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Flentke GR, Wilkie TE, Baulch J, Huang Y, Smith SM. Alcohol exposure suppresses ribosome biogenesis and causes nucleolar stress in cranial neural crest cells. PLoS One 2024; 19:e0304557. [PMID: 38941348 PMCID: PMC11213321 DOI: 10.1371/journal.pone.0304557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 05/14/2024] [Indexed: 06/30/2024] Open
Abstract
Prenatal alcohol exposure (PAE) causes cognitive impairment and a distinctive craniofacial dysmorphology, due in part to apoptotic losses of the pluripotent cranial neural crest cells (CNCs) that form facial bones and cartilage. We previously reported that PAE rapidly represses expression of >70 ribosomal proteins (padj = 10-E47). Ribosome dysbiogenesis causes nucleolar stress and activates p53-MDM2-mediated apoptosis. Using primary avian CNCs and the murine CNC line O9-1, we tested whether nucleolar stress and p53-MDM2 signaling mediates this apoptosis. We further tested whether haploinsufficiency in genes that govern ribosome biogenesis, using a blocking morpholino approach, synergizes with alcohol to worsen craniofacial outcomes in a zebrafish model. In both avian and murine CNCs, pharmacologically relevant alcohol exposure (20mM, 2hr) causes the dissolution of nucleolar structures and the loss of rRNA synthesis; this nucleolar stress persisted for 18-24hr. This was followed by reduced proliferation, stabilization of nuclear p53, and apoptosis that was prevented by overexpression of MDM2 or dominant-negative p53. In zebrafish embryos, low-dose alcohol or morpholinos directed against ribosomal proteins Rpl5a, Rpl11, and Rps3a, the Tcof homolog Nolc1, or mdm2 separately caused modest craniofacial malformations, whereas these blocking morpholinos synergized with low-dose alcohol to reduce and even eliminate facial elements. Similar results were obtained using a small molecule inhibitor of RNA Polymerase 1, CX5461, whereas p53-blocking morpholinos normalized craniofacial outcomes under high-dose alcohol. Transcriptome analysis affirmed that alcohol suppressed the expression of >150 genes essential for ribosome biogenesis. We conclude that alcohol causes the apoptosis of CNCs, at least in part, by suppressing ribosome biogenesis and invoking a nucleolar stress that initiates their p53-MDM2 mediated apoptosis. We further note that the facial deficits that typify PAE and some ribosomopathies share features including reduced philtrum, upper lip, and epicanthal distance, suggesting the facial deficits of PAE represent, in part, a ribosomopathy.
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Affiliation(s)
- George R. Flentke
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States of America
| | - Thomas E. Wilkie
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States of America
| | - Josh Baulch
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States of America
| | - Yanping Huang
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States of America
| | - Susan M. Smith
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States of America
- Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States of America
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Ghamari M, Mehrab Mohseni M, Taheri M, Neishabouri SM, Shirvani-Farsani Z. Abnormal expression of long non-coding RNAs RMRP, CTC-487M23.5, and DGCR5 in the peripheral blood of patients with Bipolar disorder. Metab Brain Dis 2024; 39:313-320. [PMID: 37962788 DOI: 10.1007/s11011-023-01316-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been recently considered as one of the regulatory mechanisms of the nervous system. Hence, lncRNAs may be considered diagnostic biomarkers for bipolar disorder (BD). We aimed to investigate the expression of RMRP, CTC-487M23.5, and DGCR5 lncRNAs in bipolar patients. The levels of these three lncRNAs were measured in peripheral blood mononuclear cells (PBMCs) of 50 BD patients and 50 healthy subjects by real-time PCR. Moreover, we performed a ROC curve analysis between the gene expression and some clinical features of BD patients. Significant upregulation of RMRP and CTC-487M23.5 and no significant change in levels of DGCR5 was observed in BD individuals compared with controls. Also, we found upregulation of RMRP and downregulation of CTC-487M23.5 and DGCR5 in females with BD. The areas under the ROC curve (AUC) for RMRP and CTC-487M23.5 lncRNAs were 0.80 and 0.61, respectively. There was no significant correlation between the expression of these three lncRNAs and clinical features in PBMCs of BD patients. These results suggest a role for RMRP and CTC-487M23.5 in the pathogenesis of bipolar disorder. Moreover, the peripheral expression of these two lncRNAs might be beneficial as potential biomarkers for BD.
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Affiliation(s)
- Melina Ghamari
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Technology, Shahid Beheshti University, Tehran, Iran
| | - Mahdieh Mehrab Mohseni
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Technology, Shahid Beheshti University, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | | | - Zeinab Shirvani-Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Technology, Shahid Beheshti University, Tehran, Iran.
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3
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Gao Y, Wang X, Luo H, Chen C, Li J, Sun R, Li D, Sun Z. Exosomal Long Non-Coding Ribonucleic Acid Ribonuclease Component of Mitochondrial Ribonucleic Acid Processing Endoribonuclease Is Defined as a Potential Non-Invasive Diagnostic Biomarker for Bladder Cancer and Facilitates Tumorigenesis via the miR-206/G6PD Axis. Cancers (Basel) 2023; 15:5305. [PMID: 37958478 PMCID: PMC10649581 DOI: 10.3390/cancers15215305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Bladder cancer (BLCA) is one of the cancers that is highly sensitive to specific non-invasive tumor biomarkers that facilitate early diagnosis. Exosome-derived long non-coding RNAs (lncRNAs) hold promise as diagnostic biomarkers for BLCA. In this study, we employed RNA-sequencing to compare the expression patterns of lncRNAs in urine exosomes from three BLCA patients and three healthy individuals. RMRP displayed the most significant differential expression. Elevated RMRP expression levels were observed in urinary and plasma exosomes from BLCA patients compared with those from healthy individuals. RMRP exhibited significant associations with certain BLCA patient clinicopathological features, including tumor stage, poor prognosis, and tumor grade. Combined diagnosis using RMRP in urine and plasma exosomes demonstrated a superior diagnostic performance with receiver operating characteristic curve analysis. RMRP was found to be related to BLCA tumor progression and the cell migration and invasion processes via the miR-206/G6PD axis both in vitro and in vivo. Mechanistically, RMRP serves as an miR-206 sponge, as suggested by dual-luciferase reporter assays and RNA immunoprecipitation. Our study suggests that the combined diagnosis of RMRP in urinary and plasma exosomes can serve as an excellent non-invasive diagnostic biomarker for BLCA patients. Additionally, targeting the RMRP/miR-206/G6PD axis holds promise as a therapeutic strategy for BLCA.
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Affiliation(s)
- Yuting Gao
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Xuan Wang
- Department of Pharmacy, Putuo People’s Hospital, School of Medicine, Tongji University, Shanghai 200060, China;
| | - Huarong Luo
- Department of Urology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China;
| | - Chen Chen
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Jing Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Ruixin Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Dong Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Zujun Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
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4
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Guo L, Salian S, Xue JY, Rath N, Rousseau J, Kim H, Ehresmann S, Moosa S, Nakagawa N, Kuroda H, Clayton-Smith J, Wang J, Wang Z, Banka S, Jackson A, Zhang YM, Wei ZJ, Hüning I, Brunet T, Ohashi H, Thomas MF, Bupp C, Miyake N, Matsumoto N, Mendoza-Londono R, Costain G, Hahn G, Di Donato N, Yigit G, Yamada T, Nishimura G, Ansel KM, Wollnik B, Hrabě de Angelis M, Mégarbané A, Rosenfeld JA, Heissmeyer V, Ikegawa S, Campeau PM. Null and missense mutations of ERI1 cause a recessive phenotypic dichotomy in humans. Am J Hum Genet 2023; 110:1068-1085. [PMID: 37352860 PMCID: PMC10357479 DOI: 10.1016/j.ajhg.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/25/2023] Open
Abstract
ERI1 is a 3'-to-5' exoribonuclease involved in RNA metabolic pathways including 5.8S rRNA processing and turnover of histone mRNAs. Its biological and medical significance remain unclear. Here, we uncover a phenotypic dichotomy associated with bi-allelic ERI1 variants by reporting eight affected individuals from seven unrelated families. A severe spondyloepimetaphyseal dysplasia (SEMD) was identified in five affected individuals with missense variants but not in those with bi-allelic null variants, who showed mild intellectual disability and digital anomalies. The ERI1 missense variants cause a loss of the exoribonuclease activity, leading to defective trimming of the 5.8S rRNA 3' end and a decreased degradation of replication-dependent histone mRNAs. Affected-individual-derived induced pluripotent stem cells (iPSCs) showed impaired in vitro chondrogenesis with downregulation of genes regulating skeletal patterning. Our study establishes an entity previously unreported in OMIM and provides a model showing a more severe effect of missense alleles than null alleles within recessive genotypes, suggesting a key role of ERI1-mediated RNA metabolism in human skeletal patterning and chondrogenesis.
