1
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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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2
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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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3
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Rodriguez K, Shargo R, Ekblad M, Sunkersett G, Karjoo S, Betensky M, Wilsey MJ. Endoscopic Assessment and Serial Balloon Dilatation in a Toddler With Dyskeratosis Congenita-Hoyeraal-Hreidarsson Syndrome Following Bone Marrow Transplant: A Case Report. JPGN REPORTS 2023; 4:e291. [PMID: 37200733 PMCID: PMC10187843 DOI: 10.1097/pg9.0000000000000291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 12/12/2022] [Indexed: 05/20/2023]
Abstract
We report a 3-year-old patient with suspected oropharyngeal graft-versus-host disease (GVHD) who developed progressive dysphagia to solids and liquids. The patient has a history of Dyskeratosis Congenita-Hoyeraal-Hreidarsson Syndrome with associated bone marrow failure requiring a nonmyeloablative matched sibling hematopoietic stem cell transplant. Esophagram revealed significant narrowing in the cricopharyngeal region. Subsequent esophagoscopy showed a proximal, high-grade pinhole esophageal stricture that was very difficult to visualize and cannulate. High-grade esophageal strictures are uncommon in very young children with GVHD. We believe the patient's underlying Dyskeratosis Congenita-Hoyeraal-Hreidarsson Syndrome in the setting of inflammatory changes seen in GVHD following hematopoietic stem cell transplant set the stage for a high-grade esophageal obstruction. The patient's symptoms improved with serial endoscopic balloon dilation.
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Affiliation(s)
- Kurt Rodriguez
- From the Johns Hopkins All Children’s Hospital, Saint Petersburg, FL
| | - Ryan Shargo
- University of South Florida, Reisterstown, MD
| | | | | | - Sara Karjoo
- From the Johns Hopkins All Children’s Hospital, Saint Petersburg, FL
| | - Marisol Betensky
- From the Johns Hopkins All Children’s Hospital, Saint Petersburg, FL
| | - Michael J. Wilsey
- From the Johns Hopkins All Children’s Hospital, Saint Petersburg, FL
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4
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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: 43] [Impact Index Per Article: 43.0] [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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5
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Niewisch MR, Giri N, McReynolds LJ, Alsaggaf R, Bhala S, Alter BP, Savage SA. Disease progression and clinical outcomes in telomere biology disorders. Blood 2022; 139:1807-1819. [PMID: 34852175 PMCID: PMC8952184 DOI: 10.1182/blood.2021013523] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/11/2021] [Indexed: 11/20/2022] Open
Abstract
Dyskeratosis congenita related telomere biology disorders (DC/TBDs) are characterized by very short telomeres caused by germline pathogenic variants in telomere biology genes. Clinical presentations can affect all organs, and inheritance patterns include autosomal dominant (AD), autosomal recessive (AR), X-linked (XLR), or de novo. This study examined the associations between mode of inheritance with phenotypes and long-term clinical outcomes. Two hundred thirty-one individuals with DC/TBDs (144 male, 86.6% known genotype, median age at diagnosis 19.4 years [range 0 to 71.6]), enrolled in the National Cancer Institute's Inherited Bone Marrow Failure Syndrome Study, underwent detailed clinical assessments and longitudinal follow-up (median follow-up 5.2 years [range 0 to 36.7]). Patients were grouped by inheritance pattern, considering AD-nonTINF2, AR/XLR, and TINF2 variants separately. Severe bone marrow failure (BMF), severe liver disease, and gastrointestinal telangiectasias were more prevalent in AR/XLR or TINF2 disease, whereas pulmonary fibrosis developed predominantly in adults with AD disease. After adjusting for age at DC/TBD diagnosis, we observed the highest cancer risk in AR/XLR individuals. At last follow-up, 42% of patients were deceased with a median overall survival (OS) of 52.8 years (95% confidence interval [CI] 45.5-57.6), and the hematopoietic cell or solid organ transplant-free median survival was 45.3 years (95% CI 37.4-52.1). Significantly better OS was present in AD vs AR/XLR/TINF2 disease (P < .01), while patients with AR/XLR and TINF2 disease had similar survival probabilities. This long-term study of the clinical manifestations of DC/TBDs creates a foundation for incorporating the mode of inheritance into evidence-based clinical care guidelines and risk stratification in patients with DC/TBDs. This trial was registered at www.clinicaltrials.gov as #NCT00027274.
