiano C, Pieraccioli M, Panzeri V, Sette C, Bielli P. c-MYC empowers transcription and productive splicing of the oncogenic splicing factor Sam68 in cancer. Nucleic Acids Res 2020; 47:6160-6171. [PMID: 31066450 PMCID: PMC6614821 DOI: 10.1093/nar/gkz344] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified the promoter region of the Sam68 gene (KHDRBS1) and the proto-oncogenic transcription factor c-MYC as a key regulator of Sam68 expression. Upregulation of Sam68 and c-MYC correlate in PCa patients. c-MYC directly binds to and activates the Sam68 promoter. Furthermore, c-MYC affects productive splicing of the nascent Sam68 transcript by modulating the transcriptional elongation rate within the gene. Importantly, c-MYC-dependent expression of Sam68 is under the tight control of external cues, such as androgens and/or mitogens. These findings uncover an unexpected coordination of transcription and splicing of Sam68 by c-MYC, which may represent a key step in PCa tumorigenesis.
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Affiliation(s)
- Cinzia Caggiano
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Marco Pieraccioli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Valentina Panzeri
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Science medical/chirurgic and translational medicine, University of Rome Sapienza,00189 Rome, Italy
| | - Claudio Sette
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy
| | - Pamela Bielli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
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Pagliarini V, Guerra M, Di Rosa V, Compagnucci C, Sette C. Combined treatment with the histone deacetylase inhibitor LBH589 and a splice-switch antisense oligonucleotide enhances SMN2 splicing and SMN expression in Spinal Muscular Atrophy cells. J Neurochem 2020; 153:264-275. [PMID: 31811660 DOI: 10.1111/jnc.14935] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/23/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022]
Abstract
Spinal muscular atrophy (SMA) is a motor neuron disease caused by loss of function mutations in the Survival Motor Neuron 1 (SMN1) gene and reduced expression of the SMN protein, leading to spinal motor neuron death, muscle weakness and atrophy. Although humans harbour the highly homologous SMN2 gene, its defective splicing regulation yields a truncated and unstable SMN protein. The first therapy for SMA was recently approved by the Food and Drug Administration and consists of an antisense oligonucleotide (Nusinersen) rendering SMN2 functional and thus improving patients' motor activity and quality of life. Nevertheless, not all patients equally respond to this therapy and the long-term tolerability and safety of Nusinersen are still unknown. Herein, in vivo splicing assays indicated that the HDAC inhibitor LBH589 is particularly efficient in rescuing the SMN2 splicing defect in SMA fibroblasts and SMA type-I mice-derived neural stem cells. Western blot analyses showed that LBH589 also causes a significant increase in SMN protein expression in SMA cells. Moreover chromatin immunoprecipitation analyses revealed that LBH589 treatment induces widespread H4 acetylation of the entire SMN2 locus and selectively favors the inclusion of the disease-linked exon 7 in SMN2 mature mRNA. The combined treatment of SMA cells with sub-optimal doses of LBH589 and of an antisense oligonucleotide that mimic Nusinersen (ASO_ISSN1) elicits additive effects on SMN2 splicing and SMN protein expression. These findings suggest that HDAC inhibitors can potentiate the activity of Nusinersen and support the notion that 'SMN-plus' combinatorial therapeutic approaches might represent an enhanced opportunity in the scenario of SMA therapy.
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Affiliation(s)
- Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.,IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
| | - Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Valentina Di Rosa
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 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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30
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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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31
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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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32
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Ni W, Xia Y, Luo L, Wen F, Hu D, Bi Y, Qi J. High expression of ALDH1A3 might independently influence poor progression-free and overall survival in patients with glioma via maintaining glucose uptake and lactate production. Cell Biol Int 2019; 44:569-582. [PMID: 31642564 DOI: 10.1002/cbin.11257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 10/19/2019] [Indexed: 12/29/2022]
Abstract
Recent studies have found that the acetaldehyde dehydrogenase 1A3 (ALDH1A3) gene is a marker of glioma stem cells. A total of 115 brain glioma specimens were collected and classified into grade I-IV, while non-tumor brain tissue specimens, taken from 12 patients of vascular malformation surgery, were used as control. ALDH1A3 gene promoter methylation in glioma tissues was detected by pyrosequencing, while immunohistochemistry and western blot were used to detect ALDH1A3 protein expressions in different grades of glioma tissues and normal brain tissues. The expression of ALDH1A3 in the glioma cell line U87 was detected by quantitative real-time polymerase chain reaction and RNA-Seq technology was applied to investigate differentially expressed genes before and after silencing the ALDH1A3 gene. Among the 115 glioma tissue specimens, 50 (43.48%) showed low and 65 (56.52%) high expression of ALDH1A3, but no expression was detected in the control. Univariate and multivariate COX regression analyses showed that the patient's tumor pathological grade, the methylation status of ALDH1A3 promoter, and the expression of ALDH1A3 protein were risk factors for progression-free survival (PFS) and overall survival (OS) (all P < 0.05) and the OS of mice with silenced ALDH1A3 in a glioma nude mouse model was prolonged. U87 experiments revealed that ALDH1A3 expression had significant effects on apoptosis, proliferation, cell cycle, mitochondrial membrane potential, glucose consumption, lactate production, invasion ability, and expression of the pyruvate kinase M2 (PKM2) and hexokinase 2 (HK2) in glioma cells. ALDH1A3 protein expression is a marker for poor PFS and OS in glioma patients.
