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Salpietro V, Maroofian R, Zaki MS, Wangen J, Ciolfi A, Barresi S, Efthymiou S, Lamaze A, Aughey GN, Al Mutairi F, Rad A, Rocca C, Calì E, Accogli A, Zara F, Striano P, Mojarrad M, Tariq H, Giacopuzzi E, Taylor JC, Oprea G, Skrahina V, Rehman KU, Abd Elmaksoud M, Bassiony M, El Said HG, Abdel-Hamid MS, Al Shalan M, Seo G, Kim S, Lee H, Khang R, Issa MY, Elbendary HM, Rafat K, Marinakis NM, Traeger-Synodinos J, Ververi A, Sourmpi M, Eslahi A, Khadivi Zand F, Beiraghi Toosi M, Babaei M, Jackson A, Bertoli-Avella A, Pagnamenta AT, Niceta M, Battini R, Corsello A, Leoni C, Chiarelli F, Dallapiccola B, Faqeih EA, Tallur KK, Alfadhel M, Alobeid E, Maddirevula S, Mankad K, Banka S, Ghayoor-Karimiani E, Tartaglia M, Chung WK, Green R, Alkuraya FS, Jepson JEC, Houlden H. Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome. Am J Hum Genet 2024; 111:200-210. [PMID: 38118446 PMCID: PMC10806450 DOI: 10.1016/j.ajhg.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023] Open
Abstract
The homologous genes GTPBP1 and GTPBP2 encode GTP-binding proteins 1 and 2, which are involved in ribosomal homeostasis. Pathogenic variants in GTPBP2 were recently shown to be an ultra-rare cause of neurodegenerative or neurodevelopmental disorders (NDDs). Until now, no human phenotype has been linked to GTPBP1. Here, we describe individuals carrying bi-allelic GTPBP1 variants that display an identical phenotype with GTPBP2 and characterize the overall spectrum of GTP-binding protein (1/2)-related disorders. In this study, 20 individuals from 16 families with distinct NDDs and syndromic facial features were investigated by whole-exome (WES) or whole-genome (WGS) sequencing. To assess the functional impact of the identified genetic variants, semi-quantitative PCR, western blot, and ribosome profiling assays were performed in fibroblasts from affected individuals. We also investigated the effect of reducing expression of CG2017, an ortholog of human GTPBP1/2, in the fruit fly Drosophila melanogaster. Individuals with bi-allelic GTPBP1 or GTPBP2 variants presented with microcephaly, profound neurodevelopmental impairment, pathognomonic craniofacial features, and ectodermal defects. Abnormal vision and/or hearing, progressive spasticity, choreoathetoid movements, refractory epilepsy, and brain atrophy were part of the core phenotype of this syndrome. Cell line studies identified a loss-of-function (LoF) impact of the disease-associated variants but no significant abnormalities on ribosome profiling. Reduced expression of CG2017 isoforms was associated with locomotor impairment in Drosophila. In conclusion, bi-allelic GTPBP1 and GTPBP2 LoF variants cause an identical, distinct neurodevelopmental syndrome. Mutant CG2017 knockout flies display motor impairment, highlighting the conserved role for GTP-binding proteins in CNS development across species.
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Affiliation(s)
- Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Jamie Wangen
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Sabina Barresi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Angelique Lamaze
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK; Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Gabriel N Aughey
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Fuad Al Mutairi
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Elisa Calì
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Andrea Accogli
- Division of Medical Genetics, Department of Pediatrics, McGill University, Montreal, Canada
| | - Federico Zara
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Unit of Pediatric Neurology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Huma Tariq
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Edoardo Giacopuzzi
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK; Genomics Research Centre, Human Technopole, Milan, Italy; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | | | - Marwa Abd Elmaksoud
- Neurology Unit, Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Mahmoud Bassiony
- Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Huda G El Said
- Department of Family Health, High Institute of Public Health, University of Alexandria, Alexandria, Egypt
| | - Mohamed S Abdel-Hamid
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Maha Al Shalan
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | | | - Hane Lee
- 3billion, Inc, Seoul, South Korea
| | | | - Mahmoud Y Issa
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Karima Rafat
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Athina Ververi
- Genetics Unit, Department of Obstetrics & Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Thessaloniki, Greece
| | | | - Atieh Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Masshad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Masshad, Iran
| | | | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | | | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Antonio Corsello
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Chiara Leoni
- Center for Rare Diseases and Birth Defects, Department of Women and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | | | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Eissa Ali Faqeih
- Unit of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Majid Alfadhel
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia; College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Kshitij Mankad
- Department of Neuroradiology, Great Ormond Street Hospital, London, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Ehsan Ghayoor-Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, University of London, St George's, Cranmer Terrace, London SW17 0RE, UK
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - James E C Jepson
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
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Catalanotto C, Barbato C, Cogoni C, Benelli D. The RNA-Binding Function of Ribosomal Proteins and Ribosome Biogenesis Factors in Human Health and Disease. Biomedicines 2023; 11:2969. [PMID: 38001969 PMCID: PMC10669870 DOI: 10.3390/biomedicines11112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The ribosome is a macromolecular complex composed of RNA and proteins that interact through an integrated and interconnected network to preserve its ancient core activities. In this review, we emphasize the pivotal role played by RNA-binding proteins as a driving force in the evolution of the current form of the ribosome, underscoring their importance in ensuring accurate protein synthesis. This category of proteins includes both ribosomal proteins and ribosome biogenesis factors. Impairment of their RNA-binding activity can also lead to ribosomopathies, which is a group of disorders characterized by defects in ribosome biogenesis that are detrimental to protein synthesis and cellular homeostasis. A comprehensive understanding of these intricate processes is essential for elucidating the mechanisms underlying the resulting diseases and advancing potential therapeutic interventions.
