1
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Ma T, Xiong ES, Lardelli RM, Lykke-Andersen J. Sm complex assembly and 5' cap trimethylation promote selective processing of snRNAs by the 3' exonuclease TOE1. Proc Natl Acad Sci U S A 2024; 121:e2315259121. [PMID: 38194449 PMCID: PMC10801842 DOI: 10.1073/pnas.2315259121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/06/2023] [Indexed: 01/11/2024] Open
Abstract
Competing exonucleases that promote 3' end maturation or degradation direct quality control of small non-coding RNAs, but how these enzymes distinguish normal from aberrant RNAs is poorly understood. The Pontocerebellar Hypoplasia 7 (PCH7)-associated 3' exonuclease TOE1 promotes maturation of canonical small nuclear RNAs (snRNAs). Here, we demonstrate that TOE1 achieves specificity toward canonical snRNAs through their Sm complex assembly and cap trimethylation, two features that distinguish snRNAs undergoing correct biogenesis from other small non-coding RNAs. Indeed, disruption of Sm complex assembly via snRNA mutations or protein depletions obstructs snRNA processing by TOE1, and in vitro snRNA processing by TOE1 is stimulated by a trimethylated cap. An unstable snRNA variant that normally fails to undergo maturation becomes fully processed by TOE1 when its degenerate Sm binding motif is converted into a canonical one. Our findings uncover the molecular basis for how TOE1 distinguishes snRNAs from other small non-coding RNAs and explain how TOE1 promotes maturation specifically of canonical snRNAs undergoing proper processing.
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Affiliation(s)
- Tiantai Ma
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Erica S. Xiong
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Rea M. Lardelli
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Jens Lykke-Andersen
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
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2
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Groen K, van der Vis JJ, van Batenburg AA, Kazemier KM, de Bruijn MJ, Stadhouders R, Arp P, Verkerk AJ, Schoemaker AE, de Bie CI, Massink MP, van Beek FT, Grutters JC, Vergouw LJ, van Moorsel CH. A new variant in the ZCCHC8 gene: diverse clinical phenotypes and expression in the lung. ERJ Open Res 2024; 10:00487-2023. [PMID: 38375433 PMCID: PMC10875464 DOI: 10.1183/23120541.00487-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/12/2023] [Indexed: 02/21/2024] Open
Abstract
Introduction Pulmonary fibrosis is a severe disease which can be familial. A genetic cause can only be found in ∼40% of families. Searching for shared novel genetic variants may aid the discovery of new genetic causes of disease. Methods Whole-exome sequencing was performed in 152 unrelated patients with a suspected genetic cause of pulmonary fibrosis from the St Antonius interstitial lung disease biobank. Variants of interest were selected by filtering for novel, potentially deleterious variants that were present in at least three unrelated pulmonary fibrosis patients. Results The novel c.586G>A p.(E196K) variant in the ZCCHC8 gene was observed in three unrelated patients: two familial patients and one sporadic patient, who was later genealogically linked to one of the families. The variant was identified in nine additional relatives with pulmonary fibrosis and other telomere-related phenotypes, such as pulmonary arterial venous malformations, emphysema, myelodysplastic syndrome, acute myeloid leukaemia and dyskeratosis congenita. One family showed incomplete segregation, with absence of the variant in one pulmonary fibrosis patient who carried a PARN variant. The majority of ZCCHC8 variant carriers showed short telomeres in blood. ZCCHC8 protein was located in different lung cell types, including alveolar type 2 (AT2) pneumocytes, the culprit cells in pulmonary fibrosis. AT2 cells showed telomere shortening and increased DNA damage, which was comparable to patients with sporadic pulmonary fibrosis and those with pulmonary fibrosis carrying a telomere-related gene variant, respectively. Discussion The ZCCHC8 c.586G>A variant confirms the involvement of ZCCHC8 in pulmonary fibrosis and short-telomere syndromes and underlines the importance of including the ZCCHC8 gene in diagnostic gene panels for these diseases.
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Affiliation(s)
- Karlijn Groen
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
| | - Joanne J. van der Vis
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
- Department of Clinical Chemistry, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
| | - Aernoud A. van Batenburg
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
| | - Karin M. Kazemier
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
- Center of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pascal Arp
- Department of Internal Medicine, Laboratory of Population Genomics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Annemieke J.M.H. Verkerk
- Department of Internal Medicine, Laboratory of Population Genomics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Angela E. Schoemaker
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Charlotte I. de Bie
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Maarten P.G. Massink
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Frouke T. van Beek
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
| | - Jan C. Grutters
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
- Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Leonie J.M. Vergouw
- Department of Internal Medicine, Laboratory of Population Genomics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Coline H.M. van Moorsel
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
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Yin J, Seo Y, Rhim J, Jin X, Kim TH, Kim SS, Hong JH, Gwak HS, Yoo H, Park JB, Kim JH. Cross-talk between PARN and EGFR-STAT3 Signaling Facilitates Self-Renewal and Proliferation of Glioblastoma Stem Cells. Cancer Res 2023; 83:3693-3709. [PMID: 37747775 DOI: 10.1158/0008-5472.can-22-3965] [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: 02/14/2023] [Revised: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
Glioblastoma is the most common type of malignant primary brain tumor and displays highly aggressive and heterogeneous phenotypes. The transcription factor STAT3 has been reported to play a key role in glioblastoma malignancy. Thus, discovering targets and functional downstream networks regulated by STAT3 that govern glioblastoma pathogenesis may lead to improved treatment strategies. In this study, we identified that poly(A)-specific ribonuclease (PARN), a key modulator of RNA metabolism, activates EGFR-STAT3 signaling to support glioblastoma stem cells (GSC). Functional integrative analysis of STAT3 found PARN as the top-scoring transcriptional target involved in RNA processing in patients with glioblastoma, and PARN expression was strongly correlated with poor patient survival and elevated malignancy. PARN positively regulated self-renewal and proliferation of GSCs through its 3'-5' exoribonuclease activity. EGFR was identified as a clinically relevant target of PARN in GSCs. PARN positively modulated EGFR by negatively regulating the EGFR-targeting miRNA miR-7, and increased EGFR expression created a positive feedback loop to increase STAT3 activation. PARN depletion in GSCs reduced infiltration and prolonged survival in orthotopic brain tumor xenografts; similar results were observed using siRNA nanocapsule-mediated PARN targeting. Pharmacological targeting of STAT3 also confirmed PARN regulation by STAT3 signaling. In sum, these results suggest that a STAT3-PARN regulatory network plays a pivotal role in tumor progression and thus may represent a target for glioblastoma therapeutics. SIGNIFICANCE A positive feedback loop comprising PARN and EGFR-STAT3 signaling supports self-renewal and proliferation of glioblastoma stem cells to drive tumor progression and can be targeted in glioblastoma therapeutics.
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Affiliation(s)
- Jinlong Yin
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Yoona Seo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Jiho Rhim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Xiong Jin
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Tae Hoon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Sung Soo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Jun-Hee Hong
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Ho-Shin Gwak
- Neuro-Oncology Clinic, National Cancer Center, Goyang, Korea
- Department of Cancer Control, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Heon Yoo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Neuro-Oncology Clinic, National Cancer Center, Goyang, Korea
| | - Jong Bae Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Jong Heon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
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4
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Huynh TN, Parker R. The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation. J Biol Chem 2023; 299:105139. [PMID: 37544646 PMCID: PMC10493513 DOI: 10.1016/j.jbc.2023.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023] Open
Abstract
The levels of non-coding RNAs (ncRNAs) are regulated by transcription, RNA processing, and RNA degradation pathways. One mechanism for the degradation of ncRNAs involves the addition of oligo(A) tails by non-canonical poly(A) polymerases, which then recruit processive sequence-independent 3' to 5' exonucleases for RNA degradation. This pathway of decay is also regulated by three 3' to 5' exoribonucleases, USB1, PARN, and TOE1, which remove oligo(A) tails and thereby can protect ncRNAs from decay in a manner analogous to the deubiquitination of proteins. Loss-of-function mutations in these genes lead to premature degradation of some ncRNAs and lead to specific human diseases such as Poikiloderma with Neutropenia (PN) for USB1, Dyskeratosis Congenita (DC) for PARN and Pontocerebellar Hypoplasia type 7 (PCH7) for TOE1. Herein, we review the biochemical properties of USB1, PARN, and TOE1, how they modulate ncRNA levels, and their roles in human diseases.
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Affiliation(s)
- Thao Ngoc Huynh
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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5
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Ma T, Xiong ES, Lardelli RM, Lykke-Andersen J. The 3' exonuclease TOE1 selectively processes snRNAs through recognition of Sm complex assembly and 5' cap trimethylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553431. [PMID: 37645788 PMCID: PMC10462049 DOI: 10.1101/2023.08.15.553431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Competing exonucleases that promote 3' end maturation or degradation direct quality control of small non-coding RNAs, but how these enzymes distinguish normal from aberrant RNAs is poorly understood. The Pontocerebellar Hypoplasia 7 (PCH7)-associated 3' exonuclease TOE1 promotes maturation of canonical small nuclear RNAs (snRNAs). Here, we demonstrate that TOE1 achieves specificity towards canonical snRNAs by recognizing Sm complex assembly and cap trimethylation, two features that distinguish snRNAs undergoing correct biogenesis from other small non-coding RNAs. Indeed, disruption of Sm complex assembly via snRNA mutations or protein depletions obstructs snRNA processing by TOE1, and in vitro snRNA processing by TOE1 is stimulated by a trimethylated cap. An unstable snRNA variant that normally fails to undergo maturation becomes fully processed by TOE1 when its degenerate Sm binding motif is converted into a canonical one. Our findings uncover the molecular basis for how TOE1 distinguishes snRNAs from other small non-coding RNAs and explain how TOE1 promotes maturation specifically of canonical snRNAs undergoing proper processing.
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Affiliation(s)
- Tiantai Ma
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Erica S Xiong
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rea M Lardelli
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jens Lykke-Andersen
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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6
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Schneider C, Bohnsack KE. Caught in the act-Visualizing ribonucleases during eukaryotic ribosome assembly. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1766. [PMID: 36254602 DOI: 10.1002/wrna.1766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 07/20/2023]
Abstract
Ribosomes are essential macromolecular machines responsible for translating the genetic information encoded in mRNAs into proteins. Ribosomes are composed of ribosomal RNAs and proteins (rRNAs and RPs) and the rRNAs fulfill both catalytic and architectural functions. Excision of the mature eukaryotic rRNAs from their precursor transcript is achieved through a complex series of endoribonucleolytic cleavages and exoribonucleolytic processing steps that are precisely coordinated with other aspects of ribosome assembly. Many ribonucleases involved in pre-rRNA processing have been identified and pre-rRNA processing pathways are relatively well defined. However, momentous advances in cryo-electron microscopy have recently enabled structural snapshots of various pre-ribosomal particles from budding yeast (Saccharomyces cerevisiae) and human cells to be captured and, excitingly, these structures not only allow pre-rRNAs to be observed before and after cleavage events, but also enable ribonucleases to be visualized on their target RNAs. These structural views of pre-rRNA processing in action allow a new layer of understanding of rRNA maturation and how it is coordinated with other aspects of ribosome assembly. They illuminate mechanisms of target recognition by the diverse ribonucleases involved and reveal how the cleavage/processing activities of these enzymes are regulated. In this review, we discuss the new insights into pre-rRNA processing gained by structural analyses and the growing understanding of the mechanisms of ribonuclease regulation. This article is categorized under: Translation > Ribosome Biogenesis RNA Processing > rRNA Processing.