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Affiliation(s)
- Wei Ni
- Department of Neurosurgery, Yunnan Cancer Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Yaoxiong Xia
- Department of Radiation Oncology, Yunnan Cancer Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Lin Luo
- Department of Neurosurgery, Yunnan Cancer Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Fan Wen
- Department of Neurosurgery, Yunnan Cancer Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Dong Hu
- Department of Neurosurgery, Yunnan Cancer Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Yuxu Bi
- Department of Neurosurgery, Yunnan Cancer Center, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Junhui Qi
- Department of Neurosurgery, Second People's Hospital of Yunnan Province, Kunming, 650021, China
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33
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Samson JM, Ravindran Menon D, Smith DE, Baird E, Kitano T, Gao D, Tan AC, Fujita M. Clinical implications of ALDH1A1 and ALDH1A3 mRNA expression in melanoma subtypes. Chem Biol Interact 2019; 314:108822. [PMID: 31580832 DOI: 10.1016/j.cbi.2019.108822] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 08/23/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022]
Abstract
Aldehyde dehydrogenase (ALDH) activity is not only a valuable marker for cancer cells with stem-like features, but also plays a vital role in drug resistance and disease progression in many tumors including melanoma. However, the precise role of ALDH activity in patient prognosis remains unclear. In this study, using the Cancer Genome Atlas (TCGA) RNA-sequencing expression data, we analyzed gene expression of ALDH isozymes in melanoma tumors to define the expression patterns and the prognostic and predictive values of these enzymes. We found that ALDH1A1 and ALDH1A3 had both higher and broader expression ranges in melanoma patients, and that ALDH1A3 expression correlated with better overall survival in metastatic melanoma. Further, stratification of the TCGA cohorts by the mutational subtypes of melanoma specifically revealed that expression of ALDH1A3 correlated with better prognosis in metastatic BRAF-mutant melanoma while expression of ALDH1A1 correlated with better prognosis in BRAF wild-type melanoma. Gene set enrichment analysis (GSEA) of these cohorts identified upregulation in oxidative phosphorylation, adipogenesis, and fatty acid metabolism signaling in ALDH1Alo patients, suggesting BRAF/MEK inhibitor resistance in that subset of patients. On the other hand, GSEA of ALDH1A3hi cohorts revealed upregulation in glycolysis, hypoxia and angiogenesis, suggesting BRAF/MEK inhibitor sensitivity in that subset of patients. Gene expression analysis using pre-treatment tumor samples supports high ALDH1A3 expression before BRAF/MEK inhibitor treatment as predictive of better treatment response in BRAF-mutant melanoma patients. Our study provides evidence that high ALDH1A3 mRNA expression is not only a prognostic marker but also a predictive marker for BRAF/MEK inhibitor treatment response in BRAF-mutant metastatic melanoma patients.
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Affiliation(s)
- Jenny Mae Samson
- Department of Dermatology, University of Colorado Denver, Aurora, CO, 80045, United States
| | - Dinoop Ravindran Menon
- Department of Dermatology, University of Colorado Denver, Aurora, CO, 80045, United States
| | - Derek E Smith
- Department of Biostatistics & Informatics, University of Colorado Denver, Aurora, CO 80045, United States
| | - Erika Baird
- Department of Dermatology, University of Colorado Denver, Aurora, CO, 80045, United States
| | - Takayuki Kitano
- Department of Dermatology, University of Colorado Denver, Aurora, CO, 80045, United States; School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0215, Japan
| | - Dexiang Gao
- Department of Biostatistics & Informatics, University of Colorado Denver, Aurora, CO 80045, United States
| | - Aik-Choon Tan
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, United States.
| | - Mayumi Fujita
- Department of Dermatology, University of Colorado Denver, Aurora, CO, 80045, United States; Denver VA Medical Center, Denver, CO, 80220, United States; Department of Immunology & Microbiology, University of Colorado Denver, Aurora, CO, 80045, United States.