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Affiliation(s)
- Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Christian Barbato
- National Research Council (CNR), Department of Sense Organs DOS, Institute of Biochemistry and Cell Biology (IBBC), Sapienza University of Rome, 00185 Rome, Italy;
| | - Carlo Cogoni
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Dario Benelli
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
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Belli V, Maiello D, Di Lorenzo C, Furia M, Vicidomini R, Turano M. New Insights into Dyskerin-CypA Interaction: Implications for X-Linked Dyskeratosis Congenita and Beyond. Genes (Basel) 2023; 14:1766. [PMID: 37761906 PMCID: PMC10531313 DOI: 10.3390/genes14091766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/27/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The highly conserved family of cyclophilins comprises multifunctional chaperones that interact with proteins and RNAs, facilitating the dynamic assembly of multimolecular complexes involved in various cellular processes. Cyclophilin A (CypA), the predominant member of this family, exhibits peptidyl-prolyl cis-trans isomerase activity. This enzymatic function aids with the folding and activation of protein structures and often serves as a molecular regulatory switch for large multimolecular complexes, ensuring appropriate inter- and intra-molecular interactions. Here, we investigated the involvement of CypA in the nucleus, where it plays a crucial role in supporting the assembly and trafficking of heterogeneous ribonucleoproteins (RNPs). We reveal that CypA is enriched in the nucleolus, where it colocalizes with the pseudouridine synthase dyskerin, the catalytic component of the multifunctional H/ACA RNPs involved in the modification of cellular RNAs and telomere stability. We show that dyskerin, whose mutations cause the X-linked dyskeratosis (X-DC) and the Hoyeraal-Hreidarsson congenital ribosomopathies, can directly interact with CypA. These findings, together with the remark that substitution of four dyskerin prolines are known to cause X-DC pathogenic mutations, lead us to indicate this protein as a CypA client. The data presented here suggest that this chaperone can modulate dyskerin activity influencing all its partecipated RNPs.
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Affiliation(s)
- Valentina Belli
- Istituto Nazionale Tumori—IRCSS—Fondazione G. Pascale, 80131 Naples, Italy;
| | - Daniela Maiello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (D.M.); (C.D.L.); (M.F.)
| | - Concetta Di Lorenzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (D.M.); (C.D.L.); (M.F.)
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Maria Furia
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (D.M.); (C.D.L.); (M.F.)
| | - Rosario Vicidomini
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mimmo Turano
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (D.M.); (C.D.L.); (M.F.)
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Smallwood K, Watt KEN, Ide S, Baltrunaite K, Brunswick C, Inskeep K, Capannari C, Adam MP, Begtrup A, Bertola DR, Demmer L, Demo E, Devinsky O, Gallagher ER, Guillen Sacoto MJ, Jech R, Keren B, Kussmann J, Ladda R, Lansdon LA, Lunke S, Mardy A, McWalters K, Person R, Raiti L, Saitoh N, Saunders CJ, Schnur R, Skorvanek M, Sell SL, Slavotinek A, Sullivan BR, Stark Z, Symonds JD, Wenger T, Weber S, Whalen S, White SM, Winkelmann J, Zech M, Zeidler S, Maeshima K, Stottmann RW, Trainor PA, Weaver KN. POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies. Am J Hum Genet 2023; 110:809-825. [PMID: 37075751 PMCID: PMC10183370 DOI: 10.1016/j.ajhg.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/21/2023] [Indexed: 04/21/2023] Open
Abstract
Heterozygous pathogenic variants in POLR1A, which encodes the largest subunit of RNA Polymerase I, were previously identified as the cause of acrofacial dysostosis, Cincinnati-type. The predominant phenotypes observed in the cohort of 3 individuals were craniofacial anomalies reminiscent of Treacher Collins syndrome. We subsequently identified 17 additional individuals with 12 unique heterozygous variants in POLR1A and observed numerous additional phenotypes including neurodevelopmental abnormalities and structural cardiac defects, in combination with highly prevalent craniofacial anomalies and variable limb defects. To understand the pathogenesis of this pleiotropy, we modeled an allelic series of POLR1A variants in vitro and in vivo. In vitro assessments demonstrate variable effects of individual pathogenic variants on ribosomal RNA synthesis and nucleolar morphology, which supports the possibility of variant-specific phenotypic effects in affected individuals. To further explore variant-specific effects in vivo, we used CRISPR-Cas9 gene editing to recapitulate two human variants in mice. Additionally, spatiotemporal requirements for Polr1a in developmental lineages contributing to congenital anomalies in affected individuals were examined via conditional mutagenesis in neural crest cells (face and heart), the second heart field (cardiac outflow tract and right ventricle), and forebrain precursors in mice. Consistent with its ubiquitous role in the essential function of ribosome biogenesis, we observed that loss of Polr1a in any of these lineages causes cell-autonomous apoptosis resulting in embryonic malformations. Altogether, our work greatly expands the phenotype of human POLR1A-related disorders and demonstrates variant-specific effects that provide insights into the underlying pathogenesis of ribosomopathies.
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Affiliation(s)
- Kelly Smallwood
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Kristina Baltrunaite
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chad Brunswick
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Katherine Inskeep
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Corrine Capannari
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Margaret P Adam
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | | | - Laurie Demmer
- Atrium Health's Levine Children's Hospital, Charlotte, NC, USA
| | - Erin Demo
- Sibley Heart Center, Atlanta, GA, USA
| | - Orrin Devinsky
- Department of Neurology, Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Emily R Gallagher
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Boris Keren
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Jennifer Kussmann
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Roger Ladda
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA, USA
| | - Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy Research Institute, 2401 Gillham Road, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, USA
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Anne Mardy
- Department of Women's Health, University of Texas Austin Dell Medical Center, Austin, TX, USA
| | | | | | - Laura Raiti
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia
| | | | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy Research Institute, 2401 Gillham Road, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, USA
| | | | - Matej Skorvanek
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic; Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Susan L Sell
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Joseph D Symonds
- Paediatric Neuroscience Research Group, Royal Hospital for Children, Glasgow G667AB, UK
| | - Tara Wenger
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sacha Weber
- CCA-AHU de génétique clinique et de neurogénétique, Service de Génétique et de Neurologie, CHU de Caen, Caen, France
| | - Sandra Whalen
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - K Nicole Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Temaj G, Saha S, Dragusha S, Ejupi V, Buttari B, Profumo E, Beqa L, Saso L. Ribosomopathies and cancer: pharmacological implications. Expert Rev Clin Pharmacol 2022; 15:729-746. [PMID: 35787725 DOI: 10.1080/17512433.2022.2098110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The ribosome is a ribonucleoprotein organelle responsible for protein synthesis, and its biogenesis is a highly coordinated process that involves many macromolecular components. Any acquired or inherited impairment in ribosome biogenesis or ribosomopathies is associated with the development of different cancers and rare genetic diseases. Interference with multiple steps of protein synthesis has been shown to promote tumor cell death. AREAS COVERED We discuss the current insights about impaired ribosome biogenesis and their secondary consequences on protein synthesis, transcriptional and translational responses, proteotoxic stress, and other metabolic pathways associated with cancer and rare diseases. Studies investigating the modulation of different therapeutic chemical entities targeting cancer in in vitro and in vivo models have also been detailed. EXPERT OPINION Despite the association between inherited mutations affecting ribosome biogenesis and cancer biology, the development of therapeutics targeting the essential cellular machinery has only started to emerge. New chemical entities should be designed to modulate different checkpoints (translating oncoproteins, dysregulation of specific ribosome-assembly machinery, ribosomal stress, and rewiring ribosomal functions). Although safe and effective therapies are lacking, consideration should also be given to using existing drugs alone or in combination for long-term safety, with known risks for feasibility in clinical trials and synergistic effects.