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Affiliation(s)
- Claudia Schneider
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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7
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Nanjappa DP, De Saffel H, Kalladka K, Arjuna S, Babu N, Prasad K, Sips P, Chakraborty A. Poly (A)-specific ribonuclease deficiency impacts oogenesis in zebrafish. Sci Rep 2023; 13:10026. [PMID: 37340076 DOI: 10.1038/s41598-023-37226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/18/2023] [Indexed: 06/22/2023] Open
Abstract
Poly (A)-specific ribonuclease (PARN) is the most important 3'-5'exonuclease involved in the process of deadenylation, the removal of poly (A) tails of mRNAs. Although PARN is primarily known for its role in mRNA stability, recent studies suggest several other functions of PARN including a role in telomere biology, non-coding RNA maturation, trimming of miRNAs, ribosome biogenesis and TP53 function. Moreover, PARN expression is de-regulated in many cancers, including solid tumours and hematopoietic malignancies. To better understand the in vivo role of PARN, we used a zebrafish model to study the physiological consequences of Parn loss-of-function. Exon 19 of the gene, which partially codes for the RNA binding domain of the protein, was targeted for CRISPR-Cas9-directed genome editing. Contrary to the expectations, no developmental defects were observed in the zebrafish with a parn nonsense mutation. Intriguingly, the parn null mutants were viable and fertile, but turned out to only develop into males. Histological analysis of the gonads in the mutants and their wild type siblings revealed a defective maturation of gonadal cells in the parn null mutants. The results of this study highlight yet another emerging function of Parn, i.e., its role in oogenesis.
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Affiliation(s)
- Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Hanna De Saffel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Krithika Kalladka
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Kishan Prasad
- Department of Pathology, KS Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Patrick Sips
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India.
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8
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Revy P, Kannengiesser C, Bertuch AA. Genetics of human telomere biology disorders. Nat Rev Genet 2023; 24:86-108. [PMID: 36151328 DOI: 10.1038/s41576-022-00527-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2022] [Indexed: 01/24/2023]
Abstract
Telomeres are specialized nucleoprotein structures at the ends of linear chromosomes that prevent the activation of DNA damage response and repair pathways. Numerous factors localize at telomeres to regulate their length, structure and function, to avert replicative senescence or genome instability and cell death. In humans, Mendelian defects in several of these factors can result in abnormally short or dysfunctional telomeres, causing a group of rare heterogeneous premature-ageing diseases, termed telomeropathies, short-telomere syndromes or telomere biology disorders (TBDs). Here, we review the TBD-causing genes identified so far and describe their main functions associated with telomere biology. We present molecular aspects of TBDs, including genetic anticipation, phenocopy, incomplete penetrance and somatic genetic rescue, which underlie the complexity of these diseases. We also discuss the implications of phenotypic and genetic features of TBDs on fundamental aspects related to human telomere biology, ageing and cancer, as well as on diagnostic, therapeutic and clinical approaches.
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Affiliation(s)
- Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Nationale contre le Cancer, Paris, France.
- Université Paris Cité, Imagine Institute, Paris, France.
| | - Caroline Kannengiesser
- APHP Service de Génétique, Hôpital Bichat, Paris, France
- Inserm U1152, Université Paris Cité, Paris, France
| | - Alison A Bertuch
- Departments of Paediatrics and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
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9
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Batista LFZ, Dokal I, Parker R. Telomere biology disorders: time for moving towards the clinic? Trends Mol Med 2022; 28:882-891. [PMID: 36057525 PMCID: PMC9509473 DOI: 10.1016/j.molmed.2022.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/19/2022]
Abstract
Telomere biology disorders (TBDs) are a group of rare diseases caused by mutations that impair telomere maintenance. Mutations that cause reduced levels of TERC/hTR, the telomerase RNA component, are found in most TBD patients and include loss-of-function mutations in hTR itself, in hTR-binding proteins [NOP10, NHP2, NAF1, ZCCHC8, and dyskerin (DKC1)], and in proteins required for hTR processing (PARN). These patients show diverse clinical presentations that most commonly include bone marrow failure (BMF)/aplastic anemia (AA), pulmonary fibrosis, and liver cirrhosis. There are no curative therapies for TBD patients. An understanding of hTR biogenesis, maturation, and degradation has identified pathways and pharmacological agents targeting the poly(A) polymerase PAPD5, which adds 3'-oligoadenosine tails to hTR to promote hTR degradation, and TGS1, which modifies the 5'-cap structure of hTR to enhance degradation, as possible therapeutic approaches. Critical next steps will be clinical trials to establish the effectiveness and potential side effects of these compounds in TBD patients.
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Affiliation(s)
- Luis F Z Batista
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Center for Genome Integrity, Washington University in St. Louis, St. Louis, MO, USA; Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, USA.
| | - Inderjeet Dokal
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Roy Parker
- Department of Biochemistry and Biofrontiers Instiute, University of Colorado, Boulder, CO, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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10
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Nagpal N, Tai AK, Nandakumar J, Agarwal S. Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13. Nucleic Acids Res 2022; 50:9413-9425. [PMID: 36018809 PMCID: PMC9458449 DOI: 10.1093/nar/gkac706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/27/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
Mutations in DKC1 (encoding dyskerin) cause telomere diseases including dyskeratosis congenita (DC) by decreasing steady-state levels of TERC, the non-coding RNA component of telomerase. How DKC1 mutations variably impact numerous other snoRNAs remains unclear, which is a barrier to understanding disease mechanisms in DC beyond impaired telomere maintenance. Here, using DC patient iPSCs, we show that mutations in the dyskerin N-terminal extension domain (NTE) dysregulate scaRNA13. In iPSCs carrying the del37L NTE mutation or engineered to carry NTE mutations via CRISPR/Cas9, but not in those with C-terminal mutations, we found scaRNA13 transcripts with aberrant 3' extensions, as seen when the exoribonuclease PARN is mutated in DC. Biogenesis of scaRNA13 was rescued by repair of the del37L DKC1 mutation by genome-editing, or genetic or pharmacological inactivation of the polymerase PAPD5, which counteracts PARN. Inspection of the human telomerase cryo-EM structure revealed that in addition to mediating intermolecular dyskerin interactions, the NTE interacts with terminal residues of the associated snoRNA, indicating a role for this domain in 3' end definition. Our results provide mechanistic insights into the interplay of dyskerin and the PARN/PAPD5 axis in the biogenesis and accumulation of snoRNAs beyond TERC, broadening our understanding of ncRNA dysregulation in human diseases.
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Affiliation(s)
- Neha Nagpal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children's Hospital; Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; Department of Pediatrics, Harvard Medical School; Manton Center for Orphan Disease Research; Harvard Initiative in RNA Medicine; Boston, MA, USA
| | - Albert K Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
- Data Intensive Studies Center, Tufts University, Medford, MA, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Suneet Agarwal
- To whom correspondence should be addressed. Tel: +1 617 919 4610; Fax: +1 617 919 3359;
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11
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Kyritsis A, Papanastasi E, Kokkori I, Maragozidis P, Chatzileontiadou DSM, Pallaki P, Labrou M, Zarogiannis SG, Chrousos GP, Vlachakis D, Gourgoulianis KI, Balatsos NAA. Integrated Deadenylase Genetic Association Network and Transcriptome Analysis in Thoracic Carcinomas. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103102. [PMID: 35630580 PMCID: PMC9145511 DOI: 10.3390/molecules27103102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
The poly(A) tail at the 3′ end of mRNAs determines their stability, translational efficiency, and fate. The shortening of the poly(A) tail, and its efficient removal, triggers the degradation of mRNAs, thus, regulating gene expression. The process is catalyzed by a family of enzymes, known as deadenylases. As the dysregulation of gene expression is a hallmark of cancer, understanding the role of deadenylases has gained additional interest. Herein, the genetic association network shows that CNOT6 and CNOT7 are the most prevalent and most interconnected nodes in the equilibrated diagram. Subsequent silencing and transcriptomic analysis identifies transcripts possibly regulated by specific deadenylases. Furthermore, several gene ontologies are enriched by common deregulated genes. Given the potential concerted action and overlapping functions of deadenylases, we examined the effect of silencing a deadenylase on the remaining ones. Our results suggest that specific deadenylases target unique subsets of mRNAs, whilst at the same time, multiple deadenylases may affect the same mRNAs with overlapping functions.
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Affiliation(s)
- Athanasios Kyritsis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
| | - Eirini Papanastasi
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Ioanna Kokkori
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Department of Pneumonology-Oncology, Theagenio Cancer Hospital, 540 07 Thessaloniki, Greece
| | - Panagiotis Maragozidis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Demetra S. M. Chatzileontiadou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Paschalina Pallaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Maria Labrou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Sotirios G. Zarogiannis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Department of Physiology, Faculty of Medicine, University of Thessaly, Biopolis, 415 00 Larissa, Greece
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (G.P.C.); (D.V.)
- UNESCO Chair on Adolescent Health Care, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Center of Clinical, Experimental Surgery and Translational Research, Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Dimitrios Vlachakis
- University Research Institute of Maternal and Child Health and Precision Medicine, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (G.P.C.); (D.V.)
- UNESCO Chair on Adolescent Health Care, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Center of Clinical, Experimental Surgery and Translational Research, Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 118 55 Athens, Greece
| | - Konstantinos I. Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
| | - Nikolaos A. A. Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
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12
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Multisystemic Manifestations in Rare Diseases: The Experience of Dyskeratosis Congenita. Genes (Basel) 2022; 13:genes13030496. [PMID: 35328050 PMCID: PMC8953471 DOI: 10.3390/genes13030496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/27/2023] Open
Abstract
Dyskeratosis congenital (DC) is the first genetic syndrome described among telomeropathies. Its classical phenotype is characterized by the mucocutaneous triad of reticulated pigmentation of skin lace, nail dystrophy and oral leukoplakia. The clinical presentation, however, is heterogeneous and serious clinical complications include bone marrow failure, hematological and solid tumors. It may also involve immunodeficiencies, dental, pulmonary and liver disorders, and other minor complication. Dyskeratosis congenita shows marked genetic heterogeneity, as at least 14 genes are responsible for the shortening of telomeres characteristic of this disease. This review discusses clinical characteristics, molecular genetics, disease evolution, available therapeutic options and differential diagnosis of dyskeratosis congenita to provide an interdisciplinary and personalized medical assessment that includes family genetic counseling.