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34
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Translating neural stem cells to neurons in the mammalian brain. Cell Death Differ 2019; 26:2495-2512. [PMID: 31551564 DOI: 10.1038/s41418-019-0411-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/05/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
The mammalian neocortex underlies our perception of sensory information, performance of motor activities, and higher-order cognition. During mammalian embryogenesis, radial glial precursor cells sequentially give rise to diverse populations of excitatory cortical neurons, followed by astrocytes and oligodendrocytes. A subpopulation of these embryonic neural precursors persists into adulthood as neural stem cells, which give rise to inhibitory interneurons and glia. Although the intrinsic mechanisms instructing the genesis of these distinct progeny have been well-studied, most work to date has focused on transcriptional, epigenetic, and cell-cycle control. Recent studies, however, have shown that posttranscriptional mechanisms also regulate the cell fate choices of transcriptionally primed neural precursors during cortical development. These mechanisms are mediated primarily by RNA-binding proteins and microRNAs that coordinately regulate mRNA translation, stability, splicing, and localization. Together, these findings point to an extensive network of posttranscriptional control and provide insight into both normal cortical development and disease. They also add another layer of complexity to brain development and raise important biological questions for future investigation.
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35
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Mariella E, Marotta F, Grassi E, Gilotto S, Provero P. The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. Front Genet 2019; 10:714. [PMID: 31475030 PMCID: PMC6707137 DOI: 10.3389/fgene.2019.00714] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/05/2019] [Indexed: 11/13/2022] Open
Abstract
In the last decades, genome-wide association studies (GWAS) have uncovered tens of thousands of associations between common genetic variants and complex diseases. However, these statistical associations can rarely be interpreted functionally and mechanistically. As the majority of the disease-associated variants are located far from coding sequences, even the relevant gene is often unclear. A way to gain insight into the relevant mechanisms is to study the genetic determinants of intermediate molecular phenotypes, such as gene expression and transcript structure. We propose a computational strategy to discover genetic variants affecting the relative expression of alternative 3′ untranslated region (UTR) isoforms, generated through alternative polyadenylation, a widespread posttranscriptional regulatory mechanism known to have relevant functional consequences. When applied to a large dataset in which whole genome and RNA sequencing data are available for 373 European individuals, 2,530 genes with alternative polyadenylation quantitative trait loci (apaQTL) were identified. We analyze and discuss possible mechanisms of action of these variants, and we show that they are significantly enriched in GWAS hits, in particular those concerning immune-related and neurological disorders. Our results point to an important role for genetically determined alternative polyadenylation in affecting predisposition to complex diseases, and suggest new ways to extract functional information from GWAS data.
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Affiliation(s)
- Elisa Mariella
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Federico Marotta
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Elena Grassi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Stefano Gilotto
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.,Center for Tranlational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
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36
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La Rosa P, Russo M, D'Amico J, Petrillo S, Aquilano K, Lettieri-Barbato D, Turchi R, Bertini ES, Piemonte F. Nrf2 Induction Re-establishes a Proper Neuronal Differentiation Program in Friedreich's Ataxia Neural Stem Cells. Front Cell Neurosci 2019; 13:356. [PMID: 31417369 PMCID: PMC6685360 DOI: 10.3389/fncel.2019.00356] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
Frataxin deficiency is the pathogenic cause of Friedreich’s Ataxia, an autosomal recessive disease characterized by the increase of oxidative stress and production of free radicals in the cell. Although the onset of the pathology occurs in the second decade of life, cognitive differences and defects in brain structure and functional activation are observed in patients, suggesting developmental defects to take place during fetal neurogenesis. Here, we describe impairments in proliferation, stemness potential and differentiation in neural stem cells (NSCs) isolated from the embryonic cortex of the Frataxin Knockin/Knockout mouse, a disease animal model whose slow-evolving phenotype makes it suitable to study pre-symptomatic defects that may manifest before the clinical onset. We demonstrate that enhancing the expression and activity of the antioxidant response master regulator Nrf2 ameliorates the phenotypic defects observed in NSCs, re-establishing a proper differentiation program.