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Affiliation(s)
| | - Sarmistha Saha
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | | | - Valon Ejupi
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Brigitta Buttari
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Elisabetta Profumo
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Lule Beqa
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Italy
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Papendorf JJ, Krüger E, Ebstein F. Proteostasis Perturbations and Their Roles in Causing Sterile Inflammation and Autoinflammatory Diseases. Cells 2022; 11:cells11091422. [PMID: 35563729 PMCID: PMC9103147 DOI: 10.3390/cells11091422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 12/17/2022] Open
Abstract
Proteostasis, a portmanteau of the words protein and homeostasis, refers to the ability of eukaryotic cells to maintain a stable proteome by acting on protein synthesis, quality control and/or degradation. Over the last two decades, an increasing number of disorders caused by proteostasis perturbations have been identified. Depending on their molecular etiology, such diseases may be classified into ribosomopathies, proteinopathies and proteasomopathies. Strikingly, most—if not all—of these syndromes exhibit an autoinflammatory component, implying a direct cause-and-effect relationship between proteostasis disruption and the initiation of innate immune responses. In this review, we provide a comprehensive overview of the molecular pathogenesis of these disorders and summarize current knowledge of the various mechanisms by which impaired proteostasis promotes autoinflammation. We particularly focus our discussion on the notion of how cells sense and integrate proteostasis perturbations as danger signals in the context of autoinflammatory diseases to provide insights into the complex and multiple facets of sterile inflammation.
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Martin ET, Blatt P, Nguyen E, Lahr R, Selvam S, Yoon HAM, Pocchiari T, Emtenani S, Siekhaus DE, Berman A, Fuchs G, Rangan P. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Dev Cell 2022; 57:883-900.e10. [PMID: 35413237 PMCID: PMC9011129 DOI: 10.1016/j.devcel.2022.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/11/2022] [Accepted: 03/10/2022] [Indexed: 01/26/2023]
Abstract
Ribosomal defects perturb stem cell differentiation, and this is the cause of ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discover that three DExD/H-box proteins govern ribosome biogenesis (RiBi) and Drosophila oogenesis. Loss of these DExD/H-box proteins, which we name Aramis, Athos, and Porthos, aberrantly stabilizes p53, arrests the cell cycle, and stalls germline stem cell (GSC) differentiation. Aramis controls cell-cycle progression by regulating translation of mRNAs that contain a terminal oligo pyrimidine (TOP) motif in their 5' UTRs. We find that TOP motifs confer sensitivity to ribosome levels that are mediated by La-related protein (Larp). One such TOP-containing mRNA codes for novel nucleolar protein 1 (Non1), a conserved p53 destabilizing protein. Upon a sufficient ribosome concentration, Non1 is expressed, and it promotes GSC cell-cycle progression via p53 degradation. Thus, a previously unappreciated TOP motif in Drosophila responds to reduced RiBi to co-regulate the translation of ribosomal proteins and a p53 repressor, coupling RiBi to GSC differentiation.
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Affiliation(s)
- Elliot T Martin
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Elaine Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roni Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sangeetha Selvam
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Hyun Ah M Yoon
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA; Albany Medical College, Albany, NY 12208, USA
| | - Tyler Pocchiari
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA; SUNY Upstate Medical University, Syracuse, NY 13210-2375, USA
| | - Shamsi Emtenani
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Daria E Siekhaus
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Andrea Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gabriele Fuchs
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA.
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA.
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8
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Groarke EM, Calado RT, Liu JM. Cell senescence and malignant transformation in the inherited bone marrow failure syndromes: Overlapping pathophysiology with therapeutic implications. Semin Hematol 2022; 59:30-37. [PMID: 35491056 PMCID: PMC9062194 DOI: 10.1053/j.seminhematol.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/19/2022] [Accepted: 01/26/2022] [Indexed: 02/02/2023]
Abstract
Fanconi anemia, telomeropathies and ribosomopathies are members of the inherited bone marrow failure syndromes, rare genetic disorders that lead to failure of hematopoiesis, developmental abnormalities, and cancer predisposition. While each disorder is caused by different genetic defects in seemingly disparate processes of DNA repair, telomere maintenance, or ribosome biogenesis, they appear to lead to a common pathway characterized by premature senescence of hematopoietic stem cells. Here we review the experimental data on senescence and inflammation underlying marrow failure and malignant transformation. We conclude with a critical assessment of current and future therapies targeting these pathways in inherited bone marrow failure syndromes patients.
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Affiliation(s)
- Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
| | - Rodrigo T Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Johnson M Liu
- Division of Hematology, Maine Medical Center, Portland, ME
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9
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Frattini A, Bolamperti S, Valli R, Cipolli M, Pinto RM, Bergami E, Frau MR, Cesaro S, Signo M, Bezzerri V, Porta G, Khan AW, Rubinacci A, Villa I. Enhanced p53 Levels Are Involved in the Reduced Mineralization Capacity of Osteoblasts Derived from Shwachman-Diamond Syndrome Subjects. Int J Mol Sci 2021; 22:ijms222413331. [PMID: 34948128 PMCID: PMC8707819 DOI: 10.3390/ijms222413331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive disorder characterized by bone marrow failure, exocrine pancreatic insufficiency, and skeletal abnormalities, caused by loss-of-function mutations in the SBDS gene, a factor involved in ribosome biogenesis. By analyzing osteoblasts from SDS patients (SDS-OBs), we show that SDS-OBs displayed reduced SBDS gene expression and reduced/undetectable SBDS protein compared to osteoblasts from healthy subjects (H-OBs). SDS-OBs cultured in an osteogenic medium displayed a lower mineralization capacity compared to H-OBs. Whole transcriptome analysis showed significant differences in the gene expression of SDS-OBs vs. H-OBs, particularly in the ossification pathway. SDS-OBs expressed lower levels of the main genes responsible for osteoblastogenesis. Of all downregulated genes, Western blot analyses confirmed lower levels of alkaline phosphatase and collagen type I in SDS-OBs than in H-OBs. Interestingly, SDS-OBs showed higher protein levels of p53, an inhibitor of osteogenesis, compared to H-OBs. Silencing of Tp53 was associated with higher collagen type I and alkaline phosphatase protein levels and an increase in SDS-OB mineralization capacity. In conclusion, our results show that the reduced capacity of SDS-OBs to mineralize is mediated, at least in part, by the high levels of p53 and highlight an important role of SBDS in osteoblast functions.