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13
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Stark C, Koskenvuo JW, Nykänen A, Seppälä EH, Myllykangas S, Lemström K, Raivio P. Monogenic gene variants in lung transplant recipients with usual interstitial pneumonia. ERJ Open Res 2022; 8:00583-2021. [PMID: 35083318 PMCID: PMC8784759 DOI: 10.1183/23120541.00583-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/09/2021] [Indexed: 12/03/2022] Open
Abstract
Aim The prevalence of monogenic disease-causing gene variants in lung transplant recipients with idiopathic pulmonary fibrosis is not fully known. Their impact on clinical outcomes before and after transplantation requires more evidence. Patients and methods We retrospectively performed sequence analysis of genes associated with pulmonary fibrosis in a cohort of 23 patients with histologically confirmed usual interstitial pneumonia that had previously undergone double lung transplantation. We evaluated the impact of confirmed molecular diagnoses on disease progression, clinical outcomes and incidence of acute rejection or chronic lung allograft dysfunction after transplantation. Results 15 patients out of 23 (65%) had a variant in a gene associated with interstitial lung disease. 11 patients (48%) received a molecular diagnosis, of which nine involved genes for telomerase function. Five diagnostic variants were found in the gene for Telomerase reverse transcriptase. Two of these variants, p.(Asp684Gly) and p.(Arg774*), seemed to be enriched in Finnish lung transplant recipients. Disease progression and the incidence of acute rejection and chronic lung allograft dysfunction was similar between patients with telomere-related disease and the rest of the study population. The incidence of renal or bone marrow insufficiency or skin malignancies did not differ between the groups. Conclusion Genetic variants are common in lung transplant recipients with pulmonary fibrosis and are most often related to telomerase function. A molecular diagnosis for telomeropathy does not seem to impact disease progression or the risk of complications or allograft dysfunction after transplantation. A molecular diagnosis is common in lung transplant recipients with usual interstitial pneumonia and frequently reveals variants in genes related to telomerase function. This finding is not associated with increased risk of allograft dysfunction.https://bit.ly/30ucMQy
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14
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Galati A, Scatolini L, Micheli E, Bavasso F, Cicconi A, Maccallini P, Chen L, Roake CM, Schoeftner S, Artandi SE, Gatti M, Cacchione S, Raffa GD. The S-adenosylmethionine analog sinefungin inhibits the trimethylguanosine synthase TGS1 to promote telomerase activity and telomere lengthening. FEBS Lett 2021; 596:42-52. [PMID: 34817067 DOI: 10.1002/1873-3468.14240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 10/16/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022]
Abstract
Mutations in many genes that control the expression, the function, or the stability of telomerase cause telomere biology disorders (TBDs), such as dyskeratosis congenita, pulmonary fibrosis, and aplastic anemia. Mutations in a subset of the genes associated with TBDs cause reductions of the telomerase RNA moiety hTR, thus limiting telomerase activity. We have recently found that loss of the trimethylguanosine synthase TGS1 increases both hTR abundance and telomerase activity and leads to telomere elongation. Here, we show that treatment with the S-adenosylmethionine analog sinefungin inhibits TGS1 activity, increases the hTR levels, and promotes telomere lengthening in different cell types. Our results hold promise for restoring telomere length in stem and progenitor cells from TBD patients with reduced hTR levels.
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Affiliation(s)
- Alessandra Galati
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Livia Scatolini
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Emanuela Micheli
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Francesca Bavasso
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Alessandro Cicconi
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Paolo Maccallini
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Lu Chen
- Cancer Signaling and Epigenetics Program-Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Caitlin M Roake
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli studi di Trieste, Italy
| | - Steven E Artandi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy.,Istituto di Biologia e Patologia Molecolari del CNR, Roma, Italy
| | - Stefano Cacchione
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Grazia D Raffa
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
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15
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Nanjappa DP, Babu N, Khanna-Gupta A, O'Donohue MF, Sips P, Chakraborty A. Poly (A)-specific ribonuclease (PARN): More than just "mRNA stock clearing". Life Sci 2021; 285:119953. [PMID: 34520768 DOI: 10.1016/j.lfs.2021.119953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the balance between the synthesis and the degradation decides the steady-state levels of messenger RNAs (mRNA). The removal of adenosine residues from the poly(A) tail, called deadenylation, is the first and the most crucial step in the process of mRNA degradation. Poly (A)-specific ribonuclease (PARN) is one such enzyme that catalyses the process of deadenylation. Although PARN has been primarily known as the regulator of the mRNA stability, recent evidence clearly suggests several other functions of PARN, including a role in embryogenesis, oocyte maturation, cell-cycle progression, telomere biology, non-coding RNA maturation and ribosome biogenesis. Also, deregulated PARN activity is shown to be a hallmark of specific disease conditions. Pathogenic variants in the PARN gene have been observed in various cancers and inherited bone marrow failure syndromes. The focus in this review is to highlight the emerging functions of PARN, particularly in the context of human diseases.
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Affiliation(s)
- Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India
| | - Arati Khanna-Gupta
- Consortium of Rare Genetic and Bone Marrow Disorders, India network@NitteDU, NITTE (Deemed to be University, Deralakatte, Mangaluru, India
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative CBI, Université de Toulouse- CNRS- UPS- Toulouse-, Dynamics and Disorders of Ribosome Synthesis, Toulouse, France
| | - Patrick Sips
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India.
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16
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Benyelles M, O'Donohue MF, Kermasson L, Lainey E, Borie R, Lagresle-Peyrou C, Nunes H, Cazelles C, Fourrage C, Ollivier E, Marcais A, Gamez AS, Morice-Picard F, Caillaud D, Pottier N, Ménard C, Ba I, Fernandes A, Crestani B, de Villartay JP, Gleizes PE, Callebaut I, Kannengiesser C, Revy P. NHP2 deficiency impairs rRNA biogenesis and causes pulmonary fibrosis and Høyeraal-Hreidarsson syndrome. Hum Mol Genet 2021; 29:907-922. [PMID: 31985013 DOI: 10.1093/hmg/ddaa011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
Telomeres are nucleoprotein structures at the end of chromosomes. The telomerase complex, constituted of the catalytic subunit TERT, the RNA matrix hTR and several cofactors, including the H/ACA box ribonucleoproteins Dyskerin, NOP10, GAR1, NAF1 and NHP2, regulates telomere length. In humans, inherited defects in telomere length maintenance are responsible for a wide spectrum of clinical premature aging manifestations including pulmonary fibrosis (PF), dyskeratosis congenita (DC), bone marrow failure and predisposition to cancer. NHP2 mutations have been so far reported only in two patients with DC. Here, we report the first case of Høyeraal-Hreidarsson syndrome, the severe form of DC, caused by biallelic missense mutations in NHP2. Additionally, we identified three unrelated patients with PF carrying NHP2 heterozygous mutations. Strikingly, one of these patients acquired a somatic mutation in the promoter of TERT that likely conferred a selective advantage in a subset of blood cells. Finally, we demonstrate that a functional deficit of human NHP2 affects ribosomal RNA biogenesis. Together, our results broaden the functional consequences and clinical spectrum of NHP2 deficiency.
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Affiliation(s)
- Maname Benyelles
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laëtitia Kermasson
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Elodie Lainey
- Hematology Laboratory, Robert DEBRE Hospital-APHP and INSERM UMR 1131-Hematology University Institute-Denis Diderot School of Medicine, Paris, France
| | - Raphael Borie
- APHP, Hôpital Bichat, Service de Pneumologie A, DHU FIRE, Paris, France.,INSERM, Unité 1152, Paris, France.,Université Paris Diderot, Paris, France
| | - Chantal Lagresle-Peyrou
- Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, Paris, France.,University of Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Hilario Nunes
- Service de Pneumologie, Centre de Référence des Maladies Pulmonaires rares, Hôpital Avicenne, AP-HP, INSERM 1272, Université Paris 13, Bobigny, France
| | - Clarisse Cazelles
- Service d'hématologie adulte, Hôpital Necker- Enfants malades, Paris, France
| | - Cécile Fourrage
- INSERM UMR 1163, Genomics platform, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Genomic Core Facility, Imagine Institute-Structure Fédérative de Recherche Necker, INSERM U1163, Paris, France
| | - Emmanuelle Ollivier
- INSERM UMR 1163, Genomics platform, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Genomic Core Facility, Imagine Institute-Structure Fédérative de Recherche Necker, INSERM U1163, Paris, France
| | - Ambroise Marcais
- Service d'hématologie Adultes, Hôpital Necker-Enfants Malades, Assistance publique hôpitaux de Paris, Paris, France, Laboratoire d'onco-hématologie, Institut Necker-Enfants Malades, INSERM U1151, Université Paris Descartes, Paris, France
| | | | - Fanny Morice-Picard
- Service de Dermatologie Pédiatrique, Centre de Reference des Maladies Rares de la Peau, CHU de Bordeaux, Bordeaux F-33076, France
| | - Denis Caillaud
- Service de Pneumologie-Allergologie, Hôpital Gabriel Montpied, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Nicolas Pottier
- Univ. Lille, CHU Lille, Institut Pasteur de Lille, EA4483-IMPECS, Lille, France
| | - Christelle Ménard
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Ibrahima Ba
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Alicia Fernandes
- Biological Resources Center, Structure Fédérative de Recherche Necker, INSERM US24, CNRS UMS3633, Assistance Publique des Hôpitaux de Paris and Institut Imagine, Paris, France
| | - Bruno Crestani
- APHP, Hôpital Bichat, Service de Pneumologie A, DHU FIRE, Paris, France
| | - Jean-Pierre de Villartay
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Caroline Kannengiesser
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
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17
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Belaya Z, Golounina O, Nikitin A, Tarbaeva N, Pigarova E, Mamedova E, Vorontsova M, Shafieva I, Demina I, Van Hul W. Multiple bilateral hip fractures in a patient with dyskeratosis congenita caused by a novel mutation in the PARN gene. Osteoporos Int 2021; 32:1227-1231. [PMID: 33244623 DOI: 10.1007/s00198-020-05758-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/20/2020] [Indexed: 10/22/2022]
Abstract
We report a case of a young male patient with clinical signs of dyskeratosis congenita who presented with multiple bilateral low-traumatic hip fractures. Whole exome sequencing (WES) showed a previously unreported mutation in the poly(A)-specific ribonuclease (PARN) gene. Zoledronic acid 5 mg over 3 years was effective at preventing further fractures. A male patient was referred to our clinic at age 24 due to multiple bilateral hip fractures. At the time of admission, the patient's height was 160 cm and weight 40 kg; bone mineral density (BMD) at the lumbar spine was normal (L1-L4 0.0 Z-score). The patient was found to have abnormal skin pigmentation, hyperkeratosis of palms and soles, nail dystrophy, and signs of bone marrow failure (BMF). Bone fragility first presented at 5 years old with a wrist fracture, followed by multiple bilateral low-traumatic hip fractures without falls from 14 to 24 years. WES showed a previously unreported mutation (NM_002582.3: c.1652delA; p.His551fs) in the poly(A)-specific ribonuclease (PARN) gene. Flow fish telomere measurement result was 5.9 (reference range 8.0-12.6), which is consistent with the DC diagnosis. Permanent fixation with internal metal rods and zoledronic acid 5 mg over 3 years was effective at preventing further fractures over 4 years of follow-up. Additionally, BMF did not progress over 4 years of observation. DC associated with PARN gene mutations might predispose to low-traumatic multiple hip fractures in adolescents and young adults. Treatment with zoledronic acid in this case was effective and safe at preventing further fractures.