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Affiliation(s)
- Piergiorgio La Rosa
- Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Marta Russo
- Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Jessica D'Amico
- Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Sara Petrillo
- Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Katia Aquilano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Daniele Lettieri-Barbato
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Riccardo Turchi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Enrico S Bertini
- Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Fiorella Piemonte
- Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
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37
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Kamieniarz-Gdula K, Proudfoot NJ. Transcriptional Control by Premature Termination: A Forgotten Mechanism. Trends Genet 2019; 35:553-564. [PMID: 31213387 PMCID: PMC7471841 DOI: 10.1016/j.tig.2019.05.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 12/26/2022]
Abstract
The concept of early termination as an important means of transcriptional control has long been established. Even so, its role in metazoan gene expression is underappreciated. Recent technological advances provide novel insights into premature transcription termination (PTT). This process is frequent, widespread, and can occur close to the transcription start site (TSS), or within the gene body. Stable prematurely terminated transcripts contribute to the transcriptome as instances of alternative polyadenylation (APA). Independently of transcript stability and function, premature termination opposes the formation of full-length transcripts, thereby negatively regulating gene expression, especially of transcriptional regulators. Premature termination can be beneficial or harmful, depending on its context. As a result, multiple factors have evolved to control this process.
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Affiliation(s)
- Kinga Kamieniarz-Gdula
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK; Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland; Center for Advanced Technology, Adam Mickiewicz University, Umultowska 89c, 61-614 Poznań, Poland.
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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38
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Vassalli G. Aldehyde Dehydrogenases: Not Just Markers, but Functional Regulators of Stem Cells. Stem Cells Int 2019; 2019:3904645. [PMID: 30733805 PMCID: PMC6348814 DOI: 10.1155/2019/3904645] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/25/2018] [Indexed: 12/26/2022] Open
Abstract
Aldehyde dehydrogenase (ALDH) is a superfamily of enzymes that detoxify a variety of endogenous and exogenous aldehydes and are required for the biosynthesis of retinoic acid (RA) and other molecular regulators of cellular function. Over the past decade, high ALDH activity has been increasingly used as a selectable marker for normal cell populations enriched in stem and progenitor cells, as well as for cell populations from cancer tissues enriched in tumor-initiating stem-like cells. Mounting evidence suggests that ALDH not only may be used as a marker for stem cells but also may well regulate cellular functions related to self-renewal, expansion, differentiation, and resistance to drugs and radiation. ALDH exerts its functional actions partly through RA biosynthesis, as all-trans RA reverses the functional effects of pharmacological inhibition or genetic suppression of ALDH activity in many cell types in vitro. There is substantial evidence to suggest that the role of ALDH as a stem cell marker comes down to the specific isoform(s) expressed in a particular tissue. Much emphasis has been placed on the ALDH1A1 and ALDH1A3 members of the ALDH1 family of cytosolic enzymes required for RA biosynthesis. ALDH1A1 and ALDH1A3 regulate cellular function in both normal stem cells and tumor-initiating stem-like cells, promoting tumor growth and resistance to drugs and radiation. An improved understanding of the molecular mechanisms by which ALDH regulates cellular function will likely open new avenues in many fields, especially in tissue regeneration and oncology.
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Affiliation(s)
- Giuseppe Vassalli
- Laboratory of Cellular and Molecular Cardiology, Cardiocentro Ticino, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Center for Molecular Cardiology, University of Zürich, Zürich, Switzerland
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39
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Gong Q, Stump MR, Zhou Z. Regulation of Kv11.1 potassium channel C-terminal isoform expression by the RNA-binding proteins HuR and HuD. J Biol Chem 2018; 293:19624-19632. [PMID: 30377250 DOI: 10.1074/jbc.ra118.003720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 10/17/2018] [Indexed: 12/19/2022] Open
Abstract
The potassium voltage-gated channel subfamily H member 2 (KCNH2) gene encodes the Kv11.1 potassium channel, which conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative polyadenylation and forms a functional, full-length Kv11.1a isoform if exon 15 is polyadenylated or a nonfunctional, C-terminally truncated Kv11.1a-USO isoform if intron 9 is polyadenylated. The molecular mechanisms that regulate Kv11.1 isoform expression are poorly understood. In this study, using HEK293 cells and reporter gene expression, pulldown assays, and RNase protection assays, we identified the RNA-binding proteins Hu antigen R (HuR) and Hu antigen D (HuD) as regulators of Kv11.1 isoform expression. We show that HuR and HuD inhibit activity at the intron 9 polyadenylation site. When co-expressed with the KCNH2 gene, HuR and HuD increased levels of the Kv11.1a isoform and decreased the Kv11.1a-USO isoform in the RNase protection assays and immunoblot analyses. In patch clamp experiments, HuR and HuD significantly increased the Kv11.1 current. siRNA-mediated knockdown of HuR protein decreased levels of the Kv11.1a isoform and increased those of the Kv11.1a-USO isoform. Our findings suggest that the relative expression levels of Kv11.1 C-terminal isoforms are regulated by the RNA-binding HuR and HuD proteins.