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Affiliation(s)
- Annalisa Frattini
- Institute for Genetic and Biomedical Research (IRGB), UOS Milano CNR, Via Fantoli, 15/16, 20138 Milano, Italy
- Department of Medicine and Surgery (DMC), Universita’ degli Studi dell’Insubria, Via J.H. Dunant, 5, 21100 Varese, Italy; (R.V.); (G.P.); (A.W.K.)
- Correspondence: ; Tel.: +39-0332217113
| | - Simona Bolamperti
- Bone Metabolism Unit, IRCCS Ospedale San Raffaele, Via Olgettina, 60, 20132 Milano, Italy; (S.B.); (M.S.); (A.R.); (I.V.)
| | - Roberto Valli
- Department of Medicine and Surgery (DMC), Universita’ degli Studi dell’Insubria, Via J.H. Dunant, 5, 21100 Varese, Italy; (R.V.); (G.P.); (A.W.K.)
| | - Marco Cipolli
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata di Verona, Piazzale Aristide Stefani, 1, 37126 Verona, Italy;
| | - Rita Maria Pinto
- Department of Onco-Hematology, Ospedale Bambino Gesù IRCCS, Piazza S.Onofrio, 4, 00165 Roma, Italy;
| | - Elena Bergami
- Pediatric Onco-Hematology, IRCCS Policlinico San Matteo, Viale Camillo Golgi, 19, 27100 Pavia, Italy;
| | - Maria Rita Frau
- Pediatrics and Intensive Neonatal Therapy, Ospedale San Francesco, Via Salvatore Mannironi, 08100 Nuoro, Italy;
| | - Simone Cesaro
- Pediatric Hematology Oncology, Ospedale Donna Bambino, Azienda Ospedaliera Universitaria Integrata, Piazzale Aristide Stefani, 1, 37126 Verona, Italy;
| | - Michela Signo
- Bone Metabolism Unit, IRCCS Ospedale San Raffaele, Via Olgettina, 60, 20132 Milano, Italy; (S.B.); (M.S.); (A.R.); (I.V.)
| | - Valentino Bezzerri
- Cystic Fibrosis Center, Azienda Ospedaliero Universitaria Ospedali Riuniti di Ancona, Via Conca, 71, 60126 Ancona, Italy;
| | - Giovanni Porta
- Department of Medicine and Surgery (DMC), Universita’ degli Studi dell’Insubria, Via J.H. Dunant, 5, 21100 Varese, Italy; (R.V.); (G.P.); (A.W.K.)
| | - Abdul Waheed Khan
- Department of Medicine and Surgery (DMC), Universita’ degli Studi dell’Insubria, Via J.H. Dunant, 5, 21100 Varese, Italy; (R.V.); (G.P.); (A.W.K.)
| | - Alessandro Rubinacci
- Bone Metabolism Unit, IRCCS Ospedale San Raffaele, Via Olgettina, 60, 20132 Milano, Italy; (S.B.); (M.S.); (A.R.); (I.V.)
| | - Isabella Villa
- Bone Metabolism Unit, IRCCS Ospedale San Raffaele, Via Olgettina, 60, 20132 Milano, Italy; (S.B.); (M.S.); (A.R.); (I.V.)
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Gay DM, Lund AH, Jansson MD. Translational control through ribosome heterogeneity and functional specialization. Trends Biochem Sci 2021; 47:66-81. [PMID: 34312084 DOI: 10.1016/j.tibs.2021.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/18/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
The conceptual origins of ribosome specialization can be traced back to the earliest days of molecular biology. Yet, this field has only recently begun to gather momentum, with numerous studies identifying distinct heterogeneous ribosome populations across multiple species and model systems. It is proposed that some of these compositionally distinct ribosomes may be functionally specialized and able to regulate the translation of specific mRNAs. Identification and functional characterization of specialized ribosomes has the potential to elucidate a novel layer of gene expression control, at the level of translation, where the ribosome itself is a key regulatory player. In this review, we discuss different sources of ribosome heterogeneity, evidence for ribosome specialization, and also the future directions of this exciting field.
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Affiliation(s)
- David M Gay
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Martin D Jansson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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11
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McCool MA, Bryant CJ, Baserga SJ. MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis. Biochem Soc Trans 2020; 48:595-612. [PMID: 32267487 DOI: 10.1042/BST20190854] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/14/2022]
Abstract
Ribosome biogenesis is the fine-tuned, essential process that generates mature ribosomal subunits and ultimately enables all protein synthesis within a cell. Novel regulators of ribosome biogenesis continue to be discovered in higher eukaryotes. While many known regulatory factors are proteins or small nucleolar ribonucleoproteins, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) are emerging as a novel modulatory layer controlling ribosome production. Here, we summarize work uncovering non-coding RNAs (ncRNAs) as novel regulators of ribosome biogenesis and highlight their links to diseases of defective ribosome biogenesis. It is still unclear how many miRNAs or lncRNAs are involved in phenotypic or pathological disease outcomes caused by impaired ribosome production, as in the ribosomopathies, or by increased ribosome production, as in cancer. In time, we hypothesize that many more ncRNA regulators of ribosome biogenesis will be discovered, which will be followed by an effort to establish connections between disease pathologies and the molecular mechanisms of this additional layer of ribosome biogenesis control.
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12
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Recasens-Alvarez C, Alexandre C, Kirkpatrick J, Nojima H, Huels DJ, Snijders AP, Vincent JP. Ribosomopathy-associated mutations cause proteotoxic stress that is alleviated by TOR inhibition. Nat Cell Biol 2021; 23:127-135. [PMID: 33495632 PMCID: PMC7116740 DOI: 10.1038/s41556-020-00626-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/16/2020] [Indexed: 02/07/2023]
Abstract
Ribosomes are multicomponent molecular machines that synthesize all of the proteins of living cells. Most of the genes that encode the protein components of ribosomes are therefore essential. A reduction in gene dosage is often viable albeit deleterious and is associated with human syndromes, which are collectively known as ribosomopathies1-3. The cell biological basis of these pathologies has remained unclear. Here, we model human ribosomopathies in Drosophila and find widespread apoptosis and cellular stress in the resulting animals. This is not caused by insufficient protein synthesis, as reasonably expected. Instead, ribosomal protein deficiency elicits proteotoxic stress, which we suggest is caused by the accumulation of misfolded proteins that overwhelm the protein degradation machinery. We find that dampening the integrated stress response4 or autophagy increases the harm inflicted by ribosomal protein deficiency, suggesting that these activities could be cytoprotective. Inhibition of TOR activity-which decreases ribosomal protein production, slows down protein synthesis and stimulates autophagy5-reduces proteotoxic stress in our ribosomopathy model. Interventions that stimulate autophagy, combined with means of boosting protein quality control, could form the basis of a therapeutic strategy for this class of diseases.