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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
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Rotana Alsaggaf
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Sonia Bhala
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
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6
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Pulmonary fibrosis in dyskeratosis congenita: a case report with a PRISMA-compliant systematic review. BMC Pulm Med 2021; 21:279. [PMID: 34479523 PMCID: PMC8418029 DOI: 10.1186/s12890-021-01645-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/25/2021] [Indexed: 12/04/2022] Open
Abstract
Background Dyskeratosis congenita (DC) is a rare genetic disorder of poor telomere maintenance. Pulmonary fibrosis (PF) related to DC is rarely reported. Case presentation A 23-year-old student presented with a four-year history of progressive cough and exertional dyspnea. Physical examination was remarkable for typical mucocutaneous abnormalities. Chest computerized tomography scan revealed interstitial fibrosis. Testing of peripheral blood leukocytes confirmed that his telomeres were 30th percentile of age-matched controls. A heterozygous missense mutation located in exon 22 of PARN gene was identified in the patient by whole exome sequencing. The patient refused danazol therapy and lung transplantation, and died of respiratory failure 2 years later. In addition, this case and 26 reported cases of DC-related PF identified through the comprehensive search of PubMed, Web of Science, WANFANG and CNKI were reviewed. Later-onset PF was observed in 11 patients (40.7%). Radiological usual interstitial pneumonia (UIP) pattern or possible UIP pattern was noted only in half of patients. However, histopathological UIP or probable UIP patterns were found in 63.6% of patients. Age at bone marrow failure (BMF) and the frequency of normal to mild thrombocytopenia in later-onset patients was significantly higher than in early-onset patients (p = 0.017 and p = 0.021, respectively). Age at PF and age at BMF in DC patients with TERC/TERT variants was significantly higher than in those with TINF2 variants or DKC1/NHP2 variants (p = 0.004 and p = 0.003, respectively). The patients with TERT/TERC/RTEL1/PARN variants had a significantly better transplant-free survival than those with TINF2 variants or DKC1/NHP2 variants (p < 0.05). Patients who underwent surgical lung biopsy had significantly worse transplant-free survival than those without lung biopsy (p = 0.042). Worse survival was found in patients with immunosuppression therapy than in those without (p = 0.012). Conclusions It is common for DC-associated PF to occur later in life without significant hematological manifestations. Mutations in the genes encoding different components of the telomere maintenance pathway were associated with clinical phenotypes and prognosis. PF caused by DC should be kept in mind by clinicians in the differential diagnosis of patients with unexplained PF and should be excluded before diagnostic surgical lung biopsy is undertaken or empirical immunosuppression therapy is prescribed. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01645-w.
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7
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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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8
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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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9
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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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10
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Schratz KE, DeZern AE. Genetic Predisposition to Myelodysplastic Syndrome in Clinical Practice. Hematol Oncol Clin North Am 2020; 34:333-356. [PMID: 32089214 PMCID: PMC7875473 DOI: 10.1016/j.hoc.2019.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Myelodysplastic syndromes (MDSs) are a heterogeneous group of marrow failure disorders that primarily affect older persons but also occur at a lower frequency in children and young adults. There is increasing recognition of an inherited predisposition to MDS as well as other myeloid malignancies for patients of all ages. Germline predisposition to MDS can occur as part of a syndrome or sporadic disease. The timely diagnosis of an underlying genetic predisposition in the setting of MDS is important. This article delineates germline genetic causes of MDS and provides a scaffold for the diagnosis and management of patients in this context.