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Affiliation(s)
- Qiuming Gong
- From the Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon 97239 and
| | - Matthew R Stump
- Department of Biology, George Fox University, Newberg, Oregon 97132
| | - Zhengfeng Zhou
- From the Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon 97239 and
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40
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The RNA binding protein Sam68 controls T helper 1 differentiation and anti-mycobacterial response through modulation of miR-29. Cell Death Differ 2018; 26:1169-1180. [PMID: 30258098 DOI: 10.1038/s41418-018-0201-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/08/2018] [Accepted: 08/27/2018] [Indexed: 12/24/2022] Open
Abstract
Polarization of naive T cells into interferon (IFN)-γ-producing T helper 1 (Th1) cells is an essential event in the inflammatory response to pathogens. Herein, we identify the RNA binding protein Sam68 as a specific modulator of Th1 differentiation. Sam68-knockout (ko) naive T cells are strongly defective in IL-12-mediated Th1 polarization and express low levels of T-bet and Eomes. Consequently, Sam68-ko Th1 cells are significantly impaired in IFN-γ production. Moreover, we found that Sam68 is required for the induction of an inflammatory Th1 response during Mycobacterium bovis Bacillus Calmette-Guerin (BCG) infection, thus limiting bacterial dissemination in the lungs. Mechanistically, Sam68 directly binds to the microRNA miR-29, a negative regulator of Th1 response, and inhibits its expression during BCG infection. These findings uncover a novel post-transcriptional mechanism required for the Th1-mediated defense against intracellular pathogens and identify a new function for Sam68 in the regulation of the immune response.
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41
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Ravanidis S, Kattan FG, Doxakis E. Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors. Int J Mol Sci 2018; 19:ijms19082280. [PMID: 30081499 PMCID: PMC6121432 DOI: 10.3390/ijms19082280] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
The timing, dosage and location of gene expression are fundamental determinants of brain architectural complexity. In neurons, this is, primarily, achieved by specific sets of trans-acting RNA-binding proteins (RBPs) and their associated factors that bind to specific cis elements throughout the RNA sequence to regulate splicing, polyadenylation, stability, transport and localized translation at both axons and dendrites. Not surprisingly, misregulation of RBP expression or disruption of its function due to mutations or sequestration into nuclear or cytoplasmic inclusions have been linked to the pathogenesis of several neuropsychiatric and neurodegenerative disorders such as fragile-X syndrome, autism spectrum disorders, spinal muscular atrophy, amyotrophic lateral sclerosis and frontotemporal dementia. This review discusses the roles of Pumilio, Staufen, IGF2BP, FMRP, Sam68, CPEB, NOVA, ELAVL, SMN, TDP43, FUS, TAF15, and TIA1/TIAR in RNA metabolism by analyzing their specific molecular and cellular function, the neurological symptoms associated with their perturbation, and their axodendritic transport/localization along with their target mRNAs as part of larger macromolecular complexes termed ribonucleoprotein (RNP) granules.