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Affiliation(s)
| | | | | | - Hisashi Nojima
- The Francis Crick Institute, London, UK
- FUJIREBIO Inc, Tokyo, Japan
| | - David J Huels
- The Francis Crick Institute, London, UK
- Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Academic Medical Center, Amsterdam, the Netherlands
- Academic Medical Center, Oncode Institute, Amsterdam, the Netherlands
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13
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Chelomina GN, Rozhkovan KV, Burundukova OL, Gorpenchenko TY, Khrolenko YA, Zhuravlev YN. Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines. Biomolecules 2020; 10:biom10101410. [PMID: 33036123 PMCID: PMC7599642 DOI: 10.3390/biom10101410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023] Open
Abstract
Long-term cultivation of Panax ginseng cell lines leads to a decreasing synthesis of the biologically active substances used in traditional medicine. To gain insight into the cellular mechanisms which may influence this process, we analyzed variations within the rDNA cluster of the Oriental ginseng cell lines. The cell lines were cultivated for 6 and 24 years; the number of nucleoli and chromosomes was analyzed. The complete 18S rDNA sequences were cloned and sequenced. The nucleotide polymorphism and phylogenetic relations of the sequences were analyzed, and the secondary structures for separate 18S rRNA regions were modeled. The 18S rDNA accumulated mutations during cell cultivation that correlate well with an increase in the number of chromosomes and nucleoli. The patterns of nucleotide diversity are culture-specific and the increasing polymorphism associates with cytosine methylation sites. The secondary structures of some 18S rRNA regions and their interaction can alter during cultivation. The phylogenetic tree topologies are particular for each cell line.The observed alterations in rDNA clusters are associated with a somaclonal variation, leading to changes in the pattern of intracellular synthesis during cell cultivation. The identified divergent rRNAs could provide additional gene expression regulation in P. ginseng cells by forming heterogeneous ribosomes.
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Affiliation(s)
- Galina N. Chelomina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
- Correspondence: ; Tel.: +7-(423)-231-0410
| | - Konstantin V. Rozhkovan
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
- Saint-Petersburg State University Clinic, St. Petersburg 190103, Russia
| | - Olga L. Burundukova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Tatiana Y. Gorpenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Yulia A. Khrolenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Yuri N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
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14
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Orgebin E, Lamoureux F, Isidor B, Charrier C, Ory B, Lézot F, Baud'huin M. Ribosomopathies: New Therapeutic Perspectives. Cells 2020; 9:E2080. [PMID: 32932838 DOI: 10.3390/cells9092080] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
Ribosomopathies are a group of rare diseases in which genetic mutations cause defects in either ribosome biogenesis or function, given specific phenotypes. Ribosomal proteins, and multiple other factors that are necessary for ribosome biogenesis (rRNA processing, assembly of subunits, export to cytoplasm), can be affected in ribosomopathies. Despite the need for ribosomes in all cell types, these diseases result mainly in tissue-specific impairments. Depending on the type of ribosomopathy and its pathogenicity, there are many potential therapeutic targets. The present manuscript will review our knowledge of ribosomopathies, discuss current treatments, and introduce the new therapeutic perspectives based on recent research. Diamond–Blackfan anemia, currently treated with blood transfusion prior to steroids, could be managed with a range of new compounds, acting mainly on anemia, such as L-leucine. Treacher Collins syndrome could be managed by various treatments, but it has recently been shown that proteasomal inhibition by MG132 or Bortezomib may improve cranial skeleton malformations. Developmental defects resulting from ribosomopathies could be also treated pharmacologically after birth. It might thus be possible to treat certain ribosomopathies without using multiple treatments such as surgery and transplants. Ribosomopathies remain an open field in the search for new therapeutic approaches based on our recent understanding of the role of ribosomes and progress in gene therapy for curing genetic disorders.
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Panoutsopoulos AA, De Crescenzo AH, Lee A, Lu AM, Ross AP, Borodinsky LN, Marcucio R, Trainor PA, Zarbalis KS. Pak1ip1 Loss-of-Function Leads to Cell Cycle Arrest, Loss of Neural Crest Cells, and Craniofacial Abnormalities. Front Cell Dev Biol 2020; 8:510063. [PMID: 32984348 PMCID: PMC7490522 DOI: 10.3389/fcell.2020.510063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
Neural crest cells (NCCs) comprise a transient progenitor cell population of neuroepithelial origin that contributes to a variety of cell types throughout vertebrate embryos including most mesenchymal cells of the cranial and facial structures. Consequently, abnormal NCC development underlies a variety of craniofacial defects including orofacial clefts, which constitute some of the most common birth defects. We previously reported the generation of manta ray (mray) mice that carry a loss-of-function allele of the gene encoding the preribosomal factor Pak1ip1. Here we describe cranioskeletal abnormalities in homozygous mray mutants that arise from a loss of NCCs after their specification. Our results show that the localized loss of cranial NCCs in the developing frontonasal prominences is caused by cell cycle arrest and cell death. In addition, and consistent with deficits in ribosome biosynthesis, homozygous mray mutants display decreased protein biosynthesis, further linking Pak1ip1 to a role in ribosome biogenesis.
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Affiliation(s)
- Alexios A Panoutsopoulos
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children - Northern California, Sacramento, CA, United States
| | - Angelo Harlan De Crescenzo
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children - Northern California, Sacramento, CA, United States
| | - Albert Lee
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children - Northern California, Sacramento, CA, United States
| | - Amelia MacKenzie Lu
- David B. Falk College of Sport and Human Dynamics - Department of Public Health, Syracuse University, Syracuse, NY, United States
| | - Adam P Ross
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children - Northern California, Sacramento, CA, United States
| | - Laura N Borodinsky
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children - Northern California, Sacramento, CA, United States.,Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Ralph Marcucio
- Department of Orthopedic Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, United States.,Department of Anatomy and Cell Biology, School of Medicine, The University of Kansas Medical Center, Kansas, KS, United States
| | - Konstantinos S Zarbalis
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children - Northern California, Sacramento, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States
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16
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Abstract
The nucleolus is a prominent, membraneless compartment found within the nucleus of eukaryotic cells. It forms around ribosomal RNA (rRNA) genes, where it coordinates the transcription, processing, and packaging of rRNA to produce ribosomal subunits. Recent efforts to characterize the biophysical properties of the nucleolus have transformed our understanding of the assembly and organization of this dynamic compartment. Indeed, soluble macromolecules condense from the nucleoplasm to form nucleoli through a process called liquid–liquid phase separation. Individual nucleolar components rapidly exchange with the nucleoplasm and separate within the nucleolus itself to form distinct subcompartments. In addition to its essential role in ribosome biogenesis, the nucleolus regulates many aspects of cell physiology, including genome organization, stress responses, senescence and lifespan. Consequently, the nucleolus is implicated in several human diseases, such as Hutchinson–Gilford progeria syndrome, Diamond–Blackfan anemia, and various forms of cancer. This Special Issue highlights new insights into the physical and molecular mechanisms that control the architecture and diverse functions of the nucleolus, and how they break down in disease.