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Affiliation(s)
- Long Guo
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China; National Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Center of Medical Genetics, Northwest Women's and Children's Hospital, the Affiliated Northwest Women's and Children's Hospital of Xi'an Jiaotong University Health Science Center, Xi'an 710003, China.
| | - Smrithi Salian
- Department of Pediatrics, CHU Sainte Justine Research Center, University of Montreal, 3175 Cote-Sainte-Catherine, Montreal, QC H3T 1C5, Canada
| | - Jing-Yi Xue
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China; Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Nicola Rath
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, German Research Center for Environmental Health, D-81377 Munich, Germany
| | - Justine Rousseau
- Department of Pediatrics, CHU Sainte Justine Research Center, University of Montreal, 3175 Cote-Sainte-Catherine, Montreal, QC H3T 1C5, Canada
| | - Hyunyun Kim
- Department of Pediatrics, CHU Sainte Justine Research Center, University of Montreal, 3175 Cote-Sainte-Catherine, Montreal, QC H3T 1C5, Canada
| | - Sophie Ehresmann
- Molecular Biology Program, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Tygerberg 7505, South Africa
| | - Norio Nakagawa
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; Department of Pediatrics, North Medical Center, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hiroshi Kuroda
- Department of Pediatrics, Kyoto City Hospital, Kyoto 604-8845, Japan
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, M13 9WL Manchester, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Juan Wang
- Department of Ultrasound, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Zheng Wang
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, M13 9WL Manchester, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, M13 9WL Manchester, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Yan-Min Zhang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an 710082, China
| | - Zhen-Jie Wei
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Irina Hüning
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany
| | - Theresa Brunet
- Institute of Human Genetics, School of Medicine, Technical University Munich, 80333 Munich, Germany; Department of Paediatric Neurology and Developmental Medicine, Hauner Children's Hospital, Ludwig Maximilian University of Munich, 80539 Munich, Germany
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Hospital, Saitama 330-8777, Japan
| | - Molly F Thomas
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Caleb Bupp
- Spectrum Health, Grand Rapids, MI 49503, USA
| | - Noriko Miyake
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Program in Genetics and Genome Biology, SickKids Research Institute, and Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Gregory Costain
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A4, Canada
| | - Gabriele Hahn
- Institute for Radiological Diagnostics, Universitätsklinikum Carl Gustav Carus Dresden, Technische Universität, 01307 Dresden, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, University Hospital, TU Dresden, 01069 Dresden, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, 37075 Göttingen, Germany; DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany
| | - Takahiro Yamada
- Department of Medical Ethics and Medical Genetics, Kyoto University School of Public Health, Kyoto 606-8501, Japan
| | - Gen Nishimura
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, 37075 Göttingen, Germany; DZHK (German Center for Cardiovascular Research), partner site Göttingen, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, 85354 Freising, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - André Mégarbané
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, 1102-2801, Lebanon and Institut Jerome Lejeune, 75015 Paris, France
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Vigo Heissmeyer
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, German Research Center for Environmental Health, D-81377 Munich, Germany; Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, 82152 Planegg-Martinsried, Germany
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte Justine Research Center, University of Montreal, 3175 Cote-Sainte-Catherine, Montreal, QC H3T 1C5, Canada.
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Kukkola HL, Utriainen P, Huttunen P, Taskinen M, Mäkitie O, Vakkilainen S. Lymphomas in cartilage-hair hypoplasia – A case series of 16 patients reveals advanced stage DLBCL as the most common form. Front Immunol 2022; 13:1004694. [PMID: 36211439 PMCID: PMC9541526 DOI: 10.3389/fimmu.2022.1004694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/12/2022] [Indexed: 12/02/2022] Open
Abstract
Background Patients with cartilage-hair hypoplasia (CHH) have an increased risk of malignancy, particularly non-Hodgkin lymphoma and basal cell carcinoma. The characteristics, clinical course, response to therapy and outcome of lymphomas in CHH remains unexplored. Methods We assessed clinical features of lymphoma cases among Finnish patients with CHH. Data were collected from the Finnish Cancer Registry, hospital records, the National Medical Databases and Cause-of-Death Registry of Statistics Finland. Results Among the 160 CHH patients, 16 (6 men, 10 women) were diagnosed with lymphoma during 1953-2016. Lymphoma was diagnosed in young adulthood (median age 26.4 years, range from 6.4 to 69.5 years), mostly in advanced stage. The most common lymphoma type was diffuse large cell B-cell lymphoma (DLBCL) (6/16, 38%). Eight patients received chemotherapy (8/16, 50%), and two of them survived. Standard lymphoma chemotherapy regimens were administered in the majority of cases. Altogether, eleven CHH patients died due to lymphomas (11/16, 69%). In almost all surviving lymphoma patients, the diagnosis was made either during routine follow-up or after evaluation for non-specific mild symptoms. Search for CHH-related clinical predictors demonstrated higher prevalence of recurrent respiratory infections, in particular otitis media, and Hirschsprung disease in patients with lymphoma. However, three patients had no clinical signs of immunodeficiency prior to lymphoma diagnosis. Conclusion DLBCL is the most common type of lymphoma in CHH. The outcome is poor probably due to advanced stage of lymphoma at the time of diagnosis. Other CHH-related manifestations poorly predicted lymphoma development, implying that all CHH patients should be regularly screened for malignancy.
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Affiliation(s)
- Hanna-Leena Kukkola
- Children and Adolescents, Pediatric Research Center, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pauliina Utriainen
- Children and Adolescents, Pediatric Research Center, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation (SCT), Children‘s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pasi Huttunen
- Children and Adolescents, Pediatric Research Center, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation (SCT), Children‘s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mervi Taskinen
- Children and Adolescents, Pediatric Research Center, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation (SCT), Children‘s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Outi Mäkitie
- Children and Adolescents, Pediatric Research Center, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Svetlana Vakkilainen
- Children and Adolescents, Pediatric Research Center, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- *Correspondence: Svetlana Vakkilainen,
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6
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Derksen M, Mertens V, Visser EA, Arts J, Vree Egberts W, Pruijn GJM. A novel experimental approach for the selective isolation and characterization of human RNase MRP. RNA Biol 2022; 19:305-312. [PMID: 35129080 PMCID: PMC8820802 DOI: 10.1080/15476286.2022.2027659] [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] [Indexed: 12/01/2022] Open
Abstract
RNase MRP is a ribonucleoprotein complex involved in the endoribonucleolytic cleavage of different RNAs. Mutations in the RNA component of the RNP are the cause of cartilage hair hypoplasia. Patients with cartilage hair hypoplasia are characterized by skeletal dysplasia. Biochemical purification of RNase MRP is desired to be able to study its biochemical function, composition and activity in both healthy and disease situations. Due to the high similarity with RNase P, a method to specifically isolate the RNase MRP complex is currently lacking. By fusing a streptavidin-binding RNA aptamer, the S1m-aptamer, to the RNase MRP RNA we have been able to compare the relative expression levels of wildtype and mutant MRP RNAs. Moreover, we were able to isolate active RNase MRP complexes. We observed that mutant MRP RNAs are expressed at lower levels and have lower catalytic activity compared to the wildtype RNA. The observation that a single nucleotide substitution at position 40 in the P3 domain but not in other domains of RNase MRP RNA severely reduced the binding of the Rpp25 protein subunit confirmed that the P3 region harbours the main binding site for this protein. Altogether, this study shows that the RNA aptamer tagging approach can be used to identify RNase MRP substrates, but also to study the effect of mutations on MRP RNA expression levels and RNase MRP composition and endoribonuclease activity.
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Affiliation(s)
- Merel Derksen
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Vicky Mertens
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Eline A. Visser
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Janine Arts
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Wilma Vree Egberts
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Ger J. M. Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
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7
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Chabronova A, van den Akker GGH, Meekels-Steinbusch MMF, Friedrich F, Cremers A, Surtel DAM, Peffers MJ, van Rhijn LW, Lausch E, Zabel B, Caron MMJ, Welting TJM. Uncovering pathways regulating chondrogenic differentiation of CHH fibroblasts. Noncoding RNA Res 2022; 6:211-224. [PMID: 34988338 PMCID: PMC8688813 DOI: 10.1016/j.ncrna.2021.12.003] [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] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 02/08/2023] Open
Abstract
Mutations in the non-coding snoRNA component of mitochondrial RNA processing endoribonuclease (RMRP) are the cause of cartilage-hair hypoplasia (CHH). CHH is a rare form of metaphyseal chondrodysplasia characterized by disproportionate short stature and abnormal growth plate development. The process of chondrogenic differentiation within growth plates of long bones is vital for longitudinal bone growth. However, molecular mechanisms behind impaired skeletal development in CHH patients remain unclear. We employed a transdifferentiation model (FDC) combined with whole transcriptome analysis to investigate the chondrogenic transdifferentiation capacity of CHH fibroblasts and to examine pathway regulation in CHH cells during chondrogenic differentiation. We established that the FDC transdifferentiation model is a relevant in vitro model of chondrogenic differentiation, with an emphasis on the terminal differentiation phase, which is crucial for longitudinal bone growth. We demonstrated that CHH fibroblasts are capable of transdifferentiating into chondrocyte-like cells, and show a reduced commitment to terminal differentiation. We also found a number of key factors of BMP, FGF, and IGF-1 signalling axes to be significantly upregulated in CHH cells during the chondrogenic transdifferentiation. Our results support postulated conclusions that RMRP has pleiotropic functions and profoundly affects multiple aspects of cell fate and signalling. Our findings shed light on the consequences of pathological CHH mutations in snoRNA RMRP during chondrogenic differentiation and the relevance and roles of non-coding RNAs in genetic diseases in general.
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Affiliation(s)
- Alzbeta Chabronova
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Guus G H van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Mandy M F Meekels-Steinbusch
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Franziska Friedrich
- Department of Pediatrics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andy Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Don A M Surtel
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Mandy J Peffers
- Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Lodewijk W van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Ekkehart Lausch
- Department of Pediatrics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernhard Zabel
- Medical Faculty, Otto van Guericke University of Magdeburg, 39106, Magdeburg, Germany
| | - Marjolein M J Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Tim J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
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8
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Huang Y, Xie B, Cao M, Lu H, Wu X, Hao Q, Zhou X. LncRNA RNA Component of Mitochondrial RNA-Processing Endoribonuclease Promotes AKT-Dependent Breast Cancer Growth and Migration by Trapping MicroRNA-206. Front Cell Dev Biol 2021; 9:730538. [PMID: 34621748 PMCID: PMC8490808 DOI: 10.3389/fcell.2021.730538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/30/2021] [Indexed: 12/30/2022] Open
Abstract
The RNA component of mitochondrial RNA-processing endoribonuclease (RMRP) was recently shown to play a role in cancer development. However, the function and mechanism of RMRP during cancer progression remain incompletely understood. Here, we report that RMRP is amplified and highly expressed in various malignant cancers, and the high level of RMRP is significantly associated with their poor prognosis, including breast cancer. Consistent with this, ectopic RMRP promotes proliferation and migration of TP53-mutated breast cancer cells, whereas depletion of RMRP leads to inhibition of their proliferation and migration. RNA-seq analysis reveals AKT as a downstream target of RMRP. Interestingly, RMRP indirectly elevates AKT expression by preventing AKT mRNA from miR-206-mediated targeting via a competitive sequestering mechanism. Remarkably, RMRP endorses breast cancer progression in an AKT-dependent fashion, as knockdown of AKT completely abolishes RMRP-induced cancer cell growth and migration. Altogether, our results unveil a novel role of the RMRP-miR-206-AKT axis in breast cancer development, providing a potential new target for developing an anti-breast cancer therapy.