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Affiliation(s)
- Stylianos Ravanidis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Fedon-Giasin Kattan
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Epaminondas Doxakis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
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Puttini S, Plaisance I, Barile L, Cervio E, Milano G, Marcato P, Pedrazzini T, Vassalli G. ALDH1A3 Is the Key Isoform That Contributes to Aldehyde Dehydrogenase Activity and Affects in Vitro Proliferation in Cardiac Atrial Appendage Progenitor Cells. Front Cardiovasc Med 2018; 5:90. [PMID: 30087899 PMCID: PMC6066537 DOI: 10.3389/fcvm.2018.00090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/25/2018] [Indexed: 12/23/2022] Open
Abstract
High aldehyde dehydrogenase (ALDHhi) activity has been reported in normal and cancer stem cells. We and others have shown previously that human ALDHhi cardiac atrial appendage cells are enriched with stem/progenitor cells. The role of ALDH in these cells is poorly understood but it may come down to the specific ALDH isoform(s) expressed. This study aimed to compare ALDHhi and ALDHlo atrial cells and to identify the isoform(s) that contribute to ALDH activity, and their functional role. Methods and Results: Cells were isolated from atrial appendage specimens from patients with ischemic and/or valvular heart disease undergoing heart surgery. ALDHhi activity assessed with the Aldefluor reagent coincided with primitive surface marker expression (CD34+). Depending on their ALDH activity, RT-PCR analysis of ALDHhi and ALDHlo cells demonstrated a differential pattern of pluripotency genes (Oct 4, Nanog) and genes for more established cardiac lineages (Nkx2.5, Tbx5, Mef2c, GATA4). ALDHhi cells, but not ALDHlo cells, formed clones and were culture-expanded. When cultured under cardiac differentiation conditions, ALDHhi cells gave rise to a higher number of cardiomyocytes compared with ALDHlo cells. Among 19 ALDH isoforms known in human, ALDH1A3 was most highly expressed in ALDHhi atrial cells. Knocking down ALDH1A3, but not ALDH1A1, ALDH1A2, ALDH2, ALDH4A1, or ALDH8A1 using siRNA decreased ALDH activity and cell proliferation in ALDHhi cells. Conversely, overexpressing ALDH1A3 with a retroviral vector increased proliferation in ALDHlo cells. Conclusions: ALDH1A3 is the key isoform responsible for ALDH activity in ALDHhi atrial appendage cells, which have a propensity to differentiate into cardiomyocytes. ALDH1A3 affects in vitro proliferation of these cells.
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Affiliation(s)
- Stefania Puttini
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland
| | - Isabelle Plaisance
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland
| | - Lucio Barile
- Cardiocentro Ticino Foundation and Swiss Institute for Regenerative Medicine, Lugano, Switzerland
| | - Elisabetta Cervio
- Cardiocentro Ticino Foundation and Swiss Institute for Regenerative Medicine, Lugano, Switzerland
| | - Giuseppina Milano
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland.,Cardiocentro Ticino Foundation and Swiss Institute for Regenerative Medicine, Lugano, Switzerland
| | - Paola Marcato
- Departments of Pathology, Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Thierry Pedrazzini
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland
| | - Giuseppe Vassalli
- Cardiovascular Department, CHUV University Hospital, Lausanne, Switzerland.,Cardiocentro Ticino Foundation and Swiss Institute for Regenerative Medicine, Lugano, Switzerland
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Rodríguez-Cazorla E, Ortuño-Miquel S, Candela H, Bailey-Steinitz LJ, Yanofsky MF, Martínez-Laborda A, Ripoll JJ, Vera A. Ovule identity mediated by pre-mRNA processing in Arabidopsis. PLoS Genet 2018; 14:e1007182. [PMID: 29329291 PMCID: PMC5785034 DOI: 10.1371/journal.pgen.1007182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/25/2018] [Accepted: 01/02/2018] [Indexed: 11/18/2022] Open
Abstract
Ovules are fundamental for plant reproduction and crop yield as they are the precursors of seeds. Therefore, ovule specification is a critical developmental program. In Arabidopsis thaliana, ovule identity is redundantly conferred by the homeotic D-class genes SHATTERPROOF1 (SHP1), SHP2 and SEEDSTICK (STK), phylogenetically related to the MADS-domain regulatory gene AGAMOUS (AG), essential in floral organ specification. Previous studies have shown that the HUA-PEP activity, comprised of a suite of RNA-binding protein (RBP) encoding genes, regulates AG pre-mRNA processing and thus flower patterning and organ identity. Here, we report that the HUA-PEP activity additionally governs ovule morphogenesis. Accordingly, in severe hua-pep backgrounds ovules transform into flower organ-like structures. These homeotic transformations are most likely due to the dramatic reduction in SHP1, SHP2 and STK activity. Our molecular and genome-wide profiling strategies revealed the accumulation of prematurely terminated transcripts of D-class genes in hua-pep mutants and reduced amounts of their respective functional messengers, which points to pre-mRNA processing misregulation as the origin of the ovule developmental defects in such backgrounds. RNA processing and transcription are coordinated by the RNA polymerase II (RNAPII) carboxyl-terminal domain (CTD). Our results show that HUA-PEP activity members can interact with the CTD regulator C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 (CPL1), supporting a co-transcriptional mode of action for the HUA-PEP activity. Our findings expand the portfolio of reproductive developmental programs in which HUA-PEP activity participates, and further substantiates the importance of RNA regulatory mechanisms (pre-mRNA co-transcriptional regulation) for correct gene expression during plant morphogenesis.