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Ertekin E, Gencturk E, Kasim M, Ulgen KO. A Drug Repurposing and Protein-Protein Interaction Network Study of Ribosomopathies Using Yeast as a Model System. OMICS 2020; 24:96-109. [PMID: 31895625 DOI: 10.1089/omi.2019.0096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ribosomopathies result in various cancers, neurodegenerative and viral diseases, and other pathologies such as Diamond-Blackfan anemia and Shwachman-Diamond syndrome. Their pathophysiology at a proteome and functional level remains to be determined. Protein networks and highly connected hub proteins for ribosome biogenesis in Saccharomyces cerevisiae offer a potential as a model system to inform future therapeutic innovation in ribosomopathies. In this context, we report a ribosome biogenesis protein-protein interaction network in S. cerevisiae, created with 1772 proteins and 22,185 physical interactions connecting them. Moreover, by network decomposition analysis, we determined the linear pathways between the transcription factors and target proteins with a view to drug repurposing. While considering only the paths containing the three C/D box proteins (Nop56, Nop58, and Nop1), the most frequently encountered proteins were Aft1, Htz1, Ssa1, Ssb1, Ssb2, Gcn5, Cka1, Tef1, Nop1, Cdc28, Act1, Krr1, Rpl8B, and Tor1, which were then identified as potential drug targets. For drug repurposing, these candidate proteins were further searched in the DrugBank to find other diseases associated with them, as well as the drugs used to treat these diseases. To support the computational results, an experimental study was conducted using in-house manufactured microfluidic bioreactor platform, while the effect of the drug temsirolimus, Tor1 inhibitor, on yeast cells was investigated by following Nop56 protein expression. In conclusion, these results inform the ways in which ribosomopathies and associated common complex human diseases materialize and how drug repurposing might accelerate therapeutic innovation through bioinformatic studies of yeast.
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Affiliation(s)
- Ege Ertekin
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | - Elif Gencturk
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | - Muge Kasim
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | - Kutlu O Ulgen
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
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18
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Abstract
Subverting the conventional concept of “the” ribosome, a wealth of information gleaned from recent studies is revealing a much more diverse and dynamic ribosomal reality than has traditionally been thought possible. A diverse array of researchers is collectively illuminating a universe of heterogeneous and adaptable ribosomes harboring differences in composition and regulatory capacity: These differences enable specialization. The expanding universe of ribosomes not only comprises an incredible richness in ribosomal specialization between species, but also within the same tissues and even cells. In this review, we discuss ribosomal heterogeneity and speculate how the emerging understanding of the ribosomal repertoire is impacting the biological sciences today. Targeting pathogen-specific and pathological “diseased” ribosomes promises to provide new treatment options for patients, and potential applications for “designer ribosomes” are within reach. Our deepening understanding of and ability to manipulate the ribosome are establishing both the technological and theoretical foundations for major advances for the 21st century and beyond.
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Affiliation(s)
- Sergey O Sulima
- Biopharmaceutical New Technologies (BioNTech) Corporation, 55131 Mainz, Germany.
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA .
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19
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Abstract
Ribosomopathies are congenital diseases with defects in ribosome assembly and are characterized by elevated cancer risks. Additionally, somatic mutations in ribosomal proteins have recently been linked to a variety of cancers. Despite a clear correlation between ribosome defects and cancer, the molecular mechanisms by which these defects promote tumorigenesis are unclear. In this review, we focus on the emerging mechanisms that link ribosomal defects in ribosomopathies to cancer progression. This includes functional "onco-specialization" of mutant ribosomes, extra-ribosomal consequences of mutations in ribosomal proteins and ribosome assembly factors, and effects of ribosomal mutations on cellular stress and metabolism. We integrate some of these recent findings in a single model that can partially explain the paradoxical transition from hypo- to hyperproliferation phenotypes, as observed in ribosomopathies. Finally, we discuss the current and potential strategies, and the associated challenges for therapeutic intervention in ribosome-mutant diseases.
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Affiliation(s)
- Sergey O Sulima
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
| | - Kim R Kampen
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
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20
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Engidaye G, Melku M, Enawgaw B. Diamond Blackfan Anemia: Genetics, Pathogenesis, Diagnosis and Treatment. EJIFCC 2019; 30:67-81. [PMID: 30881276 PMCID: PMC6416817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Diamond Blackfan Anaemia (DBA) is a sporadic inherited anemia with broad spectrum of anomalies that are presented soon after delivery. It is inherited mainly in autosomal dominant inheritance manner and caused by mutations and deletions in either large or small ribosomal protein genes that results in an imbalance between the biosynthesis of rRNA and ribosomal proteins, eventually the activation and stabilization of p53. Diagnosing DBA is usually problematic due to a partial phenotype and its wide inconsistency in its clinical expression; however, molecular studies have identified a heterozygous mutated gene in up to 50% of the DBA cases and corticosteroid drugs are the backbone treatment options of DBA. Anomalies in bone marrow function in DBA cases are broadly associated with both congenital and acquired bone marrow failure syndromes in human. In this review different literatures were searched in Medline (eg. PubMed, PMC, Hinari, Google scholar), OMIM, EMBASE by using search engines (Google, Yahoo, Baidu Ask.com) and searching was performed by using search key words (DBA, ribosomopathies, Bone Marrow Failure Syndromes, pure red cell aplasia). Only human studies were included. This review is summarizing the current understandings of DBA.