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Affiliation(s)
- Z Belaya
- Endocrinology Research Centre, Moscow, Russia.
| | - O Golounina
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - A Nikitin
- Federal Research and Clinical Center FMBA of Russia, Moscow, Russia
| | - N Tarbaeva
- Endocrinology Research Centre, Moscow, Russia
| | - E Pigarova
- Endocrinology Research Centre, Moscow, Russia
| | - E Mamedova
- Endocrinology Research Centre, Moscow, Russia
| | | | - I Shafieva
- Department of Endocrinology and Osteoporosis, Clinics of the Federal State Budgetary Educational Institution of Higher Education "Samara State Medical University" of the Ministry of Health of the Russian Federation, Samara, Russia
| | - I Demina
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - W Van Hul
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
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18
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Chemical inhibition of PAPD5/7 rescues telomerase function and hematopoiesis in dyskeratosis congenita. Blood Adv 2021; 4:2717-2722. [PMID: 32559291 DOI: 10.1182/bloodadvances.2020001848] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/15/2020] [Indexed: 12/24/2022] Open
Abstract
Dyskeratosis congenita (DC) is a pediatric bone marrow failure syndrome caused by germline mutations in telomere biology genes. Mutations in DKC1 (the most commonly mutated gene in DC), the 3' region of TERC, and poly(A)-specific ribonuclease (PARN) cause reduced levels of the telomerase RNA component (TERC) by reducing its stability and accelerating TERC degradation. We have previously shown that depleting wild-type DKC1 levels by RNA interference or expression of the disease-associated A353V mutation in the DKC1 gene leads to decay of TERC, modulated by 3'-end oligoadenylation by noncanonical poly(A) polymerase 5 (PAPD5) followed by 3' to 5' degradation by EXOSC10. Furthermore, the constitutive genetic silencing of PAPD5 is sufficient to rescue TERC levels, restore telomerase function, and elongate telomeres in DKC1_A353V mutant human embryonic stem cells (hESCs). Here, we tested a novel PAPD5/7 inhibitor (RG7834), which was originally discovered in screens against hepatitis B viral loads in hepatic cells. We found that treatment with RG7834 rescues TERC levels, restores correct telomerase localization in DKC1 and PARN-depleted cells, and is sufficient to elongate telomeres in DKC1_A353V hESCs. Finally, treatment with RG7834 significantly improved definitive hematopoietic potential from DKC1_A353V hESCs, indicating that the chemical inhibition of PAPD5 is a potential therapy for patients with DC and reduced TERC levels.
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19
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Telomere biology disorder prevalence and phenotypes in adults with familial hematologic and/or pulmonary presentations. Blood Adv 2021; 4:4873-4886. [PMID: 33035329 DOI: 10.1182/bloodadvances.2020001721] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Telomere biology disorders (TBDs) present heterogeneously, ranging from infantile bone marrow failure associated with very short telomeres to adult-onset interstitial lung disease (ILD) with normal telomere length. Yield of genetic testing and phenotypic spectra for TBDs caused by the expanding list of telomere genes in adults remain understudied. Thus, we screened adults aged ≥18 years with a personal and/or family history clustering hematologic disorders and/or ILD enrolled on The University of Chicago Inherited Hematologic Disorders Registry for causative variants in 13 TBD genes. Sixteen (10%) of 153 probands carried causative variants distributed among TERT (n = 6), TERC (n = 4), PARN (n = 5), or RTEL1 (n = 1), of which 19% were copy number variants. The highest yield (9 of 22 [41%]) was in families with mixed hematologic and ILD presentations, suggesting that ILD in hematology populations and hematologic abnormalities in ILD populations warrant TBD genetic testing. Four (3%) of 117 familial hematologic disorder families without ILD carried TBD variants, making TBD second to only DDX41 in frequency for genetic diagnoses in this population. Phenotypes of 17 carriers with heterozygous PARN variants included 4 (24%) with hematologic abnormalities, 67% with lymphocyte telomere lengths measured by flow cytometry and fluorescence in situ hybridization at or above the 10th percentile, and a high penetrance for ILD. Alternative etiologies for cytopenias and/or ILD such as autoimmune features were noted in multiple TBD families, emphasizing the need to maintain clinical suspicion for a TBD despite the presence of alternative explanations.
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20
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Nagpal N, Agarwal S. Telomerase RNA processing: Implications for human health and disease. Stem Cells 2020; 38:10.1002/stem.3270. [PMID: 32875693 PMCID: PMC7917152 DOI: 10.1002/stem.3270] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/11/2020] [Indexed: 11/11/2022]
Abstract
Telomeres are composed of repetitive DNA sequences that are replenished by the enzyme telomerase to maintain the self-renewal capacity of stem cells. The RNA component of human telomerase (TERC) is the essential template for repeat addition by the telomerase reverse transcriptase (TERT), and also serves as a scaffold for several factors comprising the telomerase ribonucleoprotein (RNP). Unique features of TERC regulation and function have been informed not only through biochemical studies but also through human genetics. Disease-causing mutations impact TERC biogenesis at several levels including RNA transcription, post-transcriptional processing, folding, RNP assembly, and trafficking. Defects in TERC reduce telomerase activity and impair telomere maintenance, thereby causing a spectrum of degenerative diseases called telomere biology disorders (TBDs). Deciphering mechanisms of TERC dysregulation have led to a broader understanding of noncoding RNA biology, and more recently points to new therapeutic strategies for TBDs. In this review, we summarize over two decades of work revealing mechanisms of human telomerase RNA biogenesis, and how its disruption causes human diseases.
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Affiliation(s)
- Neha Nagpal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Initiative for RNA Medicine and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Boston, Massachusetts
| | - Suneet Agarwal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Initiative for RNA Medicine and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Boston, Massachusetts
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21
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Yan YB. Diverse functions of deadenylases in DNA damage response and genomic integrity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1621. [PMID: 32790161 DOI: 10.1002/wrna.1621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022]
Abstract
DNA damage response (DDR) is a coordinated network of diverse cellular processes including the detection, signaling, and repair of DNA lesions, the adjustment of metabolic network and cell fate determination. To deal with the unavoidable DNA damage caused by either endogenous or exogenous stresses, the cells need to reshape the gene expression profile to allow efficient transcription and translation of DDR-responsive messenger RNAs (mRNAs) and to repress the nonessential mRNAs. A predominant method to adjust RNA fate is achieved by modulating the 3'-end oligo(A) or poly(A) length via the opposing actions of polyadenylation and deadenylation. Poly(A)-specific ribonuclease (PARN) and the carbon catabolite repressor 4 (CCR4)-Not complex, the major executors of deadenylation, are indispensable to DDR and genomic integrity in eukaryotic cells. PARN modulates cell cycle progression by regulating the stabilities of mRNAs and microRNA (miRNAs) involved in the p53 pathway and contributes to genomic stability by affecting the biogenesis of noncoding RNAs including miRNAs and telomeric RNA. The CCR4-Not complex is involved in diverse pathways of DDR including transcriptional regulation, signaling pathways, mRNA stabilities, translation regulation, and protein degradation. The RNA targets of deadenylases are tuned by the DDR signaling pathways, while in turn the deadenylases can regulate the levels of DNA damage-responsive proteins. The mutual feedback between deadenylases and the DDR signaling pathways allows the cells to precisely control DDR by dynamically adjusting the levels of sensors and effectors of the DDR signaling pathways. Here, the diverse functions of deadenylases in DDR are summarized and the underlying mechanisms are proposed according to recent findings. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
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22
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Lardelli RM, Lykke-Andersen J. Competition between maturation and degradation drives human snRNA 3' end quality control. Genes Dev 2020; 34:989-1001. [PMID: 32499401 PMCID: PMC7328512 DOI: 10.1101/gad.336891.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/29/2020] [Indexed: 12/11/2022]
Abstract
Polymerases and exonucleases act on 3' ends of nascent RNAs to promote their maturation or degradation but how the balance between these activities is controlled to dictate the fates of cellular RNAs remains poorly understood. Here, we identify a central role for the human DEDD deadenylase TOE1 in distinguishing the fates of small nuclear (sn)RNAs of the spliceosome from unstable genome-encoded snRNA variants. We found that TOE1 promotes maturation of all regular RNA polymerase II transcribed snRNAs of the major and minor spliceosomes by removing posttranscriptional oligo(A) tails, trimming 3' ends, and preventing nuclear exosome targeting. In contrast, TOE1 promotes little to no maturation of tested U1 variant snRNAs, which are instead targeted by the nuclear exosome. These observations suggest that TOE1 is positioned at the center of a 3' end quality control pathway that selectively promotes maturation and stability of regular snRNAs while leaving snRNA variants unprocessed and exposed to degradation in what could be a widespread mechanism of RNA quality control given the large number of noncoding RNAs processed by DEDD deadenylases.
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Affiliation(s)
- Rea M Lardelli
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
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23
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Dejene EA, Li Y, Showkatian Z, Ling H, Seto E. Regulation of poly(a)-specific ribonuclease activity by reversible lysine acetylation. J Biol Chem 2020; 295:10255-10270. [PMID: 32457045 DOI: 10.1074/jbc.ra120.012552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN) is a 3'-exoribonuclease that plays an important role in regulating the stability and maturation of RNAs. Recently, PARN has been found to regulate the maturation of the human telomerase RNA component (hTR), a noncoding RNA required for telomere elongation. Specifically, PARN cleaves the 3'-end of immature, polyadenylated hTR to form the mature, nonpolyadenylated template. Despite PARN's critical role in mediating telomere maintenance, little is known about how PARN's function is regulated by post-translational modifications. In this study, using shRNA- and CRISPR/Cas9-mediated gene silencing and knockout approaches, along with 3'-exoribonuclease activity assays and additional biochemical methods, we examined whether PARN is post-translationally modified by acetylation and what effect acetylation has on PARN's activity. We found PARN is primarily acetylated by the acetyltransferase p300 at Lys-566 and deacetylated by sirtuin1 (SIRT1). We also revealed how acetylation of PARN can decrease its enzymatic activity both in vitro, using a synthetic RNA probe, and in vivo, by quantifying endogenous levels of adenylated hTR. Furthermore, we also found that SIRT1 can regulate levels of adenylated hTR through PARN. The findings of our study uncover a mechanism by which PARN acetylation and deacetylation regulate its enzymatic activity as well as levels of mature hTR. Thus, PARN's acetylation status may play a role in regulating telomere length.
