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Towler BP, Newbury SF. Regulation of cytoplasmic RNA stability: Lessons from Drosophila. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1499. [PMID: 30109918 DOI: 10.1002/wrna.1499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/06/2018] [Accepted: 07/01/2018] [Indexed: 12/19/2022]
Abstract
The process of RNA degradation is a critical level of regulation contributing to the control of gene expression. In the last two decades a number of studies have shown the specific and targeted nature of RNA decay and its importance in maintaining homeostasis. The key players within the pathways of RNA decay are well conserved with their mutation or disruption resulting in distinct phenotypes as well as human disease. Model organisms including Drosophila melanogaster have played a substantial role in elucidating the mechanisms conferring control over RNA stability. A particular advantage of this model organism is that the functions of ribonucleases can be assessed in the context of natural cells within tissues in addition to individual immortalized cells in culture. Drosophila RNA stability research has demonstrated how the cytoplasmic decay machines, such as the exosome, Dis3L2 and Xrn1, are responsible for regulating specific processes including apoptosis, proliferation, wound healing and fertility. The work discussed here has begun to identify specific mRNA transcripts that appear sensitive to specific decay pathways representing mechanisms through which the ribonucleases control mRNA stability. Drosophila research has also contributed to our knowledge of how specific RNAs are targeted to the ribonucleases including AU rich elements, miRNA targeting and 3' tailing. Increased understanding of these mechanisms is critical to elucidating the control elicited by the cytoplasmic ribonucleases which is relevant to human disease. This article is categorized under: RNA in Disease and Development > RNA in Development RNA Turnover and Surveillance > Regulation of RNA Stability RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Benjamin P Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Sarah F Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
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2
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Ryu D, Kim HJ, Joung JG, Lee HO, Bae JS, Kim SJ, Kim H, Park WY, Kim K. Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker. Oncotarget 2018; 7:47127-47133. [PMID: 27223072 PMCID: PMC5216929 DOI: 10.18632/oncotarget.9478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/28/2016] [Indexed: 12/11/2022] Open
Abstract
Immunoglobulin M multiple myeloma (IgM MM) is an extremely rare subtype of multiple myeloma with a poor clinical outcome. In this study, bone marrow aspirates of MM patients, including two cases of IgM MM, were analyzed by whole exome sequencing and RNA sequencing. Recurrent somatic mutations in the NRAS, KRAS, CCND1, DIS3, and TP53 genes were found in IgM MM and other types of MM, in agreement with previous studies. Overall transcription profiles of IgM and other types of MM clustered together, but separate from normal blood or peripheral plasma cells. Among the differentially expressed genes in IgM MM, IRF4 was highly expressed in IgM as well as in a subset of other types of MM patients. Thus, IRF4 is an independent prognostic factor for general MM patients. Taken together, the somatic mutation and transcriptome profiles support the idea that IgM MM can be classified as an aggressive MM subtype.
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Affiliation(s)
- Daeun Ryu
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jin Kim
- Department of Laboratory Medicine & Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hae-Ock Lee
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Seol Bae
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Haesu Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kihyun Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Towler BP, Jones CI, Harper KL, Waldron JA, Newbury SF. A novel role for the 3'-5' exoribonuclease Dis3L2 in controlling cell proliferation and tissue growth. RNA Biol 2016; 13:1286-1299. [PMID: 27630034 PMCID: PMC5207379 DOI: 10.1080/15476286.2016.1232238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In a complex organism, cell proliferation and apoptosis need to be precisely controlled in order for tissues to develop correctly. Excessive cell proliferation can lead to diseases such as cancer. We have shown that the exoribonuclease Dis3L2 is required for the correct regulation of proliferation in a natural tissue within the model organism Drosophila melanogaster. Dis3L2 is a member of a highly conserved family of exoribonucleases that degrade RNA in a 3′-5′ direction. We show that knockdown of dis3L2 in the Drosophila wing imaginal discs results in substantial wing overgrowth due to increased cellular proliferation rather than an increase in cell size. Imaginal discs are specified in the embryo before proliferating and differentiating to form the adult structures of the fly. Using RNA-seq we identified a small set of mRNAs that are sensitive to Dis3L2 activity. Of the mRNAs which increase in levels and are therefore potential targets of Dis3L2, we identified 2 that change at the post-transcriptional level but not at the transcriptional level, namely CG2678 (a transcription factor) and pyrexia (a TRP cation channel). We also demonstrate a compensatory effect between Dis3L2 and the 5′-3′ exoribonuclease Pacman demonstrating that these 2 exoribonucleases function to regulate opposing pathways within the developing tissue. This work provides the first description of the molecular and developmental consequences of Dis3L2 inactivation in a non-human animal model. The work is directly relevant to the understanding of human overgrowth syndromes such as Perlman syndrome.