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Affiliation(s)
- Getabalew Engidaye
- Amhara Regional State Debre Berhan Health Science College, Debre Berhan, Ethiopia, Department of Hematology & Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Ethiopia
| | - Mulugeta Melku
- Department of Hematology & Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Ethiopia
| | - Bamlaku Enawgaw
- Department of Hematology & Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Ethiopia,Corresponding author: Bamlaku Enawgaw Department of Hematology & Immunohematology School of Biomedical and Laboratory Sciences College of Medicine and Health Sciences University of Gondar Ethiopia E-mail:
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21
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Abstract
Multifaceted relations link ribosome biogenesis to cancer. Ribosome biogenesis takes place in the nucleolus. Clarifying the mechanisms involved in this nucleolar function and its relationship with cell proliferation: (1) allowed the understanding of the reasons for the nucleolar changes in cancer cells and their exploitation in tumor pathology, (2) defined the importance of the inhibition of ribosome biogenesis in cancer chemotherapy and (3) focused the attention on alterations of ribosome biogenesis in the pathogenesis of cancer. This review summarizes the research milestones regarding these relevant relationships between ribosome biogenesis and cancer. The structure and function of the nucleolus will also be briefly described.
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Affiliation(s)
- Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
| | - Davide Treré
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
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22
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Abstract
Ribosomes, which synthesize the proteins of a cell, comprise ribosomal RNA and ribosomal proteins, which coassemble hierarchically during a process termed ribosome biogenesis. Historically, biochemical and molecular biology approaches have revealed how preribosomal particles form and mature in consecutive steps, starting in the nucleolus and terminating after nuclear export into the cytoplasm. However, only recently, due to the revolution in cryo-electron microscopy, could pseudoatomic structures of different preribosomal particles be obtained. Together with in vitro maturation assays, these findings shed light on how nascent ribosomes progress stepwise along a dynamic biogenesis pathway. Preribosomes assemble gradually, chaperoned by a myriad of assembly factors and small nucleolar RNAs, before they reach maturity and enter translation. This information will lead to a better understanding of how ribosome synthesis is linked to other cellular pathways in humans and how it can cause diseases, including cancer, if disturbed.
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Affiliation(s)
- Jochen Baßler
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany; ,
| | - Ed Hurt
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany; ,
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23
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Abstract
Ribosomes have been long considered as executors of the translational program. The fact that ribosomes can control the translation of specific mRNAs or entire cellular programs is often neglected. Ribosomopathies, inherited diseases with mutations in ribosomal factors, show tissue specific defects and cancer predisposition. Studies of ribosomopathies have paved the way to the concept that ribosomes may control translation of specific mRNAs. Studies in Drosophila and mice support the existence of heterogeneous ribosomes that differentially translate mRNAs to coordinate cellular programs. Recent studies have now shown that ribosomal activity is not only a critical regulator of growth but also of metabolism. For instance, glycolysis and mitochondrial function have been found to be affected by ribosomal availability. Also, ATP levels drop in models of ribosomopathies. We discuss findings highlighting the relevance of ribosome heterogeneity in physiological and pathological conditions, as well as the possibility that in rate-limiting situations, ribosomes may favor some translational programs. We discuss the effects of ribosome heterogeneity on cellular metabolism, tumorigenesis and aging. We speculate a scenario in which ribosomes are not only executors of a metabolic program but act as modulators.
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Affiliation(s)
- Piera Calamita
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Milan, Italy.,Dipartimento di Bioscienze, Università Degli Studi Di Milano, Milan, Italy
| | - Guido Gatti
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Milan, Italy.,Dipartimento di Bioscienze, Università Degli Studi Di Milano, Milan, Italy
| | - Annarita Miluzio
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Alessandra Scagliola
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Milan, Italy.,Dipartimento di Bioscienze, Università Degli Studi Di Milano, Milan, Italy
| | - Stefano Biffo
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Milan, Italy.,Dipartimento di Bioscienze, Università Degli Studi Di Milano, Milan, Italy
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24
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Aubert M, O'Donohue MF, Lebaron S, Gleizes PE. Pre-Ribosomal RNA Processing in Human Cells: From Mechanisms to Congenital Diseases. Biomolecules 2018; 8:biom8040123. [PMID: 30356013 PMCID: PMC6315592 DOI: 10.3390/biom8040123] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomal RNAs, the most abundant cellular RNA species, have evolved as the structural scaffold and the catalytic center of protein synthesis in every living organism. In eukaryotes, they are produced from a long primary transcript through an intricate sequence of processing steps that include RNA cleavage and folding and nucleotide modification. The mechanisms underlying this process in human cells have long been investigated, but technological advances have accelerated their study in the past decade. In addition, the association of congenital diseases to defects in ribosome synthesis has highlighted the central place of ribosomal RNA maturation in cell physiology regulation and broadened the interest in these mechanisms. Here, we give an overview of the current knowledge of pre-ribosomal RNA processing in human cells in light of recent progress and discuss how dysfunction of this pathway may contribute to the physiopathology of congenital diseases.
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Affiliation(s)
- Maxime Aubert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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25
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Merkuri F, Fish JL. Developmental processes regulate craniofacial variation in disease and evolution. Genesis 2018; 57:e23249. [PMID: 30207415 DOI: 10.1002/dvg.23249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 12/30/2022]
Abstract
Variation in development mediates phenotypic differences observed in evolution and disease. Although the mechanisms underlying phenotypic variation are still largely unknown, recent research suggests that variation in developmental processes may play a key role. Developmental processes mediate genotype-phenotype relationships and consequently play an important role regulating phenotypes. In this review, we provide an example of how shared and interacting developmental processes may explain convergence of phenotypes in spliceosomopathies and ribosomopathies. These data also suggest a shared pathway to disease treatment. We then discuss three major mechanisms that contribute to variation in developmental processes: genetic background (gene-gene interactions), gene-environment interactions, and developmental stochasticity. Finally, we comment on evolutionary alterations to developmental processes, and the evolution of disease buffering mechanisms.
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Affiliation(s)
- Fjodor Merkuri
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
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26
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Núñez Villacís L, Wong MS, Ferguson LL, Hein N, George AJ, Hannan KM. New Roles for the Nucleolus in Health and Disease. Bioessays 2018; 40:e1700233. [PMID: 29603296 DOI: 10.1002/bies.201700233] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/02/2018] [Indexed: 12/31/2022]
Abstract
Over the last decade, our appreciation of the importance of the nucleolus for cellular function has progressed from the ordinary to the extraordinary. We no longer think of the nucleolus as simply the site of ribosome production, or a dynamic subnuclear body noted by pathologists for its changes in size and shape with malignancy. Instead, the nucleolus has emerged as a key controller of many cellular processes that are fundamental to normal cell homeostasis and the target for dysregulation in many human diseases; in some cases, independent of its functions in ribosome biogenesis. These extra-nucleolar or new functions, which we term "non-canonical" to distinguish them from the more traditional role of the nucleolus in ribosome synthesis, are the focus of this review. In particular, we explore how these non-canonical functions may provide novel insights into human disease and in some cases new targets for therapeutic development.