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Affiliation(s)
- Yingdan Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bangxiang Xie
- Beijing Institute of Hepatology, Beijing You An Hospital, Capital Medical University, Beijing, China.,Beijing Engineering Research Center for Precision Medicine and Transformation of Hepatitis and Liver Cancer, Beijing, China
| | - Mingming Cao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hua Lu
- Department of Biochemistry & Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Xiaohua Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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9
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Abstract
The tumor suppressor p53 prevents tumorigenesis, while inactivation of p53 promotes cancer development and drug resistance. Here, we identify that a long noncoding RNA, the RNA component of mitochondrial RNA-processing endoribonuclease (RMRP), promotes growth and proliferation of colorectal cancer cells by inhibiting p53 activity. Mechanistically, RMRP retains SNRPA1 in the nucleus, thus preventing its lysosomal degradation. The nuclear SNRPA1 then prompts MDM2-mediated p53 ubiquitination and degradation. Remarkably, RMRP expression is induced by poly (ADP-ribose) polymerase (PARP) inhibitors, a group of targeted anticancer drugs, through the transcription factor C/EBPβ. Targeting RMRP significantly enhances sensitivity of colorectal cancer cells to PARP inhibition by reactivating p53. Our study provides a possible mechanism underling tumor resistance to PARP inhibitors. p53 inactivation is highly associated with tumorigenesis and drug resistance. Here, we identify a long noncoding RNA, the RNA component of mitochondrial RNA-processing endoribonuclease (RMRP), as an inhibitor of p53. RMRP is overexpressed and associated with an unfavorable prognosis in colorectal cancer. Ectopic RMRP suppresses p53 activity by promoting MDM2-induced p53 ubiquitination and degradation, while depletion of RMRP activates the p53 pathway. RMRP also promotes colorectal cancer growth and proliferation in a p53-dependent fashion in vitro and in vivo. This anti-p53 action of RMRP is executed through an identified partner protein, SNRPA1. RMRP can interact with SNRPA1 and sequester it in the nucleus, consequently blocking its lysosomal proteolysis via chaperone-mediated autophagy. The nuclear SNRPA1 then interacts with p53 and enhances MDM2-induced proteasomal degradation of p53. Remarkably, ablation of SNRPA1 completely abrogates RMRP regulation of p53 and tumor cell growth, indicating that SNRPA1 is indispensable for the anti-p53 function of RMRP. Interestingly and significantly, poly (ADP-ribose) polymerase (PARP) inhibitors induce RMRP expression through the transcription factor C/EBPβ, and RMRP confers tumor resistance to PARP inhibition by preventing p53 activation. Altogether, our study demonstrates that RMRP plays an oncogenic role by inactivating p53 via SNRPA1 in colorectal cancer.
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10
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Szmyd B, Mlynarski W, Pastorczak A. Genetic predisposition to lymphomas: Overview of rare syndromes and inherited familial variants. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108386. [PMID: 34893151 DOI: 10.1016/j.mrrev.2021.108386] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 05/14/2021] [Accepted: 06/03/2021] [Indexed: 01/19/2023]
Abstract
Approximately 10 % of malignancies occur in carriers of germline mutations predisposing to cancer. A high risk of developing lymphomas has been noted in many primary immunodeficiencies, including DNA repair disorders. Moreover, implementation of next-generation sequencing has recently enabled to uncover rare genetic variants predisposing patients to lymphoid neoplasms. Some patients harboring inherited predisposition to lymphomas require dedicated clinical management, which will contribute to effective cancer treatment and to the prevention of potential severe toxicities and secondary malignancies. In line with that, our review summarizes the natural history of lymphoid tumors developing on different germline genetic backgrounds and discusses the progress that has been made toward successfully treating these malignancies.
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Affiliation(s)
- Bartosz Szmyd
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland.
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland.
| | - Agata Pastorczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland.
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11
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Hussen BM, Azimi T, Hidayat HJ, Taheri M, Ghafouri-Fard S. Long Non-coding RNA RMRP in the Pathogenesis of Human Disorders. Front Cell Dev Biol 2021; 9:676588. [PMID: 33996836 PMCID: PMC8120005 DOI: 10.3389/fcell.2021.676588] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/12/2021] [Indexed: 12/17/2022] Open
Abstract
RNA component of mitochondrial RNA processing endoribonuclease (RMRP) is a non-coding transcript firstly acknowledged for its association with the cartilage-hair hypoplasia (CHH) syndrome, a rare autosomal recessive condition. This transcript has been spotted in both nucleus and mitochondria. In addition to its role in the pathogenesis of CHH, RMRP participates in the pathogenesis of cancers. Independent studies in bladder cancer, colon cancer, hepatocellular carcinoma, lung cancer, breast carcinoma and multiple myeloma have confirmed the oncogenic effects of RMRP. Mechanistically, RMRP serves as a sponge for some miRNAs such as miR-206, miR-613, and miR-217. In addition to these miRNAs, expressions of tens of miRNAs have been altered following RMRP silencing, implying the vast extent of RMRP/miRNA network. In the present narrative review, we explain the role of RMRP in the development of cancers and some other non-malignant disorders.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Tahereh Azimi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahadddin University-Erbil, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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12
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Kaliatsi EG, Giarimoglou N, Stathopoulos C, Stamatopoulou V. Non-Coding RNA-Driven Regulation of rRNA Biogenesis. Int J Mol Sci 2020; 21:E9738. [PMID: 33419375 PMCID: PMC7766524 DOI: 10.3390/ijms21249738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/30/2022] Open
Abstract
Ribosomal RNA (rRNA) biogenesis takes place in the nucleolus, the most prominent condensate of the eukaryotic nucleus. The proper assembly and integrity of the nucleolus reflects the accurate synthesis and processing of rRNAs which in turn, as major components of ribosomes, ensure the uninterrupted flow of the genetic information during translation. Therefore, the abundant production of rRNAs in a precisely functional nucleolus is of outmost importance for the cell viability and requires the concerted action of essential enzymes, associated factors and epigenetic marks. The coordination and regulation of such an elaborate process depends on not only protein factors, but also on numerous regulatory non-coding RNAs (ncRNAs). Herein, we focus on RNA-mediated mechanisms that control the synthesis, processing and modification of rRNAs in mammals. We highlight the significance of regulatory ncRNAs in rRNA biogenesis and the maintenance of the nucleolar morphology, as well as their role in human diseases and as novel druggable molecular targets.
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Affiliation(s)
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| | - Vassiliki Stamatopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
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13
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Abstract
In this review, Yeganeh et al. summarize different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms. RNA polymerase (Pol) III is responsible for transcription of different noncoding genes in eukaryotic cells, whose RNA products have well-defined functions in translation and other biological processes for some, and functions that remain to be defined for others. For all of them, however, new functions are being described. For example, Pol III products have been reported to regulate certain proteins such as protein kinase R (PKR) by direct association, to constitute the source of very short RNAs with regulatory roles in gene expression, or to control microRNA levels by sequestration. Consistent with these many functions, deregulation of Pol III transcribed genes is associated with a large variety of human disorders. Here we review different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms.
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Affiliation(s)
- Meghdad Yeganeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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14
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Hayward RJ, Marsh JW, Humphrys MS, Huston WM, Myers GSA. Chromatin accessibility dynamics of Chlamydia-infected epithelial cells. Epigenetics Chromatin 2020; 13:45. [PMID: 33109274 PMCID: PMC7590614 DOI: 10.1186/s13072-020-00368-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/15/2020] [Indexed: 01/08/2023] Open
Abstract
Chlamydia are Gram-negative, obligate intracellular bacterial pathogens responsible for a broad spectrum of human and animal diseases. In humans, Chlamydia trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and is the causative agent of trachoma (infectious blindness) in disadvantaged populations. Over the course of its developmental cycle, Chlamydia extensively remodels its intracellular niche and parasitises the host cell for nutrients, with substantial resulting changes to the host cell transcriptome and proteome. However, little information is available on the impact of chlamydial infection on the host cell epigenome and global gene regulation. Regions of open eukaryotic chromatin correspond to nucleosome-depleted regions, which in turn are associated with regulatory functions and transcription factor binding. We applied formaldehyde-assisted isolation of regulatory elements enrichment followed by sequencing (FAIRE-Seq) to generate temporal chromatin maps of C. trachomatis-infected human epithelial cells in vitro over the chlamydial developmental cycle. We detected both conserved and distinct temporal changes to genome-wide chromatin accessibility associated with C. trachomatis infection. The observed differentially accessible chromatin regions include temporally-enriched sets of transcription factors, which may help shape the host cell response to infection. These regions and motifs were linked to genomic features and genes associated with immune responses, re-direction of host cell nutrients, intracellular signalling, cell-cell adhesion, extracellular matrix, metabolism and apoptosis. This work provides another perspective to the complex response to chlamydial infection, and will inform further studies of transcriptional regulation and the epigenome in Chlamydia-infected human cells and tissues.
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Affiliation(s)
- Regan J Hayward
- The ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - James W Marsh
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wilhelmina M Huston
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Garry S A Myers
- The ithree Institute, University of Technology Sydney, Sydney, NSW, Australia. .,School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.
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15
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Venturi G, Montanaro L. How Altered Ribosome Production Can Cause or Contribute to Human Disease: The Spectrum of Ribosomopathies. Cells 2020; 9:E2300. [PMID: 33076379 PMCID: PMC7602531 DOI: 10.3390/cells9102300] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
A number of different defects in the process of ribosome production can lead to a diversified spectrum of disorders that are collectively identified as ribosomopathies. The specific factors involved may either play a role only in ribosome biogenesis or have additional extra-ribosomal functions, making it difficult to ascribe the pathogenesis of the disease specifically to an altered ribosome biogenesis, even if the latter is clearly affected. We reviewed the available literature in the field from this point of view with the aim of distinguishing, among ribosomopathies, the ones due to specific alterations in the process of ribosome production from those characterized by a multifactorial pathogenesis.