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Affiliation(s)
- Eden A Dejene
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.,George Washington University Cancer Center, Washington, D.C., USA
| | - Yixuan Li
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.,George Washington University Cancer Center, Washington, D.C., USA
| | - Zahra Showkatian
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.,George Washington University Cancer Center, Washington, D.C., USA
| | - Hongbo Ling
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.,George Washington University Cancer Center, Washington, D.C., USA
| | - Edward Seto
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA .,George Washington University Cancer Center, Washington, D.C., USA
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24
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Small-Molecule PAPD5 Inhibitors Restore Telomerase Activity in Patient Stem Cells. Cell Stem Cell 2020; 26:896-909.e8. [PMID: 32320679 DOI: 10.1016/j.stem.2020.03.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/21/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022]
Abstract
Genetic lesions that reduce telomerase activity inhibit stem cell replication and cause a range of incurable diseases, including dyskeratosis congenita (DC) and pulmonary fibrosis (PF). Modalities to restore telomerase in stem cells throughout the body remain unclear. Here, we describe small-molecule PAPD5 inhibitors that demonstrate telomere restoration in vitro, in stem cell models, and in vivo. PAPD5 is a non-canonical polymerase that oligoadenylates and destabilizes telomerase RNA component (TERC). We identified BCH001, a specific PAPD5 inhibitor that restored telomerase activity and telomere length in DC patient induced pluripotent stem cells. When human blood stem cells engineered to carry DC-causing PARN mutations were xenotransplanted into immunodeficient mice, oral treatment with a repurposed PAPD5 inhibitor, the dihydroquinolizinone RG7834, rescued TERC 3' end maturation and telomere length. These findings pave the way for developing systemic telomere therapeutics to counteract stem cell exhaustion in DC, PF, and possibly other aging-related diseases.
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25
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Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN). Cells 2020; 9:cells9010162. [PMID: 31936572 PMCID: PMC7017053 DOI: 10.3390/cells9010162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 12/21/2022] Open
Abstract
Translation is spatiotemporally regulated and endoplasmic reticulum (ER)-associated mRNAs are generally in efficient translation. It is unclear whether the ER-associated mRNAs are deadenylated or degraded on the ER surface in situ or in the cytosol. Here, we showed that ER possessed active deadenylases, particularly the poly(A)-specific ribonuclease (PARN), in common cell lines and mouse tissues. Consistently, purified recombinant PARN exhibited a strong ability to insert into the Langmuir monolayer and liposome. ER-anchored PARN was found to be able to reshape the poly(A) length profile of the ER-associated RNAs by suppressing long poly(A) tails without significantly influencing the cytosolic RNAs. The shortening of long poly(A) tails did not affect global translation efficiency, which suggests that the non-specific action of PARN towards long poly(A) tails was beyond the scope of translation regulation on the ER surface. Transcriptome sequencing analysis indicated that the ER-anchored PARN trigged the degradation of a small subset of ER-enriched transcripts. The ER-anchored PARN modulated the translation of its targets by redistributing ribosomes to heavy polysomes, which suggests that PARN might play a role in dynamic ribosome reallocation. During DNA damage response, MK2 phosphorylated PARN-Ser557 to modulate PARN translocation from the ER to cytosol. The ER-anchored PARN modulated DNA damage response and thereby cell viability by promoting the decay of ER-associated MDM2 transcripts with low ribosome occupancy. These findings revealed that highly regulated communication between mRNA degradation rate and translation efficiency is present on the ER surface in situ and PARN might contribute to this communication by modulating the dynamic ribosome reallocation between transcripts with low and high ribosome occupancies.
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26
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Nieto B, Gaspar SG, Moriggi G, Pestov DG, Bustelo XR, Dosil M. Identification of distinct maturation steps involved in human 40S ribosomal subunit biosynthesis. Nat Commun 2020; 11:156. [PMID: 31919354 PMCID: PMC6952385 DOI: 10.1038/s41467-019-13990-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/11/2019] [Indexed: 02/02/2023] Open
Abstract
Technical problems intrinsic to the purification of preribosome intermediates have limited our understanding of ribosome biosynthesis in humans. Addressing this issue is important given the implication of this biological process in human disease. Here we report a preribosome purification and tagging strategy that overcomes some of the existing technical difficulties. Using these tools, we find that the pre-40S precursors go through two distinct maturation phases inside the nucleolus and follow a regulatory step that precedes late maturation in the cytoplasm. This regulatory step entails the intertwined actions of both PARN (a metazoan-specific ribonuclease) and RRP12 (a phylogenetically conserved 40S biogenesis factor that has acquired additional functional features in higher eukaryotes). Together, these results demonstrate the usefulness of this purification method for the dissection of ribosome biogenesis in human cells. They also identify distinct maturation stages and metazoan-specific regulatory mechanisms involved in the generation of the human 40S ribosomal subunit. Ribosome synthesis is a complex multi-step process. Here the authors present a method that allows the efficient isolation and characterization of the preribosomal complexes formed along the entire ribosome synthesis pathway in human cells.
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Affiliation(s)
- Blanca Nieto
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Sonia G Gaspar
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Giulia Moriggi
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08084, USA
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Departamento de Bioquímica y Biología Molecular, University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.
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27
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Lauhasurayotin S, Cuvelier GD, Klaassen RJ, Fernandez CV, Pastore YD, Abish S, Rayar M, Steele M, Jardine L, Breakey VR, Brossard J, Sinha R, Silva M, Goodyear L, Lipton JH, Michon B, Corriveau-Bourque C, Sung L, Shabanova I, Li H, Zlateska B, Dhanraj S, Cada M, Scherer SW, Dror Y. Reanalysing genomic data by normalized coverage values uncovers CNVs in bone marrow failure gene panels. NPJ Genom Med 2019; 4:30. [PMID: 31839986 PMCID: PMC6901453 DOI: 10.1038/s41525-019-0104-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/04/2019] [Indexed: 11/09/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) are genetically heterogeneous disorders with cytopenia. Many IBMFSs also feature physical malformations and an increased risk of cancer. Point mutations can be identified in about half of patients. Copy number variation (CNVs) have been reported; however, the frequency and spectrum of CNVs are unknown. Unfortunately, current genome-wide methods have major limitations since they may miss small CNVs or may have low sensitivity due to low read depths. Herein, we aimed to determine whether reanalysis of NGS panel data by normalized coverage value could identify CNVs and characterize them. To address this aim, DNA from IBMFS patients was analyzed by a NGS panel assay of known IBMFS genes. After analysis for point mutations, heterozygous and homozygous CNVs were searched by normalized read coverage ratios and specific thresholds. Of the 258 tested patients, 91 were found to have pathogenic point variants. NGS sample data from 165 patients without pathogenic point mutations were re-analyzed for CNVs; 10 patients were found to have deletions. Diamond Blackfan anemia genes most commonly exhibited heterozygous deletions, and included RPS19, RPL11, and RPL5. A diagnosis of GATA2-related disorder was made in a patient with myelodysplastic syndrome who was found to have a heterozygous GATA2 deletion. Importantly, homozygous FANCA deletion were detected in a patient who could not be previously assigned a specific syndromic diagnosis. Lastly, we identified compound heterozygousity for deletions and pathogenic point variants in RBM8A and PARN genes. All deletions were validated by orthogonal methods. We conclude that careful analysis of normalized coverage values can detect CNVs in NGS panels and should be considered as a standard practice prior to do further investigations.
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Affiliation(s)
- Supanun Lauhasurayotin
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Geoff D Cuvelier
- 3Pediatric Hematology-Oncology-Bone Marrow Transplantation, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB Canada
| | - Robert J Klaassen
- 4Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON Canada
| | | | | | - Sharon Abish
- 7Pediatric Hematology Oncology, Montreal Children's Hospital, Montreal, QC Canada
| | - Meera Rayar
- 8Division of Hematology/Oncology, UBC & B.C. Children's Hospital, Vancouver, BC Canada
| | | | - Lawrence Jardine
- 10Children's Hospital, London Health Sciences Centre, London, ON Canada
| | - Vicky R Breakey
- 11Department of Pediatrics, McMaster University, Hamilton, ON Canada
| | - Josee Brossard
- 12Centre hospitalier universitaire, Sherbrooke, QC Canada
| | - Roona Sinha
- 13Royal University Hospital, Saskatoon, SK Canada
| | | | - Lisa Goodyear
- 15Pediatric Hematology/Oncology, Janeway Child Health Centre, St. John's, NF Canada
| | - Jeffrey H Lipton
- 16Allogeneic Blood and Marrow Transplant Program, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON Canada
| | - Bruno Michon
- 17Centre Hospitalier Universitaire de Quebec, Sainte-Foy, QC Canada
| | | | - Lillian Sung
- 19Population Health Sciences, Research Institute, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Iren Shabanova
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Hongbing Li
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Bozana Zlateska
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Santhosh Dhanraj
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,20Institute of Medical Science, University of Toronto, Toronto, ON Canada
| | - Michaela Cada
- 2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Stephen W Scherer
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,21McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Yigal Dror
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada.,20Institute of Medical Science, University of Toronto, Toronto, ON Canada
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28
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1571. [PMID: 31657151 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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29
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Son A, Park JE, Kim VN. PARN and TOE1 Constitute a 3' End Maturation Module for Nuclear Non-coding RNAs. Cell Rep 2019; 23:888-898. [PMID: 29669292 DOI: 10.1016/j.celrep.2018.03.089] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 12/27/2017] [Accepted: 03/20/2018] [Indexed: 10/17/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A) tails. Rather, they promote the maturation of nuclear small non-coding RNAs (ncRNAs). PARN and TOE1 act redundantly on some ncRNAs, most prominently small Cajal body-specific RNAs (scaRNAs). scaRNAs are strongly downregulated when PARN and TOE1 are compromised together, leading to defects in small nuclear RNA (snRNA) pseudouridylation. They also function redundantly in the biogenesis of telomerase RNA component (TERC), which shares sequence motifs found in H/ACA box scaRNAs. Our findings extend the knowledge of nuclear ncRNA biogenesis, and they provide insights into the pathology of PARN/TOE1-associated genetic disorders whose therapeutic treatments are currently unavailable.
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Affiliation(s)
- Ahyeon Son
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Eun Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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30
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Dodson LM, Baldan A, Nissbeck M, Gunja SMR, Bonnen PE, Aubert G, Birchansky S, Virtanen A, Bertuch AA. From incomplete penetrance with normal telomere length to severe disease and telomere shortening in a family with monoallelic and biallelic PARN pathogenic variants. Hum Mutat 2019; 40:2414-2429. [PMID: 31448843 DOI: 10.1002/humu.23898] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/24/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
PARN encodes poly(A)-specific ribonuclease. Biallelic and monoallelic PARN variants are associated with Hoyeraal-Hreidarsson syndrome/dyskeratosis congenita and idiopathic pulmonary fibrosis (IPF), respectively. The molecular features associated with incomplete penetrance of PARN-associated IPF have not been described. We report a family with a rare missense, p.Y91C, and a novel insertion, p.(I274*), PARN variant. We found PARN p.Y91C had reduced deadenylase activity and the p.(I274*) transcript was depleted. Detailed analysis of the consequences of these variants revealed that, while PARN protein was lowest in the severely affected biallelic child who had the shortest telomeres, it was also reduced in his mother with the p.(I274*) variant but telomeres at the 50th percentile. Increased adenylation of telomerase RNA, human telomerase RNA, and certain small nucleolar RNAs, and impaired ribosomal RNA maturation were observed in cells derived from the severely affected biallelic carrier, but not in the other, less affected biallelic carrier, who had less severely shortened telomeres, nor in the monoallelic carriers who were unaffected and had telomeres ranging from the 1st to the 50th percentiles. We identified hsa-miR-202-5p as a potential negative regulator of PARN. We propose one or more genetic modifiers influence the impact of PARN variants on its targets and this underlies incomplete penetrance of PARN-associated disease.