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Affiliation(s)
| | - Samanta Ortuño-Miquel
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Alicante, Spain
| | - Lindsay J. Bailey-Steinitz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Martin F. Yanofsky
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Antonio Martínez-Laborda
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (AV); (JJR)
| | - Antonio Vera
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
- * E-mail: (AV); (JJR)
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44
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Svetoni F, De Paola E, La Rosa P, Mercatelli N, Caporossi D, Sette C, Paronetto MP. Post-transcriptional regulation of FUS and EWS protein expression by miR-141 during neural differentiation. Hum Mol Genet 2018; 26:2732-2746. [PMID: 28453628 DOI: 10.1093/hmg/ddx160] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/21/2017] [Indexed: 12/31/2022] Open
Abstract
Brain development involves proliferation, migration and specification of neural progenitor cells, culminating in neuronal circuit formation. Mounting evidence indicates that improper regulation of RNA binding proteins (RBPs), including members of the FET (FUS, EWS, TAF15) family, results in defective cortical development and/or neurodegenerative disorders. However, in spite of their physiological relevance, the precise pattern of FET protein expression in developing neurons is largely unknown. Herein, we found that FUS, EWS and TAF15 expression is differentially regulated during brain development, both in time and in space. In particular, our study identifies a fine-tuned regulation of FUS and EWS during neuronal differentiation, whereas TAF15 appears to be more constitutively expressed. Mechanistically FUS and EWS protein expression is regulated at the post-transcriptional level during neuron differentiation and brain development. Moreover, we identified miR-141 as a key regulator of these FET proteins that modulate their expression levels in differentiating neuronal cells. Thus, our studies uncover a novel link between post-transcriptional regulation of FET proteins expression and neurogenesis.
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Affiliation(s)
- Francesca Svetoni
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Elisa De Paola
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Piergiorgio La Rosa
- Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Neri Mercatelli
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Daniela Caporossi
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy
| | - Claudio Sette
- Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
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45
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46
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Alternative polyadenylation of ZEB1 promotes its translation during genotoxic stress in pancreatic cancer cells. Cell Death Dis 2017; 8:e3168. [PMID: 29120411 PMCID: PMC5775412 DOI: 10.1038/cddis.2017.562] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 01/16/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by extremely poor prognosis. The standard chemotherapeutic drug, gemcitabine, does not offer significant improvements for PDAC management due to the rapid acquisition of drug resistance by patients. Recent evidence indicates that epithelial-to-mesenchymal transition (EMT) of PDAC cells is strictly associated to early metastasization and resistance to chemotherapy. However, it is not exactly clear how EMT is related to drug resistance or how chemotherapy influences EMT. Herein, we found that ZEB1 is the only EMT-related transcription factor that clearly segregates mesenchymal and epithelial PDAC cell lines. Gemcitabine treatment caused upregulation of ZEB1 protein through post-transcriptional mechanisms in mesenchymal PDAC cells within a context of global inhibition of protein synthesis. The increase in ZEB1 protein correlates with alternative polyadenylation of the transcript, leading to shortening of the 3' untranslated region (UTR) and deletion of binding sites for repressive microRNAs. Polysome profiling indicated that shorter ZEB1 transcripts are specifically retained on the polysomes of PDAC cells during genotoxic stress, while most mRNAs, including longer ZEB1 transcripts, are depleted. Thus, our findings uncover a novel layer of ZEB1 regulation through 3'-end shortening of its transcript and selective association with polysomes under genotoxic stress, strongly suggesting that PDAC cells rely on upregulation of ZEB1 protein expression to withstand hostile environments.