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Affiliation(s)
- Giulia Venturi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy
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16
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Vakkilainen S, Taskinen M, Mäkitie O. Immunodeficiency in cartilage-hair hypoplasia: Pathogenesis, clinical course and management. Scand J Immunol 2020; 92:e12913. [PMID: 32506568 DOI: 10.1111/sji.12913] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022]
Abstract
Cartilage-hair hypoplasia (CHH) is an autosomal recessive syndromic immunodeficiency with skeletal dysplasia, short stature, hypotrichosis, variable degree of immune dysfunction and increased incidence of anaemia, Hirschsprung disease and malignancy. CHH is caused by variants in the RMRP gene, encoding the untranslated RNA molecule of the mitochondrial RNA-processing endoribonuclease, which participates in for example cell cycle regulation and telomere maintenance. Recent studies have expanded our understanding of the complex pathogenesis of CHH. Immune dysfunction has a major impact on clinical course and prognosis. Clinical features of immune dysfunction are highly variable, progressive and include infections, lung disease, immune dysregulation and malignancy. Mortality is increased compared with the general population, due to infections, malignancy and pulmonary disease. Several risk factors for early mortality have been reported in the Finnish CHH cohort and can be used to guide management. Newborn screening for severe combined immunodeficiency can possibly be of prognostic value in CHH. Regular follow-up by a multidisciplinary team should be implemented to address immune dysfunction in all patients with CHH, also in asymptomatic cases. Haematopoietic stem cell transplantation can cure immune dysfunction, but its benefits in mildly symptomatic patients with CHH remain debatable. Further research is needed to understand the mechanisms behind the variability of clinical features, to search for potential molecular treatment targets, to examine and validate risk factors for early mortality outside the Finnish CHH cohort and to develop management guidelines. This review focuses on the pathogenesis, clinical course and management of CHH.
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Affiliation(s)
- Svetlana Vakkilainen
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mervi Taskinen
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Outi Mäkitie
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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17
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Ojha S, Malla S, Lyons SM. snoRNPs: Functions in Ribosome Biogenesis. Biomolecules 2020; 10:biom10050783. [PMID: 32443616 PMCID: PMC7277114 DOI: 10.3390/biom10050783] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023] Open
Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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18
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Kampen KR, Sulima SO, Vereecke S, De Keersmaecker K. Hallmarks of ribosomopathies. Nucleic Acids Res 2020; 48:1013-1028. [PMID: 31350888 PMCID: PMC7026650 DOI: 10.1093/nar/gkz637] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Ribosomopathies are diseases caused by defects in ribosomal constituents or in factors with a role in ribosome assembly. Intriguingly, congenital ribosomopathies display a paradoxical transition from early symptoms due to cellular hypo-proliferation to an elevated cancer risk later in life. Another association between ribosome defects and cancer came into view after the recent discovery of somatic mutations in ribosomal proteins and rDNA copy number changes in a variety of tumor types, giving rise to somatic ribosomopathies. Despite these clear connections between ribosome defects and cancer, the molecular mechanisms by which defects in this essential cellular machinery are oncogenic only start to emerge. In this review, the impact of ribosomal defects on the cellular function and their mechanisms of promoting oncogenesis are described. In particular, we discuss the emerging hallmarks of ribosomopathies such as the appearance of ‘onco-ribosomes’ that are specialized in translating oncoproteins, dysregulation of translation-independent extra-ribosomal functions of ribosomal proteins, rewired cellular protein and energy metabolism, and extensive oxidative stress leading to DNA damage. We end by integrating these findings in a model that can provide an explanation how ribosomopathies could lead to the transition from hypo- to hyper-proliferation in bone marrow failure syndromes with elevated cancer risk.
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Affiliation(s)
- Kim R Kampen
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Sergey O Sulima
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Stijn Vereecke
- 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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19
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Abnormal Newborn Screening Follow-up for Severe Combined Immunodeficiency in an Amish Cohort with Cartilage-Hair Hypoplasia. J Clin Immunol 2020; 40:321-328. [PMID: 31903518 DOI: 10.1007/s10875-019-00739-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Abstract
Cartilage-hair hypoplasia (CHH) is an autosomal recessive, short limb skeletal dysplasia with a variable immunologic phenotype. The spectrum of immune function ranges from clinically normal to severe combined immunodeficiency (SCID). Multiple studies have shown that abnormal immune parameters may not predict severe outcomes. Newborn screening (NBS) using T cell receptor excision circle (TREC) assay can now effectively identify infants with severe T cell deficiency who are at risk for SCID. NBS has allowed for cost-effective identification of patients with SCID and improved outcomes with hematopoietic stem cell transplant (HSCT). Ohio reports two abnormal TREC results: decreased and absent TREC. This study evaluated the laboratory and clinical differences in eight Amish patients with CHH with an abnormal TREC result on the NBS. There were four patients with absent TREC and four patients with decreased TREC. The absent TREC patients had lower CD3, CD4, naïve CD4, CD8 cells, and phytohemagglutinin (PHA)-induced lymphocyte proliferation. Three patients with absent TREC were diagnosed with SCID and two underwent successful HSCT. Patients with absent TREC experienced more CHH-related morbidity including anemia requiring transfusion, Hirschsprung's disease, and failure to thrive. No patients with decreased TREC required HSCT. Our study indicates that CHH patients with absent TREC tend to have more severe immunological and clinical phenotype than patients with decreased TREC. Confirmation of these trends in a larger group would guide providers and parents in a timely referral for HSCT, or cost-effective surveillance monitoring of children with a life-threatening illness.
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20
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付 洪. Multifunction of LncRNA RMRP RNA. Biophysics (Nagoya-shi) 2020. [DOI: 10.12677/biphy.2020.82002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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21
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Sun X, Zhang R, Liu M, Chen H, Chen L, Luo F, Zhang D, Huang J, Li F, Ni Z, Qi H, Su N, Jin M, Yang J, Tan Q, Du X, Chen B, Huang H, Chen S, Yin L, Xu X, Deng C, Luo L, Xie Y, Chen L. Rmrp Mutation Disrupts Chondrogenesis and Bone Ossification in Zebrafish Model of Cartilage-Hair Hypoplasia via Enhanced Wnt/β-Catenin Signaling. J Bone Miner Res 2019; 34:2101-2116. [PMID: 31237961 DOI: 10.1002/jbmr.3820] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 01/09/2023]
Abstract
Cartilage-hair hypoplasia (CHH) is an autosomal recessive metaphyseal chondrodysplasia characterized by bone dysplasia and many other highly variable features. The gene responsible for CHH is the RNA component of the mitochondrial RNA-processing endoribonuclease (RMRP) gene. Currently, the pathogenesis of osteochondrodysplasia and extraskeletal manifestations in CHH patients remains incompletely understood; in addition, there are no viable animal models for CHH. We generated an rmrp KO zebrafish model to study the developmental mechanisms of CHH. We found that rmrp is required for the patterning and shaping of pharyngeal arches. Rmrp mutation inhibits the intramembranous ossification of skull bones and promotes vertebrae ossification. The abnormalities of endochondral bone ossification are variable, depending on the degree of dysregulated chondrogenesis. Moreover, rmrp mutation inhibits cell proliferation and promotes apoptosis through dysregulating the expressions of cell-cycle- and apoptosis-related genes. We also demonstrate that rmrp mutation upregulates canonical Wnt/β-catenin signaling; the pharmacological inhibition of Wnt/β-catenin could partially alleviate the chondrodysplasia and increased vertebrae mineralization in rmrp mutants. Our study, by establishing a novel zebrafish model for CHH, partially reveals the underlying mechanism of CHH, hence deepening our understanding of the role of rmrp in skeleton development.
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Affiliation(s)
- Xianding Sun
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ruobin Zhang
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Mi Liu
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Hangang Chen
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liang Chen
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Fengtao Luo
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Dali Zhang
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Junlan Huang
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Fangfang Li
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Zhenhong Ni
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Huabing Qi
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Nan Su
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Min Jin
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jing Yang
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Qiaoyan Tan
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Xiaolan Du
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Bo Chen
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Haiyang Huang
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Shuai Chen
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liangjun Yin
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Xiaoling Xu
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chuxia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Lingfei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Yangli Xie
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Lin Chen
- Laboratory of Wound Repair and Rehabilitation, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
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22
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Vakkilainen S, Skoog T, Einarsdottir E, Middleton A, Pekkinen M, Öhman T, Katayama S, Krjutškov K, Kovanen PE, Varjosalo M, Lindqvist A, Kere J, Mäkitie O. The human long non-coding RNA gene RMRP has pleiotropic effects and regulates cell-cycle progression at G2. Sci Rep 2019; 9:13758. [PMID: 31551465 PMCID: PMC6760211 DOI: 10.1038/s41598-019-50334-6] [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: 09/05/2018] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
RMRP was the first non-coding nuclear RNA gene implicated in a disease. Its mutations cause cartilage-hair hypoplasia (CHH), an autosomal recessive skeletal dysplasia with growth failure, immunodeficiency, and a high risk for malignancies. This study aimed to gain further insight into the role of RNA Component of Mitochondrial RNA Processing Endoribonuclease (RMRP) in cellular physiology and disease pathogenesis. We combined transcriptome analysis with single-cell analysis using fibroblasts from CHH patients and healthy controls. To directly assess cell cycle progression, we followed CHH fibroblasts by pulse-labeling and time-lapse microscopy. Transcriptome analysis identified 35 significantly upregulated and 130 downregulated genes in CHH fibroblasts. The downregulated genes were significantly connected to the cell cycle. Multiple other pathways, involving regulation of apoptosis, bone and cartilage formation, and lymphocyte function, were also affected, as well as PI3K-Akt signaling. Cell-cycle studies indicated that the CHH cells were delayed specifically in the passage from G2 phase to mitosis. Our findings expand the mechanistic understanding of CHH, indicate possible pathways for therapeutic intervention and add to the limited understanding of the functions of RMRP.