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Affiliation(s)
- Lois M Dodson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alessandro Baldan
- Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Mikael Nissbeck
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sethu M R Gunja
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Geraldine Aubert
- Repeat Diagnostics Inc., North Vancouver, British Columbia, Canada
| | - Sherri Birchansky
- Department of Radiology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Anders Virtanen
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Alison A Bertuch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
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31
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Niewisch MR, Savage SA. An update on the biology and management of dyskeratosis congenita and related telomere biology disorders. Expert Rev Hematol 2019; 12:1037-1052. [PMID: 31478401 DOI: 10.1080/17474086.2019.1662720] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Telomere biology disorders (TBDs) encompass a group of illnesses caused by germline mutations in genes regulating telomere maintenance, resulting in very short telomeres. Possible TBD manifestations range from complex multisystem disorders with onset in childhood such as dyskeratosis congenita (DC), Hoyeraal-Hreidarsson syndrome, Revesz syndrome and Coats plus to adults presenting with one or two DC-related features.Areas covered: The discovery of multiple genetic causes and inheritance patterns has led to the recognition of a spectrum of clinical features affecting multiple organ systems. Patients with DC and associated TBDs are at high risk of bone marrow failure, cancer, liver and pulmonary disease. Recently, vascular diseases, including pulmonary arteriovenous malformations and gastrointestinal telangiectasias, have been recognized as additional manifestations. Diagnostics include detection of very short leukocyte telomeres and germline genetic testing. Hematopoietic cell transplantation and lung transplantation are the only current therapeutic modalities but are complicated by numerous comorbidities. This review summarizes the pathophysiology underlying TBDs, associated clinical features, management recommendations and therapeutic options.Expert opinion: Understanding TBDs as complex, multisystem disorders with a heterogenous genetic background and diverse phenotypes, highlights the importance of clinical surveillance and the urgent need to develop new therapeutic strategies to improve health outcomes.
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Affiliation(s)
- Marena R Niewisch
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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32
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Deng T, Huang Y, Weng K, Lin S, Li Y, Shi G, Chen Y, Huang J, Liu D, Ma W, Songyang Z. TOE1 acts as a 3' exonuclease for telomerase RNA and regulates telomere maintenance. Nucleic Acids Res 2019; 47:391-405. [PMID: 30371886 PMCID: PMC6326811 DOI: 10.1093/nar/gky1019] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 10/14/2018] [Indexed: 12/14/2022] Open
Abstract
In human cells, telomeres are elongated by the telomerase complex that contains the reverse transcriptase hTERT and RNA template TERC/hTR. Poly(A)-specific ribonuclease (PARN) is known to trim hTR precursors by removing poly(A) tails. However, the precise mechanism of hTR 3′ maturation remains largely unknown. Target of Egr1 (TOE1) is an Asp-Glu-Asp-Asp (DEDD) domain containing deadenylase that is mutated in the human disease Pontocerebella Hypoplasia Type 7 (PCH7) and implicated in snRNA and hTR processing. We have previously found TOE1 to localize specifically in Cajal bodies, where telomerase RNP complex assembly takes place. In this study, we showed that TOE1 could interact with hTR and the telomerase complex. TOE1-deficient cells accumulated hTR precursors, including oligoadenylated and 3′-extended forms, which was accompanied by impaired telomerase activity and shortened telomeres. Telomerase activity in TOE1-deficient cells could be rescued by wild-type TOE1 but not the catalytically inactive mutant. Our results suggest that hTR 3′ end processing likely involves multiple exonucleases that work in parallel and/or sequentially, where TOE1 may function non-redundantly as a 3′-to-5′ exonuclease in conjunction with PARN. Our study highlights a mechanistic link between TOE1 mutation, improper hTR processing and telomere dysfunction in diseases such as PCH7.
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Affiliation(s)
- Tingting Deng
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Yan Huang
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Kai Weng
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou 510623, China
| | - Song Lin
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Yujing Li
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Guang Shi
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Yali Chen
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Junjiu Huang
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Dan Liu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Wenbin Ma
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhou Songyang
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China.,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Benyelles M, Episkopou H, O'Donohue M, Kermasson L, Frange P, Poulain F, Burcu Belen F, Polat M, Bole‐Feysot C, Langa‐Vives F, Gleizes P, de Villartay J, Callebaut I, Decottignies A, Revy P. Impaired telomere integrity and rRNA biogenesis in PARN-deficient patients and knock-out models. EMBO Mol Med 2019; 11:e10201. [PMID: 31273937 PMCID: PMC6609912 DOI: 10.15252/emmm.201810201] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/24/2019] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
PARN, poly(A)-specific ribonuclease, regulates the turnover of mRNAs and the maturation and stabilization of the hTR RNA component of telomerase. Biallelic PARN mutations were associated with Høyeraal-Hreidarsson (HH) syndrome, a rare telomere biology disorder that, because of its severity, is likely not exclusively due to hTR down-regulation. Whether PARN deficiency was affecting the expression of telomere-related genes was still unclear. Using cells from two unrelated HH individuals carrying novel PARN mutations and a human PARN knock-out (KO) cell line with inducible PARN complementation, we found that PARN deficiency affects both telomere length and stability and down-regulates the expression of TRF1, TRF2, TPP1, RAP1, and POT1 shelterin transcripts. Down-regulation of dyskerin-encoding DKC1 mRNA was also observed and found to result from p53 activation in PARN-deficient cells. We further showed that PARN deficiency compromises ribosomal RNA biogenesis in patients' fibroblasts and cells from heterozygous Parn KO mice. Homozygous Parn KO however resulted in early embryonic lethality that was not overcome by p53 KO. Our results refine our knowledge on the pleiotropic cellular consequences of PARN deficiency.
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Affiliation(s)
- Maname Benyelles
- Laboratory of Genome Dynamics in the Immune SystemINSERM, UMR 1163ParisFrance
- Laboratoire labellisé LigueImagine InstituteParis Descartes–Sorbonne Paris Cite UniversityParisFrance
| | | | - Marie‐Françoise O'Donohue
- Laboratoire de Biologie Moléculaire EucaryoteCentre de Biologie Intégrative (CBI)CNRS, UPSUniversité de ToulouseToulouseFrance
| | - Laëtitia Kermasson
- Laboratory of Genome Dynamics in the Immune SystemINSERM, UMR 1163ParisFrance
- Laboratoire labellisé LigueImagine InstituteParis Descartes–Sorbonne Paris Cite UniversityParisFrance
| | - Pierre Frange
- EA 7327, Université Paris Descartes, Sorbonne Paris‐CitéParisFrance
- Laboratoire de Microbiologie clinique & Unité d'ImmunologieHématologie et Rhumatologie PédiatriquesAP‐HP, Hôpital Necker, Enfants MaladesParisFrance
| | - Florian Poulain
- de Duve InstituteUniversité catholique de LouvainBrusselsBelgium
| | - Fatma Burcu Belen
- Pediatric HematologyFaculty of MedicineBaskent UniversityAnkaraTurkey
| | - Meltem Polat
- Pediatric Infectious DiseasesDepartment of Pediatric Infectious DiseasesPamukkale University Medical FacultyDenizliTurkey
| | - Christine Bole‐Feysot
- INSERM, UMR 1163Genomics platform, Imagine InstituteParis Descartes–Sorbonne Paris Cité UniversityParisFrance
- Genomic Core FacilityImagine Institute‐Structure Fédérative de Recherche NeckerINSERM U1163ParisFrance
| | | | - Pierre‐Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire EucaryoteCentre de Biologie Intégrative (CBI)CNRS, UPSUniversité de ToulouseToulouseFrance
| | - Jean‐Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune SystemINSERM, UMR 1163ParisFrance
- Laboratoire labellisé LigueImagine InstituteParis Descartes–Sorbonne Paris Cite UniversityParisFrance
| | - Isabelle Callebaut
- Muséum National d'Histoire NaturelleUMR CNRS 7590Institut de Minéralogiede Physique des Matériaux et de Cosmochimie, IMPMCSorbonne UniversitéParisFrance
| | | | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune SystemINSERM, UMR 1163ParisFrance
- Laboratoire labellisé LigueImagine InstituteParis Descartes–Sorbonne Paris Cite UniversityParisFrance
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Telomere Gene Therapy: Polarizing Therapeutic Goals for Treatment of Various Diseases. Cells 2019; 8:cells8050392. [PMID: 31035374 PMCID: PMC6563133 DOI: 10.3390/cells8050392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
Modulation of telomerase maintenance by gene therapy must meet two polarizing requirements to achieve different therapeutic outcomes: Anti-aging/regenerative applications require upregulation, while anticancer applications necessitate suppression of various genes integral to telomere maintenance (e.g., telomerase, telomerase RNA components, and shelterin complex). Patients suffering from aging-associated illnesses often exhibit telomere attrition, which promotes chromosomal instability and cellular senescence, thus requiring the transfer of telomere maintenance-related genes to improve patient outcomes. However, reactivation and overexpression of telomerase are observed in 85% of cancer patients; this process is integral to cancer immortality. Thus, telomere-associated genes in the scope of cancer gene therapy must be inactivated or inhibited to induce anticancer effects. These contradicting requirements for achieving different therapeutic outcomes mean that any vector-mediated upregulation of telomere-associated genes must be accompanied by rigorous evaluation of potential oncogenesis. Thus, this review aims to discuss how telomere-associated genes are being targeted or utilized in various gene therapy applications and provides some insight into currently available safety hazard assessments.
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35
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Zhang D, Zhou Z, Abu-Hijleh M, Batra K, Xing C, Garcia CK. Homozygous Rare PARN Missense Mutation in Familial Pulmonary Fibrosis. Am J Respir Crit Care Med 2019; 199:797-799. [PMID: 30525901 PMCID: PMC6423103 DOI: 10.1164/rccm.201809-1632le] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- David Zhang
- University of Texas Southwestern Medical CenterDallas, Texas
| | - Zhengyang Zhou
- University of Texas Southwestern Medical CenterDallas, Texas
| | | | - Kiran Batra
- University of Texas Southwestern Medical CenterDallas, Texas
| | - Chao Xing
- University of Texas Southwestern Medical CenterDallas, Texas
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36
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Shukla S, Bjerke GA, Muhlrad D, Yi R, Parker R. The RNase PARN Controls the Levels of Specific miRNAs that Contribute to p53 Regulation. Mol Cell 2019; 73:1204-1216.e4. [PMID: 30770239 DOI: 10.1016/j.molcel.2019.01.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/08/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022]
Abstract
PARN loss-of-function mutations cause a severe form of the hereditary disease dyskeratosis congenita (DC). PARN deficiency affects the stability of non-coding RNAs such as human telomerase RNA (hTR), but these effects do not explain the severe disease in patients. We demonstrate that PARN deficiency affects the levels of numerous miRNAs in human cells. PARN regulates miRNA levels by stabilizing either mature or precursor miRNAs by removing oligo(A) tails added by the poly(A) polymerase PAPD5, which if remaining recruit the exonuclease DIS3L or DIS3L2 to degrade the miRNA. PARN knockdown destabilizes multiple miRNAs that repress p53 translation, which leads to an increase in p53 accumulation in a Dicer-dependent manner, thus explaining why PARN-defective patients show p53 accumulation. This work also reveals that DIS3L and DIS3L2 are critical 3' to 5' exonucleases that regulate miRNA stability, with the addition and removal of 3' end extensions controlling miRNA levels in the cell.