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Affiliation(s)
- Benjamin P Towler
- a Brighton and Sussex Medical School, University of Sussex , Brighton , UK
| | | | - Kirsty L Harper
- a Brighton and Sussex Medical School, University of Sussex , Brighton , UK
| | - Joseph A Waldron
- a Brighton and Sussex Medical School, University of Sussex , Brighton , UK
| | - Sarah F Newbury
- a Brighton and Sussex Medical School, University of Sussex , Brighton , UK
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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Correction: Modulating the RNA Processing and Decay by the Exosome: Altering Rrp44/Dis3 Activity and End-Product. PLoS One 2015; 10:e0136810. [PMID: 26295475 PMCID: PMC4546634 DOI: 10.1371/journal.pone.0136810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Weißbach S, Langer C, Puppe B, Nedeva T, Bach E, Kull M, Bargou R, Einsele H, Rosenwald A, Knop S, Leich E. The molecular spectrum and clinical impact of DIS3 mutations in multiple myeloma. Br J Haematol 2014; 169:57-70. [PMID: 25521164 DOI: 10.1111/bjh.13256] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/04/2014] [Indexed: 01/09/2023]
Abstract
Multiple myeloma (MM) is a plasma cell neoplasm that presents with a major biological and clinical heterogeneity. We here investigated the spectrum of clonal and subclonal mutations of DIS3, an active part of the exosome complex, that may play a role in the development or progression of MM. The whole coding sequence of DIS3 was subjected to deep sequencing in 81 uniformly-treated MM patients and 12 MM cell lines and the overall occurrence of DIS3 mutations as well as the presence of DIS3 mutations in minor and major subclones were correlated with cytogenetic alterations and clinical parameters. Our study identified DIS3 mutations in 9/81 patients that were associated with 13q14 deletions and IGH translocations on the cytogenetic level. Specifically, we detected seven novel somatic DIS3 single nucleotide variants (SNVs) and defined three hot spot mutations within the RNB domain. Lastly, we found a trend towards a shorter median overall survival for patients with DIS3 mutations, and patients carrying DIS3 mutations in minor subclones of their tumours showed a significantly worse response to therapy compared to patients with DIS3 mutations in the major subclone.
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Affiliation(s)
- Susann Weißbach
- Institute of Pathology, University of Würzburg, Comprehensive Cancer Center Mainfranken (CCC MF), Würzburg, Germany
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Exosome analysis: a promising biomarker system with special attention to saliva. J Membr Biol 2014; 247:1129-36. [PMID: 25135166 DOI: 10.1007/s00232-014-9717-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/25/2014] [Indexed: 01/10/2023]
Abstract
Today, exosome-related studies have become a focus in science and technology. Recently, three scientists won the Nobel Prize for determining the mechanisms of exosomal transport, making exosomes a promising biomarker system for disease diagnosis and treatment. This review provides a general introduction of exosomes and explores the recent progress on the function, application, isolation, and identification of exosomes as biomarkers in blood and other body fluids, especially in saliva. Detailed information of exosomal proteins and RNAs is discussed in the paper because of their ability to determine the function of exosomes. Due to their noninvasive assessment for quick and convenient diagnosis of diseases, salivary exosomes may well be promising biomarkers.
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8
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Faehnle CR, Walleshauser J, Joshua-Tor L. Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway. Nature 2014; 514:252-256. [PMID: 25119025 PMCID: PMC4192074 DOI: 10.1038/nature13553] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/02/2014] [Indexed: 12/28/2022]
Abstract
The pluripotency factor Lin28 inhibits the biogenesis of the let-7 family of mammalian microRNAs1–4. Lin28 is highly expressed in embryonic stem cells and has a fundamental role in regulation of development5, glucose metabolism6 and tissue regeneration7. Alternatively, Lin28 overexpression is correlated with the onset of numerous cancers8, while let-7, a tumor suppressor, silences several human oncogenes5. Lin28 binds to precursor let-7 (pre-let-7) hairpins9, triggering the 3' oligo-uridylation activity of TUT4/710–12. The oligoU tail added to pre-let-7 serves as a decay signal, as it is rapidly degraded by Dis3L213,14, a homolog of the catalytic subunit of the RNA exosome. The molecular basis of Lin28 mediated recruitment of TUT4/7 to pre-let-7 and its subsequent degradation by Dis3L2 is largely unknown. To examine the mechanism of Dis3L2 substrate recognition we determined the structure of mouse Dis3L2 in complex with an oligoU RNA to mimic the uridylated tail of pre-let-7. Three RNA binding domains form an open funnel on one face of the catalytic domain that allows RNA to navigate a path to the active site different from its exosome counterpart. The resulting path reveals an extensive network of uracil-specific interactions spanning the first twelve nucleotides of an oligoU-tailed RNA. We identify three U-specificity zones that explain how Dis3L2 recognizes, binds and processes uridylated pre-let-7 in the final step of the Lin28/let-7 pathway.
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Affiliation(s)
- Christopher R Faehnle
- W. M. Keck Structural Biology Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.,Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jack Walleshauser
- W. M. Keck Structural Biology Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.,Watson School of Biological Science 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.,Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.,Watson School of Biological Science 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.,Howard Hughes Medical Institute 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.,Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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9
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Matos RG, Bárria C, Moreira RN, Barahona S, Domingues S, Arraiano CM. The importance of proteins of the RNase II/RNB-family in pathogenic bacteria. Front Cell Infect Microbiol 2014; 4:68. [PMID: 24918089 PMCID: PMC4042491 DOI: 10.3389/fcimb.2014.00068] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/09/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rute G Matos
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cátia Bárria
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Ricardo N Moreira
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Susana Barahona
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Susana Domingues
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cecília M Arraiano
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
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