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Affiliation(s)
- Svetlana Vakkilainen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland. .,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.
| | - Tiina Skoog
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Anna Middleton
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Minna Pekkinen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland
| | - Tiina Öhman
- Institute of Biotechnology, and Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Competence Centre on Health Technologies, Tartu, Estonia
| | - Panu E Kovanen
- Department of Pathology, University of Helsinki, and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, and Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Medical and Molecular Genetics, King's College, London, UK
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Molecular Medicine and Surgery, Karolinska Institutet and Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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23
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Son HJ, Choi EJ, Yoo NJ, Lee SH. Somatic mutations in long-non-coding RNA RMRP in acute leukemias. Pathol Res Pract 2019; 215:152647. [PMID: 31564567 DOI: 10.1016/j.prp.2019.152647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/15/2019] [Indexed: 11/16/2022]
Affiliation(s)
- Hyun Ji Son
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Eun Ji Choi
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Nam Jin Yoo
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sug Hyung Lee
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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24
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Razmara E, Bitaraf A, Yousefi H, Nguyen TH, Garshasbi M, Cho WCS, Babashah S. Non-Coding RNAs in Cartilage Development: An Updated Review. Int J Mol Sci 2019; 20:E4475. [PMID: 31514268 PMCID: PMC6769748 DOI: 10.3390/ijms20184475] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023] Open
Abstract
In the development of the skeleton, the long bones are arising from the process of endochondral ossification (EO) in which cartilage is replaced by bone. This complex process is regulated by various factors including genetic, epigenetic, and environmental elements. It is recognized that DNA methylation, higher-order chromatin structure, and post-translational modifications of histones regulate the EO. With emerging understanding, non-coding RNAs (ncRNAs) have been identified as another mode of EO regulation, which is consist of microRNAs (miRNAs or miRs) and long non-coding RNAs (lncRNAs). There is expanding experimental evidence to unlock the role of ncRNAs in the differentiation of cartilage cells, as well as the pathogenesis of several skeletal disorders including osteoarthritis. Cutting-edge technologies such as epigenome-wide association studies have been employed to reveal disease-specific patterns regarding ncRNAs. This opens a new avenue of our understanding of skeletal cell biology, and may also identify potential epigenetic-based biomarkers. In this review, we provide an updated overview of recent advances in the role of ncRNAs especially focus on miRNA and lncRNA in the development of bone from cartilage, as well as their roles in skeletal pathophysiology.
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Affiliation(s)
- Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran
| | - Amirreza Bitaraf
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran
| | - Hassan Yousefi
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA 70112, USA
| | - Tina H Nguyen
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA 70112, USA
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran
| | | | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran.
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25
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Tahmasebi S, Khoutorsky A, Mathews MB, Sonenberg N. Translation deregulation in human disease. Nat Rev Mol Cell Biol 2019; 19:791-807. [PMID: 30038383 DOI: 10.1038/s41580-018-0034-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Advances in sequencing and high-throughput techniques have provided an unprecedented opportunity to interrogate human diseases on a genome-wide scale. The list of disease-causing mutations is expanding rapidly, and mutations affecting mRNA translation are no exception. Translation (protein synthesis) is one of the most complex processes in the cell. The orchestrated action of ribosomes, tRNAs and numerous translation factors decodes the information contained in mRNA into a polypeptide chain. The intricate nature of this process renders it susceptible to deregulation at multiple levels. In this Review, we summarize current evidence of translation deregulation in human diseases other than cancer. We discuss translation-related diseases on the basis of the molecular aberration that underpins their pathogenesis (including tRNA dysfunction, ribosomopathies, deregulation of the integrated stress response and deregulation of the mTOR pathway) and describe how deregulation of translation generates the phenotypic variability observed in these disorders.
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Affiliation(s)
- Soroush Tahmasebi
- Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada. .,Department of Biochemistry, McGill University, Montreal, Quebec, Canada. .,Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA.
| | - Arkady Khoutorsky
- Department of Anesthesia and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Nahum Sonenberg
- Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada. .,Department of Biochemistry, McGill University, Montreal, Quebec, Canada.
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26
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Promoter Mutation Analysis of Long-Non-coding RNA RMRP Gene in Solid Tumors. Pathol Oncol Res 2019; 26:2809-2810. [PMID: 31422524 DOI: 10.1007/s12253-019-00723-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022]
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27
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Vakkilainen S, Costantini A, Taskinen M, Wartiovaara-Kautto U, Mäkitie O. 'Metaphyseal dysplasia without hypotrichosis' can present with late-onset extraskeletal manifestations. J Med Genet 2019; 57:18-22. [PMID: 31413121 PMCID: PMC6929920 DOI: 10.1136/jmedgenet-2019-106131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/14/2019] [Accepted: 06/22/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND Metaphyseal dysplasia without hypotrichosis (MDWH) is a rare form of chondrodysplasia with no extraskeletal manifestations. MDWH is caused by RMRP mutations, but it is differentiated from the allelic condition cartilage-hair hypoplasia (CHH), which in addition to chondrodysplasia is characterised by thin hair, immunodeficiency and increased risk of malignancy. The long-term outcome of MDWH remains unknown. OBJECTIVE We diagnosed severe agranulocytosis in a subject with RMRP mutations and normal hair. Based on this observation, we hypothesised that MDWH may, similar to CHH, associate with immune deficiency and malignancy. METHODS We collected clinical and laboratory data for a cohort of 80 patients with RMRP mutations followed for over 30 years and analysed outcome data for those with features consistent with MDWH. RESULTS In our cohort, we identified 10 patients with skeletal but no extraskeletal features during preschool age. Eight of these patients developed malignancy or clinically significant immunodeficiency during follow-up. Two of them died during chemotherapy for malignancy. At the time of the first extraskeletal manifestation, patients were school aged, 20, 43 and 50 years old. Laboratory signs of immunodeficiency (impaired lymphocyte proliferative responses) were demonstrated in four patients before the onset of symptoms. The patient outside this cohort, who had RMRP mutations, skeletal dysplasia, normal hair and severe agranulocytosis at 18 years of age, underwent haematopoietic stem cell transplantation. CONCLUSIONS MDWH can present with severe late-onset extraskeletal manifestations and thus should be reclassified and managed as CHH.
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Affiliation(s)
- Svetlana Vakkilainen
- New Children's Hospital, Pediatric Research Center, University of Helsinki and HUS Helsinki University Hospital, Helsinki, Finland .,Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
| | - Alice Costantini
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Mervi Taskinen
- New Children's Hospital, Pediatric Research Center, University of Helsinki and HUS Helsinki University Hospital, Helsinki, Finland
| | - Ulla Wartiovaara-Kautto
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center and University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics / Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Outi Mäkitie
- New Children's Hospital, Pediatric Research Center and Institute of Genetics, University of Helsinki and HUS Helsinki University Hospital and Folkhälsan Research Center, Helsinki, Finland.,Department of Molecular Medicine and Surgery and Center for Molecular Medicine and Department of Clinical Genetics, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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28
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Teng Y, Ding M, Wang X, Li H, Guo Q, Yan J, Gao L. LncRNA RMRP accelerates hypoxia-induced injury by targeting miR-214-5p in H9c2 cells. J Pharmacol Sci 2019; 142:69-78. [PMID: 31839421 DOI: 10.1016/j.jphs.2019.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/28/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To elucidate the function of lncRNA RMRP in hypoxia-induced acute myocardial infarction (AMI) in vitro and explore its underlying mechanism. METHODS Hypoxic injury was confirmed by measurement of cell viability, LDH release, migration, invasion, and apoptosis in H9c2 cells. The interactions between RMRP and miR-214-5p as well as miR-214-5p and p53 were also investigated. RESULTS Hypoxia treatment significantly induced cell damage in H9c2 cells, accompanied with the up-regulation of RMRP expressions. Transfection of RMRP siRNA remarkably attenuated hypoxia-induced injury by enhancing cell viability, migration and invasion, and reducing cell apoptosis and LDH release; whereas, enforced expression of RMRP aggravated hypoxia-induced injury. Furthermore, RMRP served as an endogenous sponge for miR-214-5p, and its expression was negatively regulated by RMRP. The effects of RMRP knockdown on hypoxia-induced injury were further enhanced with miR-214-5p overexpression, but significantly abrogated with miR-214-5p silence. Moreover, p53 was verified as a direct target of miR-214-5p, and functional investigation revealed that RMRP regulated hypoxia-induced injury via modulating p53 signaling pathway, which was partially mediated by miR-214-5p. CONCLUSION Our findings demonstrated the novel molecular mechanism of RMRP/miR-214-5p/p53 axis on the regulation of hypoxia-induced myocardial injury in H9c2 cells, which might provide potential therapeutic targets for AMI treatment.