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Affiliation(s)
- Siddharth Shukla
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Glen A Bjerke
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Rui Yi
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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37
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The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN. Nat Commun 2018; 9:5430. [PMID: 30575725 PMCID: PMC6303318 DOI: 10.1038/s41467-018-07822-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/23/2018] [Indexed: 01/08/2023] Open
Abstract
Human telomerase RNA (hTR) is transcribed as a precursor that is then posttranscriptionally modified and processed. A fraction of the transcripts is oligoadenylated by TRAMP and either processed into the mature hTR or degraded by the exosome. Here, we characterize the processing of 3′ extended forms of varying length by PARN and RRP6. We show that tertiary RNA interactions unique to the longer transcripts favor RNA degradation, whereas H/ACA RNP assembly stimulates productive processing. Interestingly, the H/ACA complex actively promotes processing in addition to protecting the mature 3′ end. Processing occurs in two steps with longer forms first being trimmed by RRP6 and shorter forms then being processed by PARN. These results reveal how RNA structure and RNP assembly affect the kinetics of processing and degradation and ultimately determine the amount of functional telomerase produced in cells. Telomerase RNA (hTR) is transcribed as a 3′-extended precursor. Here the authors examine the processing of hTR precursors of various lengths and show that processing occurs in distinct steps involving different nucleases PARN and RRP6.
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38
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Aubert M, O'Donohue MF, Lebaron S, Gleizes PE. Pre-Ribosomal RNA Processing in Human Cells: From Mechanisms to Congenital Diseases. Biomolecules 2018; 8:biom8040123. [PMID: 30356013 PMCID: PMC6315592 DOI: 10.3390/biom8040123] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomal RNAs, the most abundant cellular RNA species, have evolved as the structural scaffold and the catalytic center of protein synthesis in every living organism. In eukaryotes, they are produced from a long primary transcript through an intricate sequence of processing steps that include RNA cleavage and folding and nucleotide modification. The mechanisms underlying this process in human cells have long been investigated, but technological advances have accelerated their study in the past decade. In addition, the association of congenital diseases to defects in ribosome synthesis has highlighted the central place of ribosomal RNA maturation in cell physiology regulation and broadened the interest in these mechanisms. Here, we give an overview of the current knowledge of pre-ribosomal RNA processing in human cells in light of recent progress and discuss how dysfunction of this pathway may contribute to the physiopathology of congenital diseases.
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Affiliation(s)
- Maxime Aubert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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Heck AM, Wilusz J. The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:a032839. [PMID: 29311343 PMCID: PMC5932591 DOI: 10.1101/cshperspect.a032839] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology.
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Affiliation(s)
- Adam M Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
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Abstract
Studies of rare and common illnesses have led to remarkable progress in the understanding of the role of telomeres (nucleoprotein complexes at chromosome ends essential for chromosomal integrity) in human disease. Telomere biology disorders encompass a growing spectrum of conditions caused by rare pathogenic germline variants in genes encoding essential aspects of telomere function. Dyskeratosis congenita, a disorder at the severe end of this spectrum, typically presents in childhood with the classic triad of abnormal skin pigmentation, nail dystrophy, and oral leukoplakia, accompanied by a very high risk of bone marrow failure, cancer, pulmonary fibrosis, and other medical problems. In contrast, the less severe end of the telomere biology disorder spectrum consists of middle-age or older adults with just one feature typically seen in dyskeratosis congenita, such as pulmonary fibrosis or bone marrow failure. In the common disease realm, large-scale molecular epidemiology studies have discovered novel associations between illnesses, such as cancer, heart disease, and mental health, and both telomere length and common genetic variants in telomere biology genes. This review highlights recent findings of telomere biology in human disease from both the rare and common disease perspectives. Multi-disciplinary collaborations between clinicians, basic scientists, and epidemiologist are essential as we seek to incorporate new telomere biology discoveries to improve health outcomes.
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Affiliation(s)
- Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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41
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RNA-binding proteins control gene expression and cell fate in the immune system. Nat Immunol 2018; 19:120-129. [PMID: 29348497 DOI: 10.1038/s41590-017-0028-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 12/19/2022]
Abstract
RNA-binding proteins (RBPs) are essential for the development and function of the immune system. They interact dynamically with RNA to control its biogenesis and turnover by transcription-dependent and transcription-independent mechanisms. In this Review, we discuss the molecular mechanisms by which RBPs allow gene expression changes to occur at different speeds and to varying degrees, and which RBPs regulate the diversity of the transcriptome and proteome. These proteins are nodes for integration of transcriptional and signaling networks and are intimately linked to intermediary metabolism. They are essential components of regulatory feedback mechanisms that maintain immune tolerance and limit inflammation. The role of RBPs in malignancy and autoimmunity has led to their emergence as targets for the development of new therapeutic modalities.
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Lata S, Marasa M, Li Y, Fasel DA, Groopman E, Jobanputra V, Rasouly H, Mitrotti A, Westland R, Verbitsky M, Nestor J, Slater LM, D'Agati V, Zaniew M, Materna-Kiryluk A, Lugani F, Caridi G, Rampoldi L, Mattoo A, Newton CA, Rao MK, Radhakrishnan J, Ahn W, Canetta PA, Bomback AS, Appel GB, Antignac C, Markowitz GS, Garcia CK, Kiryluk K, Sanna-Cherchi S, Gharavi AG. Whole-Exome Sequencing in Adults With Chronic Kidney Disease: A Pilot Study. Ann Intern Med 2018; 168:100-109. [PMID: 29204651 PMCID: PMC5947852 DOI: 10.7326/m17-1319] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The utility of whole-exome sequencing (WES) for the diagnosis and management of adult-onset constitutional disorders has not been adequately studied. Genetic diagnostics may be advantageous in adults with chronic kidney disease (CKD), in whom the cause of kidney failure often remains unknown. OBJECTIVE To study the diagnostic utility of WES in a selected referral population of adults with CKD. DESIGN Observational cohort. SETTING A major academic medical center. PATIENTS 92 adults with CKD of unknown cause or familial nephropathy or hypertension. MEASUREMENTS The diagnostic yield of WES and its potential effect on clinical management. RESULTS Whole-exome sequencing provided a diagnosis in 22 of 92 patients (24%), including 9 probands with CKD of unknown cause and encompassing 13 distinct genetic disorders. Among these, loss-of-function mutations were identified in PARN in 2 probands with tubulointerstitial fibrosis. PARN mutations have been implicated in a short telomere syndrome characterized by lung, bone marrow, and liver fibrosis; these findings extend the phenotype of PARN mutations to renal fibrosis. In addition, review of the American College of Medical Genetics actionable genes identified a pathogenic BRCA2 mutation in a proband who was diagnosed with breast cancer on follow-up. The results affected clinical management in most identified cases, including initiation of targeted surveillance, familial screening to guide donor selection for transplantation, and changes in therapy. LIMITATION The small sample size and recruitment at a tertiary care academic center limit generalizability of findings among the broader CKD population. CONCLUSION Whole-exome sequencing identified diagnostic mutations in a substantial number of adults with CKD of many causes. Further study of the utility of WES in the evaluation and care of patients with CKD in additional settings is warranted. PRIMARY FUNDING SOURCE New York State Empire Clinical Research Investigator Program, Renal Research Institute, and National Human Genome Research Institute of the National Institutes of Health.
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Affiliation(s)
- Sneh Lata
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Maddalena Marasa
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Yifu Li
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - David A Fasel
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Emily Groopman
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Vaidehi Jobanputra
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Hila Rasouly
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Adele Mitrotti
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Rik Westland
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Miguel Verbitsky
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Jordan Nestor
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Lindsey M Slater
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Vivette D'Agati
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Marcin Zaniew
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Anna Materna-Kiryluk
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Francesca Lugani
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Gianluca Caridi
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Luca Rampoldi
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Aditya Mattoo
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Chad A Newton
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Maya K Rao
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Jai Radhakrishnan
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Wooin Ahn
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Pietro A Canetta
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Andrew S Bomback
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Gerald B Appel
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Corinne Antignac
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Glen S Markowitz
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Christine K Garcia
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Krzysztof Kiryluk
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Simone Sanna-Cherchi
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Ali G Gharavi
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
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Kropski JA, Reiss S, Markin C, Brown KK, Schwartz DA, Schwarz MI, Loyd JE, Phillips JA, Blackwell TS, Cogan JD. Rare Genetic Variants in PARN Are Associated with Pulmonary Fibrosis in Families. Am J Respir Crit Care Med 2017; 196:1481-1484. [PMID: 28414520 DOI: 10.1164/rccm.201703-0635le] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Sara Reiss
- 1 Vanderbilt University Medical Center Nashville, Tennessee
| | - Cheryl Markin
- 1 Vanderbilt University Medical Center Nashville, Tennessee
| | | | - David A Schwartz
- 2 National Jewish Health Denver, Colorado.,3 University of Colorado Denver, School of Medicine Denver, Colorado and
| | - Marvin I Schwarz
- 3 University of Colorado Denver, School of Medicine Denver, Colorado and
| | - James E Loyd
- 1 Vanderbilt University Medical Center Nashville, Tennessee
| | | | - Timothy S Blackwell
- 1 Vanderbilt University Medical Center Nashville, Tennessee.,4 Department of Veterans Affairs Medical Center Nashville, Tennessee
| | - Joy D Cogan
- 1 Vanderbilt University Medical Center Nashville, Tennessee
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Bizarro J, Meier UT. Inherited SHQ1 mutations impair interaction with NAP57/dyskerin, a major target in dyskeratosis congenita. Mol Genet Genomic Med 2017; 5:805-808. [PMID: 29178645 PMCID: PMC5702568 DOI: 10.1002/mgg3.314] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/12/2017] [Accepted: 06/14/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The inherited bone marrow failure syndrome dyskeratosis congenita (DC) is most frequently caused by mutations in DKC1 (MIM# 300126), the gene encoding NAP57 (aka dyskerin). The typically missense mutations modulate the interaction of NAP57 with its chaperone SHQ1, but no DC mutations have been identified in SHQ1 (MIM# 613663). Here, we report on two compound heterozygous mutations in SHQ1 in a patient with a severe neurological disorder including cerebellar degeneration. METHODS The SHQ1 mutations were identified by patient exome sequencing. The impact of the mutations was assessed in pulldown assays with recombinant NAP57. RESULTS The SHQ1 mutations were the only set of mutations consistent with an autosomal recessive mode of inheritance. The mutations map to the SHQ1-NAP57 interface and impair the interaction of the recombinant SHQ1 variants with NAP57. CONCLUSION Intrauterine growth retardation and the neurological phenotype of the patient are reminiscent of the severe clinical variant of DC, the Hoyeraal-Hreidarsson syndrome (HH). Hence, SHQ1 screening may be warranted in patients with inherited bone marrow failure syndromes.