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Affiliation(s)
- Lorena Núñez Villacís
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, The Australian National University, Acton, 2601, Australia
| | - Mei S Wong
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, The Australian National University, Acton, 2601, Australia.,Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Center, Melbourne, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Australia
| | - Laura L Ferguson
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, The Australian National University, Acton, 2601, Australia
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, The Australian National University, Acton, 2601, Australia
| | - Amee J George
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, The Australian National University, Acton, 2601, Australia.,School of Biomedical Sciences, University of Queensland, St Lucia, 4067, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, 3010, Australia
| | - Katherine M Hannan
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, The Australian National University, Acton, 2601, Australia.,Department of Biochemistry, The University of Melbourne, Parkville, 3010, Australia
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27
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Affiliation(s)
- Sergey O Sulima
- Department of Oncology, KU Leuven, University of Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, University of Leuven, Leuven Cancer Institute, Leuven, Belgium
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28
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Abstract
Ribosomes are essential, highly complex machines responsible for protein synthesis in all growing cells. Because of their importance, the process of building these machines is intricately regulated. Although the proteins involved in regulating ribosome biogenesis are just beginning to be understood, especially in human cells, the consequences for dysregulating this process have been even less studied. Such interruptions in ribosome synthesis result in a collection of human disorders known as ribosomopathies. Ribosomopathies, which occur due to mutations in proteins involved in the global process of ribosome biogenesis, result in tissue-specific defects. The questions posed by this dichotomy and the steps taken to address these questions are therefore the focus of this review: How can tissue-specific disorders result from alterations in global processes? Could ribosome specialization account for this difference?
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29
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Olombrada M, Lázaro-Gorines R, López-Rodríguez JC, Martínez-Del-Pozo Á, Oñaderra M, Maestro-López M, Lacadena J, Gavilanes JG, García-Ortega L. Fungal Ribotoxins: A Review of Potential Biotechnological Applications. Toxins (Basel) 2017; 9:E71. [PMID: 28230789 DOI: 10.3390/toxins9020071] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 12/20/2022] Open
Abstract
Fungi establish a complex network of biological interactions with other organisms in nature. In many cases, these involve the production of toxins for survival or colonization purposes. Among these toxins, ribotoxins stand out as promising candidates for their use in biotechnological applications. They constitute a group of highly specific extracellular ribonucleases that target a universally conserved sequence of RNA in the ribosome, the sarcin-ricin loop. The detailed molecular study of this family of toxic proteins over the past decades has highlighted their potential in applied research. Remarkable examples would be the recent studies in the field of cancer research with promising results involving ribotoxin-based immunotoxins. On the other hand, some ribotoxin-producer fungi have already been studied in the control of insect pests. The recent role of ribotoxins as insecticides could allow their employment in formulas and even as baculovirus-based biopesticides. Moreover, considering the important role of their target in the ribosome, they can be used as tools to study how ribosome biogenesis is regulated and, eventually, may contribute to a better understanding of some ribosomopathies.
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30
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Abstract
A veritable explosion of primary research papers within the past 10 years focuses on nucleolar and ribosomal stress, and for good reason: with ribosome biosynthesis consuming ~80% of a cell’s energy, nearly all metabolic and signaling pathways lead ultimately to or from the nucleolus. We begin by describing p53 activation upon nucleolar stress resulting in cell cycle arrest or apoptosis. The significance of this mechanism cannot be understated, as oncologists are now inducing nucleolar stress strategically in cancer cells as a potential anti-cancer therapy. We also summarize the human ribosomopathies, syndromes in which ribosome biogenesis or function are impaired leading to birth defects or bone narrow failures; the perplexing problem in the ribosomopathies is why only certain cells are affected despite the fact that the causative mutation is systemic. We then describe p53-independent nucleolar stress, first in yeast which lacks p53, and then in other model metazoans that lack MDM2, the critical E3 ubiquitin ligase that normally inactivates p53. Do these presumably ancient p53-independent nucleolar stress pathways remain latent in human cells? If they still exist, can we use them to target >50% of known human cancers that lack functional p53?
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Affiliation(s)
- Allison James
- a Department of Biological Sciences; Louisiana State University; Baton Rouge, LA USA
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31
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Abstract
The p53 tumor suppressor gene is the most frequently mutated gene in cancer. Significant progress has been made to discern the importance of p53 in coordinating cellular responses to DNA damage, oncogene activation, and other stresses. Noncoding RNAs are RNA molecules functioning without being translated into proteins. In this work, we discuss the dichotomy of p53 regulation by noncoding RNAs with four unconventional questions. First, is overexpression of microRNAs responsible for p53 inactivation in the absence of p53 mutation? Second, are there somatic mutations in the noncoding regions of the p53 gene? Third, is there a germline mutant in the noncoding regions of the p53 gene that predisposes carriers to cancer? Fourth, can p53 activation mediated by a noncoding RNA mutation cause cancer? This work highlights the prominence of noncoding RNAs in p53 dysregulation and tumorigenesis.
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Affiliation(s)
- Qipan Deng
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, 319 Abraham Flexner Way, Louisville, KY 40202, USA
| | - Lindsey Becker
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, 319 Abraham Flexner Way, Louisville, KY 40202, USA
| | - Xiaodong Ma
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, 319 Abraham Flexner Way, Louisville, KY 40202, USA
| | - Xiaoming Zhong
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China
| | - Ken Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth Ramos
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, 319 Abraham Flexner Way, Louisville, KY 40202, USA
| | - Yong Li
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, 319 Abraham Flexner Way, Louisville, KY 40202, USA School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
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32
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Abstract
Neural crest cells (NCCs) are a transient, migratory cell population, which originates during neurulation at the neural folds and contributes to the majority of tissues, including the mesenchymal structures of the craniofacial skeleton. The deregulation of the complex developmental processes that guide migration, proliferation, and differentiation of NCCs may result in a wide range of pathological conditions grouped together as neurocristopathies. Recently, due to their multipotent properties neural crest stem cells have received considerable attention as a possible source for stem cell based regenerative therapies. This exciting prospect underlines the need to further explore the developmental programs that guide NCC differentiation. This review explores the particular importance of ribosome biogenesis defects in this context since a specific interface between ribosomopathies and neurocristopathies exists as evidenced by disorders such as Treacher-Collins-Franceschetti syndrome (TCS) and Diamond-Blackfan anemia (DBA).
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Affiliation(s)
- Adam P Ross
- Department of Pathology and Laboratory Medicine, Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, University of California at Davis Sacramento, CA, USA
| | - Konstantinos S Zarbalis
- Department of Pathology and Laboratory Medicine, Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, University of California at Davis Sacramento, CA, USA
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