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Affiliation(s)
- Yan Teng
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China.
| | - Ming Ding
- Department of Critical Care Medicine, The Fourth People's Hospital of Shaanxi Province, Xi'an, Shaanxi, 710043, PR China
| | - Xiaojian Wang
- Department of Critical Care Medicine, Chang'an District Hospital of the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710100, PR China
| | - Hao Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Qinyue Guo
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Jinqi Yan
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Lan Gao
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
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29
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Wang Y, Luo X, Liu Y, Han G, Sun D. Long noncoding RNA RMRP promotes proliferation and invasion via targeting miR‐1‐3p in non–small‐cell lung cancer. J Cell Biochem 2019; 120:15170-15181. [PMID: 31050363 DOI: 10.1002/jcb.28779] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/30/2018] [Accepted: 01/09/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Yi Wang
- Department of Clinical Laboratory The Third Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
| | - Xigang Luo
- Department of Clinical Laboratory The Third Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
| | - Yang Liu
- Department of Clinical Laboratory The Third Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
| | - Guanying Han
- Department of Medical The First Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
| | - Dapeng Sun
- Department of Medical The First Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
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30
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Sulima SO, Kampen KR, De Keersmaecker K. Cancer Biogenesis in Ribosomopathies. Cells 2019; 8:E229. [PMID: 30862070 PMCID: PMC6468915 DOI: 10.3390/cells8030229] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/23/2022] Open
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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31
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Steinbusch MMF, Caron MMJ, Surtel DAM, van den Akker GGH, van Dijk PJ, Friedrich F, Zabel B, van Rhijn LW, Peffers MJ, Welting TJM. The antiviral protein viperin regulates chondrogenic differentiation via CXCL10 protein secretion. J Biol Chem 2019; 294:5121-5136. [PMID: 30718282 PMCID: PMC6442052 DOI: 10.1074/jbc.ra119.007356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/29/2019] [Indexed: 01/10/2023] Open
Abstract
Viperin (also known as radical SAM domain–containing 2 (RSAD2)) is an interferon-inducible and evolutionary conserved protein that participates in the cell's innate immune response against a number of viruses. Viperin mRNA is a substrate for endoribonucleolytic cleavage by RNase mitochondrial RNA processing (MRP) and mutations in the RNase MRP small nucleolar RNA (snoRNA) subunit of the RNase MRP complex cause cartilage-hair hypoplasia (CHH), a human developmental condition characterized by metaphyseal chondrodysplasia and severe dwarfism. It is unknown how CHH-pathogenic mutations in RNase MRP snoRNA interfere with skeletal development, and aberrant processing of RNase MRP substrate RNAs is thought to be involved. We hypothesized that viperin plays a role in chondrogenic differentiation. Using immunohistochemistry, real-time quantitative PCR, immunoblotting, ELISA, siRNA-mediated gene silencing, plasmid-mediated gene overexpression, label-free MS proteomics, and promoter reporter bioluminescence assays, we discovered here that viperin is expressed in differentiating chondrocytic cells and regulates their protein secretion and the outcome of chondrogenic differentiation by influencing transforming growth factor β (TGF-β)/SMAD family 2/3 (SMAD2/3) activity via C-X-C motif chemokine ligand 10 (CXCL10). Of note, we observed disturbances in this viperin–CXCL10–TGF-β/SMAD2/3 axis in CHH chondrocytic cells. Our results indicate that the antiviral protein viperin controls chondrogenic differentiation by influencing secretion of soluble proteins and identify a molecular route that may explain impaired chondrogenic differentiation of cells from individuals with CHH.
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Affiliation(s)
- Mandy M F Steinbusch
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
| | - Marjolein M J Caron
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
| | - Don A M Surtel
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
| | | | - Paul J van Dijk
- the Department of Anatomy and Embryology, Maastricht University, NL-6202 AZ Maastricht, The Netherlands
| | - Franziska Friedrich
- the University Heart Centre Freiburg, Faculty of Medicine, University of Freiburg, Institute for Experimental Cardiovascular Medicine, 79110 Freiburg, Germany
| | - Bernhard Zabel
- the Medical Faculty, Otto van Guericke University of Magdeburg, 39106 Magdeburg, Germany, and
| | - Lodewijk W van Rhijn
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
| | - Mandy J Peffers
- the Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Tim J M Welting
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
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32
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付 洪. Research Advances of the Long Non-Coding RNA RMRP RNA Promoting the Osteoblastic Differentiation. Biophysics (Nagoya-shi) 2019. [DOI: 10.12677/biphy.2019.73005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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33
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Abstract
Mitochondria are cytosolic organelles essential for generating energy and maintaining cell homeostasis. Despite their critical function, the handful of proteins expressed by the mitochondrial genome is insufficient to maintain mitochondrial structure or activity. Accordingly, mitochondrial metabolism is fully dependent on factors encoded by the nuclear DNA, including many proteins synthesized in the cytosol and imported into mitochondria via established mechanisms. However, there is growing evidence that mammalian mitochondria can also import cytosolic noncoding RNA via poorly understood processes. Here, we summarize our knowledge of mitochondrial RNA, discuss recent progress in understanding the molecular mechanisms and functional impact of RNA import into mitochondria, and identify rising challenges and opportunities in this rapidly evolving field.
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Affiliation(s)
- Kyoung Mi Kim
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
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34
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Cavaillé J. Box C/D small nucleolar RNA genes and the Prader-Willi syndrome: a complex interplay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28296064 DOI: 10.1002/wrna.1417] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 12/22/2022]
Abstract
The nucleolus of mammalian cells contains hundreds of box C/D small nucleolar RNAs (SNORDs). Through their ability to base pair with ribosomal RNA precursors, most play important roles in the synthesis and/or activity of ribosomes, either by guiding sequence-specific 2'-O-methylations or by facilitating RNA folding and cleavages. A growing number of SNORD genes with elusive functions have been discovered recently. Intriguingly, the vast majority of them are located in two large, imprinted gene clusters at human chromosome region 15q11q13 (the SNURF-SNRPN domain) and at 14q32 (the DLK1-DIO3 domain) where they are expressed, respectively, only from the paternally and maternally inherited alleles. These placental mammal-specific SNORD genes have many features of the canonical SNORDs that guide 2'-O-methylations, yet they lack obvious complementarity with ribosomal RNAs and, surprisingly, they are processed from large, tandemly repeated genes expressed preferentially in the brain. This review summarizes our understanding of the biology of these peculiar SNORD genes, focusing particularly on SNORD115 and SNORD116 in the SNURF-SNRPN domain. It examines the growing evidence that altered levels of these SNORDs and/or their host-gene transcripts may be a primary cause of Prader-Willi syndrome (PWS; a rare disorder characterized by overeating and obesity) as well as abnormalities in signaling through the 5-HT2C serotonin receptor. Finally, the hypothesis that PWS may be a ribosomopathy (ribosomal disease) is also discussed. WIREs RNA 2017, 8:e1417. doi: 10.1002/wrna.1417 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jérôme Cavaillé
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse; UPS and CNRS, LMBE, Toulouse, France
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35
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Aubert G, Strauss KA, Lansdorp PM, Rider NL. Defects in lymphocyte telomere homeostasis contribute to cellular immune phenotype in patients with cartilage-hair hypoplasia. J Allergy Clin Immunol 2017; 140:1120-1129.e1. [PMID: 28126377 DOI: 10.1016/j.jaci.2016.11.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/18/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND Mutations in the long noncoding RNA RNase component of the mitochondrial RNA processing endoribonuclease (RMRP) give rise to the autosomal recessive condition cartilage-hair hypoplasia (CHH). The CHH disease phenotype has some overlap with dyskeratosis congenita, a well-known "telomere disorder." RMRP binds the telomerase reverse transcriptase (catalytic subunit) in some cell lines, raising the possibility that RMRP might play a role in telomere biology. OBJECTIVE We sought to determine whether a telomere phenotype is present in immune cells from patients with CHH and explore mechanisms underlying these observations. METHODS We assessed proliferative capacity and telomere length using flow-fluorescence in situ hybridization (in situ hybridization and flow cytometry) of primary lymphocytes from patients with CHH, carrier relatives, and control subjects. The role of telomerase holoenzyme components in gene expression and activity were assessed by using quantitative PCR and the telomere repeat amplification protocol from PBMCs and enriched lymphocyte cultures. RESULTS Lymphocyte cultures from patients with CHH display growth defects in vitro, which is consistent with an immune deficiency cellular phenotype. Here we show that telomere length and telomerase activity are impaired in primary lymphocyte subsets from patients with CHH. Notably, telomerase activity is affected in a gene dose-dependent manner when comparing heterozygote RMRP carriers with patients with CHH. Telomerase deficiency in patients with CHH is not mediated by abnormal telomerase gene transcript levels relative to those of endogenous genes. CONCLUSION These findings suggest that telomere deficiency is implicated in the CHH disease phenotype through an as yet unidentified mechanism.
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Affiliation(s)
- Geraldine Aubert
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada; Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; European Research Institute on the Biology of Aging, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.
| | - Nicholas L Rider
- Section of Immunology, Allergy and Rheumatology, Texas Children's Hospital, Baylor College of Medicine, Houston, Tex.
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Castilla-Cortázar I, Rodríguez De Ita J, Martín-Estal I, Castorena F, Aguirre GA, García de la Garza R, Elizondo MI. Clinical and molecular diagnosis of a cartilage-hair hypoplasia with IGF-1 deficiency. Am J Med Genet A 2016; 173:537-540. [PMID: 27862957 PMCID: PMC6586044 DOI: 10.1002/ajmg.a.38052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/27/2016] [Indexed: 01/20/2023]
Abstract
Cartilage-hair hypoplasia syndrome (CHH) is a rare autosomal recessive condition characterized by metaphyseal chondrodysplasia and characteristic hair, together with a myriad of other symptoms, being most common immunodeficiency and gastrointestinal complications. A 15-year-old Mexican male initially diagnosed with Hirschsprung disease and posterior immunodeficiency, presents to our department for genetic and complementary evaluation for suspected CHH. Physical, biochemical, and genetic studies confirmed CHH together with IGF-1 deficiency. For this reason, we propose IGF-1 replacement therapy for its well-known actions on hematopoiesis, immune function and maturation, and metabolism. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Inma Castilla-Cortázar
- Escuela Nacional de Medicina, CITES, Tecnologico de Monterrey, Monterey, Neuvo Leon, Mexico.,Fundacion para la Investigacion, HM Hospitales, Madrid, Spain
| | | | - Irene Martín-Estal
- Escuela Nacional de Medicina, CITES, Tecnologico de Monterrey, Monterey, Neuvo Leon, Mexico
| | - Fabiola Castorena
- Escuela Nacional de Medicina, CITES, Tecnologico de Monterrey, Monterey, Neuvo Leon, Mexico
| | - Gabriel A Aguirre
- Escuela Nacional de Medicina, CITES, Tecnologico de Monterrey, Monterey, Neuvo Leon, Mexico
| | | | - Martha I Elizondo
- Escuela Nacional de Medicina, CITES, Tecnologico de Monterrey, Monterey, Neuvo Leon, Mexico
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Shukla S, Parker R. Hypo- and Hyper-Assembly Diseases of RNA-Protein Complexes. Trends Mol Med 2016; 22:615-628. [PMID: 27263464 DOI: 10.1016/j.molmed.2016.05.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 12/14/2022]
Abstract
A key aspect of cellular function is the proper assembly and utilization of ribonucleoproteins (RNPs). Recent studies have shown that hyper- or hypo-assembly of various RNPs can lead to human diseases. Defects in the formation of RNPs lead to 'RNP hypo-assembly diseases', which can be caused by RNA degradation outcompeting RNP assembly. By contrast, excess RNP assembly, either in higher order RNP granules, or due to the expression of repeat-containing RNAs, can lead to 'RNP hyper-assembly diseases'. Here, we discuss the most recent advances in understanding the cause of disease onset, as well as potential therapies from the aspect of modulating RNP assembly in the cell, which presents a novel route to the treatment of these diseases.