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Affiliation(s)
- Jonathan Bizarro
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461
| | - U Thomas Meier
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461
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45
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Montellese C, Montel-Lehry N, Henras AK, Kutay U, Gleizes PE, O'Donohue MF. Poly(A)-specific ribonuclease is a nuclear ribosome biogenesis factor involved in human 18S rRNA maturation. Nucleic Acids Res 2017; 45:6822-6836. [PMID: 28402503 PMCID: PMC5499762 DOI: 10.1093/nar/gkx253] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/03/2017] [Indexed: 01/28/2023] Open
Abstract
The poly-A specific ribonuclease (PARN), initially characterized for its role in mRNA catabolism, supports the processing of different types of non-coding RNAs including telomerase RNA. Mutations in PARN are linked to dyskeratosis congenita and pulmonary fibrosis. Here, we show that PARN is part of the enzymatic machinery that matures the human 18S ribosomal RNA (rRNA). Consistent with its nucleolar steady-state localization, PARN is required for 40S ribosomal subunit production and co-purifies with 40S subunit precursors. Depletion of PARN or expression of a catalytically-compromised PARN mutant results in accumulation of 3΄ extended 18S rRNA precursors. Analysis of these processing intermediates reveals a defect in 3΄ to 5΄ trimming of the internal transcribed spacer 1 (ITS1) region, subsequent to endonucleolytic cleavage at site E. Consistent with a function of PARN in exonucleolytic trimming of 18S-E pre-rRNA, recombinant PARN can process the corresponding ITS1 RNA fragment in vitro. Trimming of 18S-E pre-rRNA by PARN occurs in the nucleus, upstream of the final endonucleolytic cleavage by the endonuclease NOB1 in the cytoplasm. These results identify PARN as a new component of the ribosome biogenesis machinery in human cells. Defects in ribosome biogenesis could therefore underlie the pathologies linked to mutations in PARN.
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Affiliation(s)
| | - Nathalie Montel-Lehry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Ulrike Kutay
- Institut für Biochemie, ETH Zurich, Zurich CH-8093, Switzerland
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
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46
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PARN Modulates Y RNA Stability and Its 3'-End Formation. Mol Cell Biol 2017; 37:MCB.00264-17. [PMID: 28760775 DOI: 10.1128/mcb.00264-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 11/20/2022] Open
Abstract
Loss-of-function mutations in 3'-to-5' exoribonucleases have been implicated in hereditary human diseases. For example, PARN mutations cause a severe form of dyskeratosis congenita (DC), wherein PARN deficiency leads to human telomerase RNA instability. Since the DC phenotype in PARN patients is even more severe than that of loss-of-function alleles in telomerase components, we hypothesized that PARN would also be required for the stability of other RNAs. Here, we show that PARN depletion reduces the levels of abundant human Y RNAs, which might contribute to the severe phenotype of DC observed in patients. Depletion of PAPD5 or the cytoplasmic exonuclease DIS3L rescues the effect of PARN depletion on Y RNA levels, suggesting that PARN stabilizes Y RNAs by removing oligoadenylated tails added by PAPD5, which would otherwise recruit DIS3L for Y RNA degradation. Through deep sequencing of 3' ends, we provide evidence that PARN can also deadenylate the U6 and RMRP RNAs without affecting their levels. Moreover, we observed widespread posttranscriptional oligoadenylation, uridylation, and guanylation of U6 and Y RNA 3' ends, suggesting that in mammalian cells, the formation of a 3' end for noncoding RNAs can be a complex process governed by the activities of various 3'-end polymerases and exonucleases.
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47
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Warren AJ. Molecular basis of the human ribosomopathy Shwachman-Diamond syndrome. Adv Biol Regul 2017; 67:109-127. [PMID: 28942353 PMCID: PMC6710477 DOI: 10.1016/j.jbior.2017.09.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 01/05/2023]
Abstract
Mutations that target the ubiquitous process of ribosome assembly paradoxically cause diverse tissue-specific disorders (ribosomopathies) that are often associated with an increased risk of cancer. Ribosomes are the essential macromolecular machines that read the genetic code in all cells in all kingdoms of life. Following pre-assembly in the nucleus, precursors of the large 60S and small 40S ribosomal subunits are exported to the cytoplasm where the final steps in maturation are completed. Here, I review the recent insights into the conserved mechanisms of ribosome assembly that have come from functional characterisation of the genes mutated in human ribosomopathies. In particular, recent advances in cryo-electron microscopy, coupled with genetic, biochemical and prior structural data, have revealed that the SBDS protein that is deficient in the inherited leukaemia predisposition disorder Shwachman-Diamond syndrome couples the final step in cytoplasmic 60S ribosomal subunit maturation to a quality control assessment of the structural and functional integrity of the nascent particle. Thus, study of this fascinating disorder is providing remarkable insights into how the large ribosomal subunit is functionally activated in the cytoplasm to enter the actively translating pool of ribosomes.
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MESH Headings
- Bone Marrow Diseases/metabolism
- Bone Marrow Diseases/pathology
- Cryoelectron Microscopy
- Exocrine Pancreatic Insufficiency/metabolism
- Exocrine Pancreatic Insufficiency/pathology
- Humans
- Lipomatosis/metabolism
- Lipomatosis/pathology
- Mutation
- Proteins/genetics
- Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Shwachman-Diamond Syndrome
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Affiliation(s)
- Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK; The Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
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48
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Waespe N, Dhanraj S, Wahala M, Tsangaris E, Enbar T, Zlateska B, Li H, Klaassen RJ, Fernandez CV, Cuvelier GDE, Wu JK, Pastore YD, Silva M, Lipton JH, Brossard J, Michon B, Abish S, Steele M, Sinha R, Belletrutti MJ, Breakey VR, Jardine L, Goodyear L, Kofler L, Cada M, Sung L, Shago M, Scherer SW, Dror Y. The clinical impact of copy number variants in inherited bone marrow failure syndromes. NPJ Genom Med 2017; 2. [PMID: 28690869 PMCID: PMC5498150 DOI: 10.1038/s41525-017-0019-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Inherited bone marrow failure syndromes comprise a genetically heterogeneous group of diseases with hematopoietic failure and a wide array of physical malformations. Copy number variants were reported in some inherited bone marrow failure syndromes. It is unclear what impact copy number variants play in patients evaluated for a suspected diagnosis of inherited bone marrow failure syndromes. Clinical and genetic data of 323 patients from the Canadian Inherited Marrow Failure Registry from 2001 to 2014, who had a documented genetic work-up, were analyzed. Cases with pathogenic copy number variants (at least 1 kilobasepairs) were compared to cases with other mutations. Genotype-phenotype correlations were performed to assess the impact of copy number variants. Pathogenic nucleotide-level mutations were found in 157 of 303 tested patients (51.8%). Genome-wide copy number variant analysis by single-nucleotide polymorphism arrays or comparative genomic hybridization arrays revealed pathogenic copy number variants in 11 of 67 patients tested (16.4%). In four of these patients, identification of copy number variant was crucial for establishing the correct diagnosis as their clinical presentation was ambiguous. Eight additional patients were identified to harbor pathogenic copy number variants by other methods. Of the 19 patients with pathogenic copy number variants, four had compound-heterozygosity of a copy number variant with a nucleotide-level mutation. Pathogenic copy number variants were associated with more extensive non-hematological organ system involvement (p = 0.0006), developmental delay (p = 0.006) and short stature (p = 0.04) compared to nucleotide-level mutations. In conclusion, a significant proportion of patients with inherited bone marrow failure syndromes harbor pathogenic copy number variants which were associated with a more extensive non-hematological phenotype in this cohort. Patients with a phenotype suggestive of inherited bone marrow failure syndromes but without identification of pathogenic nucleotide-level mutations should undergo specific testing for copy number variants. Copy number variation in patients with inherited bone marrow failure syndromes (IBMFSs) is associated with more severe clinical symptoms. In addition to persistently low levels of red blood cells, white blood cells and/ or platelets, patients with IBMFSs also present varying degrees of physical malformations. Most cases are associated with single base-pair mutations in the DNA sequence, but Canadian researchers led by Yigal Dror at The Hospital for Sick Children in Toronto, have found that whole sections of the genome are deleted or repeated in an important proportion of patients. Those carrying copy number variants (CNV) presented more commonly with developmental delay, short stature and defects in more organ systems, than patients with point mutations. CNV analysis of patients with suspected IBMFSs could aid early disease evaluation and management.
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Affiliation(s)
- Nicolas Waespe
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Santhosh Dhanraj
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Manju Wahala
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elena Tsangaris
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Tom Enbar
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bozana Zlateska
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Hongbing Li
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Robert J Klaassen
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Geoff D E Cuvelier
- Pediatric Hematology/Oncology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
| | - John K Wu
- Division of Hematology/Oncology, UBC & B.C. Children's Hospital, Vancouver, BC, Canada
| | | | | | - Jeffrey H Lipton
- Allogeneic Blood and Marrow Transplant Program, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Joseé Brossard
- Centre Hospitalier Universitaire, Sherbrooke, QC, Canada
| | - Bruno Michon
- Centre Hospitalier Universitaire, Québec, QC, Canada
| | - Sharon Abish
- Pediatric Hematology Oncology, Montreal Children's Hospital, Montreal, QC, Canada
| | | | - Roona Sinha
- Royal University Hospital, Saskatoon, SK, Canada
| | | | - Vicky R Breakey
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Lawrence Jardine
- Children's Hospital, London Health Sciences Centre, London, ON, Canada
| | - Lisa Goodyear
- Pediatric Hematology/Oncology, Janeway Child Health Centre, St. John's, NF, Canada
| | - Liat Kofler
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michaela Cada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Lillian Sung
- Population Health Sciences, Research Institute, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mary Shago
- Cytogenetics Laboratory, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Yigal Dror
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
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Control of Cellular Aging, Tissue Function, and Cancer by p53 Downstream of Telomeres. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026088. [PMID: 28289249 DOI: 10.1101/cshperspect.a026088] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Telomeres, the nucleoprotein complex at the ends of eukaryotic chromosomes, perform an essential cellular role in part by preventing the chromosomal end from initiating a DNA-damage response. This function of telomeres can be compromised as telomeres erode either as a consequence of cell division in culture or as a normal part of cellular ageing in proliferative tissues. Telomere dysfunction in this context leads to DNA-damage signaling and activation of the tumor-suppressor protein p53, which then can prompt either cellular senescence or apoptosis. By culling cells with dysfunctional telomeres, p53 plays a critical role in protecting tissues against the effects of critically short telomeres. However, as telomere dysfunction worsens, p53 likely exacerbates short telomere-driven tissue failure diseases, including pulmonary fibrosis, aplastic anemia, and liver cirrhosis. In cells lacking p53, unchecked telomere shortening drives chromosomal end-to-end fusions and cycles of chromosome fusion-bridge-breakage. Incipient cancer cells confronting these telomere barriers must disable p53 signaling to avoid senescence and eventually up-regulate telomerase to achieve cellular immortality. The recent findings of highly recurrent activating mutations in the promoter for the telomerase reverse transcriptase (TERT) gene in diverse human cancers, together with the widespread mutations in p53 in cancer, provide support for the idea that circumvention of a telomere-p53 checkpoint is essential for malignant progression in human cancer.
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Abstract
Abstract
There is an Inside Blood Commentary on this article in this issue.
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