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47
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Lennox AL, Mao H, Silver DL. RNA on the brain: emerging layers of post-transcriptional regulation in cerebral cortex development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 28837264 DOI: 10.1002/wdev.290] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Embryonic development is a critical period during which neurons of the brain are generated and organized. In the developing cerebral cortex, this requires complex processes of neural progenitor proliferation, neuronal differentiation, and migration. Each step relies upon highly regulated control of gene expression. In particular, RNA splicing, stability, localization, and translation have emerged as key post-transcriptional regulatory nodes of mouse corticogenesis. Trans-regulators of RNA metabolism, including microRNAs (miRs) and RNA-binding proteins (RBPs), orchestrate diverse steps of cortical development. These trans-factors function either individually or cooperatively to influence RNAs, often of similar classes, termed RNA regulons. New technological advances raise the potential for an increasingly sophisticated understanding of post-transcriptional control in the developing neocortex. Many RNA-binding factors are also implicated in neurodevelopmental diseases of the cortex. Therefore, elucidating how RBPs and miRs converge to influence mRNA expression in progenitors and neurons will give valuable insights into mechanisms of cortical development and disease. WIREs Dev Biol 2018, 7:e290. doi: 10.1002/wdev.290 This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory RNA Nervous System Development > Vertebrates: Regional Development Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cells and Disease.
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Affiliation(s)
- Ashley L Lennox
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Hanqian Mao
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
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48
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Li N, Hébert S, Song J, Kleinman CL, Richard S. Transcriptome profiling in preadipocytes identifies long noncoding RNAs as Sam68 targets. Oncotarget 2017; 8:81994-82005. [PMID: 29137239 PMCID: PMC5669865 DOI: 10.18632/oncotarget.17813] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/17/2017] [Indexed: 11/25/2022] Open
Abstract
The KH-type RNA binding protein Sam68 is required for adipogenesis. We have previously shown that Sam68-deficient mice have a lean phenotype and are protected against dietary-induced obesity due to defects in mTOR and S6K1 alternative splicing. Herein we profiled the transcriptome of Sam68 wild type and deficient 3T3-L1 mouse preadipocytes. We identified 652 protein-coding genes and 9 ncRNAs that were significantly altered with the loss of Sam68. As expected, downregulated genes were significantly associated with GO terms linked to cell migration, motility, and fat cell differentiation, while upregulated genes were mostly associated with GO terms linked to neurogenesis. Of the lncRNAs, we identified Hotair, Mir155hg, as well as two new lncRNAs (SR-lncRNA-1 and SR-lncRNA-2) that were regulated by Sam68, and contained consensus Sam68 binding sites. RNA stability assays showed that Sam68-deficiency decreased the half-life of Hotair, and increased the half-lives of Mir155hg and SR-lncRNA-2, while the stability of SR-lncRNA-1 was unaffected. Depletion of Hotair and SR-lncRNA-1 in wild type 3T3-L1 cells led to defects in adipogenesis, whereas depletion of SR-lncRNA-2 in Sam68-deficient 3T3-L1 cells partially rescued the adipogenesis defect observed in these cells. Collectively, our findings define a new role for Sam68 as a regulator of lncRNAs during adipogenic differentiation.
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Affiliation(s)
- Naomi Li
- Segal Cancer Center, Sir Mortimer B Davis Jewish General Hospital, Lady Davis Institute for Medical Research, Montréal, Québec H3T 1E2, Canada.,Department of Medicine, McGill University, Montréal, Québec H3A 1A1, Canada.,Department of Oncology, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Steven Hébert
- Segal Cancer Center, Sir Mortimer B Davis Jewish General Hospital, Lady Davis Institute for Medical Research, Montréal, Québec H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Jingwen Song
- Segal Cancer Center, Sir Mortimer B Davis Jewish General Hospital, Lady Davis Institute for Medical Research, Montréal, Québec H3T 1E2, Canada.,Department of Medicine, McGill University, Montréal, Québec H3A 1A1, Canada.,Department of Oncology, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Claudia L Kleinman
- Segal Cancer Center, Sir Mortimer B Davis Jewish General Hospital, Lady Davis Institute for Medical Research, Montréal, Québec H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Stéphane Richard
- Segal Cancer Center, Sir Mortimer B Davis Jewish General Hospital, Lady Davis Institute for Medical Research, Montréal, Québec H3T 1E2, Canada.,Department of Medicine, McGill University, Montréal, Québec H3A 1A1, Canada.,Department of Oncology, McGill University, Montréal, Québec H3A 1A1, Canada
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49
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Faulty RNA splicing: consequences and therapeutic opportunities in brain and muscle disorders. Hum Genet 2017; 136:1215-1235. [DOI: 10.1007/s00439-017-1802-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
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