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Affiliation(s)
- Siddharth Shukla
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Cherkaoui Jaouad I, Laarabi FZ, Chafai Elalaoui S, Lyonnet S, Henrion-Caude A, Sefiani A. Novel Mutation and Structural RNA Analysis of the Noncoding RNase MRP Gene in Cartilage-Hair Hypoplasia. Mol Syndromol 2015; 6:77-82. [PMID: 26279652 DOI: 10.1159/000430970] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 11/19/2022] Open
Abstract
Cartilage-hair hypoplasia (CHH) is an autosomal recessive disorder which is characterized by bone metaphysis anomalies with manifestations that include short stature, defective cellular immunity, and predisposition to several cancers. It is caused by mutations in RMRP, which is transcribed as an RNA component of the mitochondrial RNA-processing ribonuclease. We report the clinical and molecular data of a Moroccan patient with CHH. Sequencing of RMRP identified 2 mutations in the patient: the known mutation g.97G>A and the variation g.27G>C, which has not been reported previously. Given the high mutational heterogeneity, the high frequency of variations in the region, and the fact that RMRP is a non-coding gene, assigning the pathogenicity to RMRP mutations remains a difficult task. Therefore, we compared the characteristics of the primary and secondary structures of mutated RMRP sequences. The location of our mutations within the secondary structure of the RMRP molecule revealed that the novel g.27G>C mutation causes a disruption in the Watson-Crick base pairing, which results in an impairment of a highly conserved P3 domain. Our work prompts considering the consequences of novel RMRP nucleotide variations on conserved RNA structures to gain insights into the pathogenicity of mutations.
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Affiliation(s)
- Imane Cherkaoui Jaouad
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V, France ; Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco, France
| | - Fatima Z Laarabi
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V, France ; Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco, France
| | - Siham Chafai Elalaoui
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V, France ; Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco, France
| | - Stanislas Lyonnet
- INSERM UMR-781, Hôpital Necker-Enfants Malades, Université Paris Descartes, France ; Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Alexandra Henrion-Caude
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V, France ; Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco, France
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Yelick PC, Trainor PA. Ribosomopathies: Global process, tissue specific defects. Rare Dis 2015; 3:e1025185. [PMID: 26442198 PMCID: PMC4590025 DOI: 10.1080/21675511.2015.1025185] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/18/2015] [Accepted: 02/26/2015] [Indexed: 01/01/2023] Open
Abstract
Disruptions in ribosomal biogenesis would be expected to have global and in fact lethal effects on a developing organism. However, mutations in ribosomal protein genes have been shown in to exhibit tissue specific defects. This seemingly contradictory finding - that globally expressed genes thought to play fundamental housekeeping functions can in fact exhibit tissue and cell type specific functions - provides new insight into roles for ribosomes, the protein translational machinery of the cell, in regulating normal development and disease. Furthermore it illustrates the surprisingly dynamic nature of processes regulating cell type specific protein translation. In this review, we discuss our current knowledge of a variety of ribosomal protein mutations associated with human disease, and models to better understand the molecular mechanisms associated with each. We use specific examples to emphasize both the similarities and differences between the effects of various human ribosomal protein mutations. Finally, we discuss areas of future study that are needed to further our understanding of the role of ribosome biogenesis in normal development, and possible approaches that can be used to treat debilitating ribosomopathy diseases.
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Affiliation(s)
| | - Paul A Trainor
- Stowers Institute ; Kansas City, MO USA ; University of Kansas Medical Center ; Kansas City, KS USA
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Riley P, Weiner DS, Leighley B, Jonah D, Morton DH, Strauss KA, Bober MB, Dicintio MS. Cartilage hair hypoplasia: characteristics and orthopaedic manifestations. J Child Orthop 2015; 9:145-52. [PMID: 25764362 PMCID: PMC4417732 DOI: 10.1007/s11832-015-0646-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 02/27/2015] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Cartilage hair hypoplasia (CHH) is a rare metaphyseal chondrodysplasia characterized by short stature and short limbs, found primarily in Amish and Finnish populations. Cartilage hair hypoplasia is caused by mutations in the RMRP gene located on chromosome 9p13.3. The disorder has several characteristic orthopaedic manifestations, including joint laxity, limited elbow extension, ankle varus, and genu varum. Immunodeficiency is of concern in most cases. Although patients exhibit orthopaedic problems, the orthopaedic literature on CHH patients is scant at best. The objective of this study was to characterize the orthopaedic manifestations of CHH based on the authors' unique access to the largest collection of CHH patients ever reported. METHODS The authors examined charts and/or radiographs in 135 cases of CHH. We analyzed the orthopaedic manifestations to better characterize and further understand the orthopaedic surgeon's role in this disorder. In addition to describing the clinical characteristics, we report on our surgical experience in caring for CHH patients. RESULTS Genu varum, with or without knee pain, is the most common reason a patient with CHH will seek orthopaedic consultation. Of the cases reviewed, 32 patients had undergone surgery, most commonly to correct genu varum. CONCLUSION This paper characterizes the orthopaedic manifestations of CHH. Characterizing this condition in the orthopaedic literature will likely assist orthopaedic surgeons in establishing a correct diagnosis and appreciating the orthopaedic manifestations. It is important that the accompanying medical conditions are appreciated and evaluated.
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Affiliation(s)
- Patrick Riley
- Department of Pediatric Orthopaedic Surgery, Akron Children’s Hospital, Akron, OH 44308 USA
| | - Dennis S. Weiner
- Department of Pediatric Orthopaedic Surgery, Akron Children’s Hospital, Akron, OH 44308 USA ,Akron Children’s Hospital, Northeast Ohio Medical University, Akron, OH 44308 USA ,Regional Skeletal Dysplasia Clinic, Akron Children’s Hospital, Akron, OH 44308 USA ,300 Locust Street, Ste. 250, Akron, OH 44302-1821 USA
| | - Bonnie Leighley
- Department of Pediatric Orthopaedic Surgery, Akron Children’s Hospital, Akron, OH 44308 USA ,Regional Skeletal Dysplasia Clinic, Akron Children’s Hospital, Akron, OH 44308 USA
| | - David Jonah
- Little People’s Research Fund, Baltimore, MD 21228 USA
| | | | | | - Michael B. Bober
- Regional Skeletal Dysplasia Clinic, Akron Children’s Hospital, Akron, OH 44308 USA ,Skeletal Dysplasia Program, Alfred I. duPont Hospital for Children, Wilmington, DE 19803 USA
| | - Martin S. Dicintio
- Department of Pediatric Orthopaedic Surgery, Akron Children’s Hospital, Akron, OH 44308 USA
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41
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Variable phenotype of severe immunodeficiencies associated with RMRP gene mutations. J Clin Immunol 2015; 35:147-57. [PMID: 25663137 DOI: 10.1007/s10875-015-0135-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/23/2015] [Indexed: 10/24/2022]
Abstract
PURPOSE Mutations in RMRP primarily give rise to Cartilage Hair Hypoplasia (CHH), a highly diverse skeletal disorder which can be associated with severe immunodeficiency. Increased availability of RMRP mutation screening has uncovered a number of infants with significant immunodeficiency but only mild or absent skeletal features. We surveyed the clinical and immunological phenotype of children who have undergone allogeneic haematopoietic stem cell transplantation for this condition in the UK. METHODS Thirteen patients with confirmed RMRP mutations underwent allogeneic stem cell transplantation (SCT) at two nationally commissioned centres using a variety of donors and conditioning regimens. Records were retrospectively reviewed. RESULTS Median time from clinical presentation to diagnosis was 12 months (range 1 to 276 months), with three infants diagnosed with severe combined immunodeficiency (SCID) without radiographical manifestations of CHH. A total of 17 allogeneic procedures were performed on 13 patients including two stem-cell top-ups. The median age at transplant was 32.4 months (range 1.5 to 125 months). Of the eleven surviving patients, median follow-up was 50 months (range 21.6 to 168 months). CONCLUSIONS RMRP mutations can cause short stature and significant immunodeficiency which can be corrected by allogeneic SCT and the diagnosis should be considered even in the absence of skeletal manifestations.
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Robles-Espinoza CD, Velasco-Herrera MDC, Hayward NK, Adams DJ. Telomere-regulating genes and the telomere interactome in familial cancers. Mol Cancer Res 2015; 13:211-22. [PMID: 25244922 PMCID: PMC4278843 DOI: 10.1158/1541-7786.mcr-14-0305] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Telomeres are repetitive sequence structures at the ends of linear chromosomes that consist of double-stranded DNA repeats followed by a short single-stranded DNA protrusion. Telomeres need to be replicated in each cell cycle and protected from DNA-processing enzymes, tasks that cells execute using specialized protein complexes such as telomerase (that includes TERT), which aids in telomere maintenance and replication, and the shelterin complex, which protects chromosome ends. These complexes are also able to interact with a variety of other proteins, referred to as the telomere interactome, to fulfill their biological functions and control signaling cascades originating from telomeres. Given their essential role in genomic maintenance and cell-cycle control, germline mutations in telomere-regulating proteins and their interacting partners have been found to underlie a variety of diseases and cancer-predisposition syndromes. These syndromes can be characterized by progressively shortening telomeres, in which carriers can present with organ failure due to stem cell senescence among other characteristics, or can also present with long or unprotected telomeres, providing an alternative route for cancer formation. This review summarizes the critical roles that telomere-regulating proteins play in cell-cycle control and cell fate and explores the current knowledge on different cancer-predisposing conditions that have been linked to germline defects in these proteins and their interacting partners.
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Affiliation(s)
| | | | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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Saito Y, Takeda J, Adachi K, Nobe Y, Kobayashi J, Hirota K, Oliveira DV, Taoka M, Isobe T. RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway. PLoS One 2014; 9:e112488. [PMID: 25401760 PMCID: PMC4234475 DOI: 10.1371/journal.pone.0112488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/17/2014] [Indexed: 01/07/2023] Open
Abstract
Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNASer-Met. To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNASer-Met, suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry–based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute “Domain 1” in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.
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Affiliation(s)
- Yuichiro Saito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Jun Takeda
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Kousuke Adachi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Yuko Nobe
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Junya Kobayashi
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Douglas V. Oliveira
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
- * E-mail:
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Batista LFZ. Telomere biology in stem cells and reprogramming. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 125:67-88. [PMID: 24993698 DOI: 10.1016/b978-0-12-397898-1.00003-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Telomerase expression in humans is restricted to different populations of stem and progenitor cells, being silenced in most somatic tissues. Efficient telomere homeostasis is essential for embryonic and adult stem cell function and therefore essential for tissue homeostasis throughout organismal life. Accordingly, the mutations in telomerase culminate in reduced stem cell function both in vivo and in vitro and have been associated with tissue dysfunction in human patients. Despite the importance of telomerase for stem cell biology, the mechanisms behind telomerase regulation during development are still poorly understood, mostly due to difficulties in acquiring and maintaining pluripotent stem cell populations in culture. In this chapter, we will analyze recent developments in this field, including the importance of efficient telomere homeostasis in different stem cell types and the role of telomerase in different techniques used for cellular reprogramming.
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Affiliation(s)
- Luis F Z Batista
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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Trainor PA, Merrill AE. Ribosome biogenesis in skeletal development and the pathogenesis of skeletal disorders. Biochim Biophys Acta Mol Basis Dis 2013; 1842:769-78. [PMID: 24252615 DOI: 10.1016/j.bbadis.2013.11.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/05/2013] [Accepted: 11/08/2013] [Indexed: 02/06/2023]
Abstract
The skeleton affords a framework and structural support for vertebrates, while also facilitating movement, protecting vital organs, and providing a reservoir of minerals and cells for immune system and vascular homeostasis. The mechanical and biological functions of the skeleton are inextricably linked to the size and shape of individual bones, the diversity of which is dependent in part upon differential growth and proliferation. Perturbation of bone development, growth and proliferation, can result in congenital skeletal anomalies, which affect approximately 1 in 3000 live births [1]. Ribosome biogenesis is integral to all cell growth and proliferation through its roles in translating mRNAs and building proteins. Disruption of any steps in the process of ribosome biogenesis can lead to congenital disorders termed ribosomopathies. In this review, we discuss the role of ribosome biogenesis in skeletal development and in the pathogenesis of congenital skeletal anomalies. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
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Affiliation(s)
- 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.
| | - Amy E Merrill
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 2013; 342:1235587. [PMID: 24092746 PMCID: PMC3947637 DOI: 10.1126/science.1235587] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating the latter. We found regions particularly sensitive to mutations ("ultrasensitive") and variants that are disruptive because of mechanistic effects on transcription-factor binding (that is, "motif-breakers"). We also found variants in regions with higher network centrality tend to be deleterious. Insertions and deletions followed a similar pattern to single-nucleotide variants, with some notable exceptions (e.g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers.
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Affiliation(s)
- Ekta Khurana
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Yao Fu
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
| | - Vincenza Colonna
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, CB10 1SA, UK
- Institute of Genetics and Biophysics, National Research Council
(CNR), 80131 Naples, Italy
| | - Xinmeng Jasmine Mu
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
| | - Hyun Min Kang
- Center for Statistical Genetics, Biostatistics, University of
Michigan, Ann Arbor, MI 48109, USA
| | - Tuuli Lappalainen
- Department of Genetic Medicine and Development, University of Geneva
Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of
Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Andrea Sboner
- Institute for Precision Medicine and the Department of Pathology and
Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian
Hospital, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute
for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021,
USA
| | - Lucas Lochovsky
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
| | - Jieming Chen
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology,
Yale University, New Haven, CT 06520, USA
| | - Arif Harmanci
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Jishnu Das
- Department of Biological Statistics and Computational Biology,
Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University,
Ithaca, NY 14853, USA
| | - Alexej Abyzov
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Suganthi Balasubramanian
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dimple Chakravarty
- Institute for Precision Medicine and the Department of Pathology and
Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian
Hospital, New York, NY 10065, USA
| | - Daniel Challis
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, CB10 1SA, UK
| | - Declan Clarke
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Uday S. Evani
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert Fragoza
- Weill Institute for Cell and Molecular Biology, Cornell University,
Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University,
Ithaca, NY 14853, USA
| | - Erik Garrison
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Richard Gibbs
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | - Zeynep H. Gümüş
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute
for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021,
USA
- Department of Physiology and Biophysics, Weill Cornell Medical
College, New York, NY, 10065, USA
| | - Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Naoki Kitabayashi
- Institute for Precision Medicine and the Department of Pathology and
Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian
Hospital, New York, NY 10065, USA
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
- Keck Biotechnology Resource Laboratory, Yale University, New Haven,
CT 06511, USA
| | - Kasper Lage
- Pediatric Surgical Research Laboratories, MassGeneral Hospital for
Children, Massachusetts General Hospital, Boston, MA 02114, USA
- Analytical and Translational Genetics Unit, Massachusetts General
Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
- Center for Biological Sequence Analysis, Department of Systems
Biology, Technical University of Denmark, Lyngby, Denmark
- Center for Protein Research, University of Copenhagen, Copenhagen,
Denmark
| | - Vaja Liluashvili
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute
for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021,
USA
- Department of Physiology and Biophysics, Weill Cornell Medical
College, New York, NY, 10065, USA
| | - Steven M. Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, NY
10065, USA
| | - Daniel G. MacArthur
- Analytical and Translational Genetics Unit, Massachusetts General
Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of
Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142,
USA
| | - Gabor Marth
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Donna Muzny
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | - Tune H. Pers
- Center for Biological Sequence Analysis, Department of Systems
Biology, Technical University of Denmark, Lyngby, Denmark
- Division of Endocrinology and Center for Basic and Translational
Obesity Research, Children’s Hospital, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Graham R. S. Ritchie
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeffrey A. Rosenfeld
- Department of Medicine, Rutgers New Jersey Medical School, Newark,
NJ 07101, USA
- IST/High Performance and Research Computing, Rutgers University
Newark, NJ 07101, USA
- Sackler Institute for Comparative Genomics, American Museum of
Natural History, New York, NY 10024, USA
| | - Cristina Sisu
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
| | - Xiaomu Wei
- Weill Institute for Cell and Molecular Biology, Cornell University,
Ithaca, NY 14853, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY
10065, USA
| | - Michael Wilson
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, CB10 1SA, UK
| | - Fuli Yu
- Baylor College of Medicine, Human Genome Sequencing Center,
Houston, TX 77030, USA
| | | | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva
Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of
Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology,
Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University,
Ithaca, NY 14853, USA
| | - Mark A. Rubin
- Institute for Precision Medicine and the Department of Pathology and
Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian
Hospital, New York, NY 10065, USA
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Cambridge, CB10 1SA, UK
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale
University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT
06520, USA
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Crahes M, Saugier-Veber P, Patrier S, Aziz M, Pirot N, Brasseur-Daudruy M, Layet V, Frébourg T, Laquerrière A. Foetal presentation of cartilage hair hypoplasia with extensive granulomatous inflammation. Eur J Med Genet 2013; 56:365-70. [DOI: 10.1016/j.ejmg.2013.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/17/2013] [Indexed: 12/01/2022]
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Taskinen M, Jeskanen L, Karjalainen-Lindsberg ML, Mäkitie A, Mäkitie O, Ranki A. Combating cancer predisposition in association with idiopathic immune deficiency: a recurrent nodal and cutaneous T-cell lymphoproliferative disease in a patient with cartilage-hair hypoplasia. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2012; 13:73-6. [PMID: 22999941 DOI: 10.1016/j.clml.2012.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 06/09/2012] [Accepted: 06/15/2012] [Indexed: 10/27/2022]
Affiliation(s)
- Mervi Taskinen
- Department of Pediatrics, Children's Hospital, Helsinki University Central Hospital, Helsinki, Finland.
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49
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Kwan A, Manning M, Zollars LK, Hoyme HE. Marked variability in the radiographic features of cartilage-hair hypoplasia: Case report and review of the literature. Am J Med Genet A 2012; 158A:2911-6. [DOI: 10.1002/ajmg.a.35604] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 07/07/2012] [Indexed: 11/07/2022]
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50
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Bernstein J, Toth EA. Yeast nuclear RNA processing. World J Biol Chem 2012; 3:7-26. [PMID: 22312453 PMCID: PMC3272586 DOI: 10.4331/wjbc.v3.i1.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 11/27/2011] [Accepted: 12/04/2011] [Indexed: 02/05/2023] Open
Abstract
Nuclear RNA processing requires dynamic and intricately regulated machinery composed of multiple enzymes and their cofactors. In this review, we summarize recent experiments using Saccharomyces cerevisiae as a model system that have yielded important insights regarding the conversion of pre-RNAs to functional RNAs, and the elimination of aberrant RNAs and unneeded intermediates from the nuclear RNA pool. Much progress has been made recently in describing the 3D structure of many elements of the nuclear degradation machinery and its cofactors. Similarly, the regulatory mechanisms that govern RNA processing are gradually coming into focus. Such advances invariably generate many new questions, which we highlight in this review.
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Affiliation(s)
- Jade Bernstein
- Jade Bernstein, Eric A Toth, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
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