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Affiliation(s)
- Kristen E Schratz
- Division of Pediatric Oncology, Johns Hopkins University School of Medicine, Bloomberg 11379, 1800 Orleans Street, Baltimore, MD 21287, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 1650 Orleans Street, Baltimore, MD 21287, USA
| | - Amy E DeZern
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 1650 Orleans Street, Baltimore, MD 21287, USA; Division of Hematologic Malignancies, Johns Hopkins University School of Medicine, CRBI Room 3M87, 1650 Orleans Street, Baltimore, MD 21287-0013, USA.
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11
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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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12
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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: 50] [Impact Index Per Article: 10.0] [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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13
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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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14
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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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15
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Abstract
Many recent advances have emerged in the telomere and telomerase fields. This Timeline article highlights the key advances that have expanded our views on the mechanistic underpinnings of telomeres and telomerase and their roles in ageing and disease. Three decades ago, the classic view was that telomeres protected the natural ends of linear chromosomes and that telomerase was a specific telomere-terminal transferase necessary for the replication of chromosome ends in single-celled organisms. While this concept is still correct, many diverse fields associated with telomeres and telomerase have substantially matured. These areas include the discovery of most of the key molecular components of telomerase, implications for limits to cellular replication, identification and characterization of human genetic disorders that result in premature telomere shortening, the concept that inhibiting telomerase might be a successful therapeutic strategy and roles for telomeres in regulating gene expression. We discuss progress in these areas and conclude with challenges and unanswered questions in the field.
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Affiliation(s)
- Jerry W Shay
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Woodring E Wright
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
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16
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Bueren JA, Quintana-Bustamante O, Almarza E, Navarro S, Río P, Segovia JC, Guenechea G. Advances in the gene therapy of monogenic blood cell diseases. Clin Genet 2019; 97:89-102. [PMID: 31231794 DOI: 10.1111/cge.13593] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/12/2019] [Accepted: 05/21/2019] [Indexed: 01/19/2023]
Abstract
Hematopoietic gene therapy has markedly progressed during the last 15 years both in terms of safety and efficacy. While a number of serious adverse events (SAE) were initially generated as a consequence of genotoxic insertions of gamma-retroviral vectors in the cell genome, no SAEs and excellent outcomes have been reported in patients infused with autologous hematopoietic stem cells (HSCs) transduced with self-inactivated lentiviral and gammaretroviral vectors. Advances in the field of HSC gene therapy have extended the number of monogenic diseases that can be treated with these approaches. Nowadays, evidence of clinical efficacy has been shown not only in primary immunodeficiencies, but also in other hematopoietic diseases, including beta-thalassemia and sickle cell anemia. In addition to the rapid progression of non-targeted gene therapies in the clinic, new approaches based on gene editing have been developed thanks to the discovery of designed nucleases and improved non-integrative vectors, which have markedly increased the efficacy and specificity of gene targeting to levels compatible with its clinical application. Based on advances achieved in the field of gene therapy, it can be envisaged that these therapies will soon be part of the therapeutic approaches used to treat life-threatening diseases of the hematopoietic system.
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Affiliation(s)
- Juan A Bueren
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Oscar Quintana-Bustamante
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Elena Almarza
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Susana Navarro
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Paula Río
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - José C Segovia
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Guillermo Guenechea
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
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17
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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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18
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Similar telomere attrition rates in androgen-treated and untreated patients with dyskeratosis congenita. Blood Adv 2019; 2:1243-1249. [PMID: 29853525 DOI: 10.1182/bloodadvances.2018016964] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 05/06/2018] [Indexed: 11/20/2022] Open
Abstract
Dyskeratosis congenita (DC) is an inherited bone marrow failure syndrome and the prototypic telomere biology disorder (TBD). Leukocyte telomere length (TL) less than the first percentile for age, measured by flow cytometry with in situ hybridization (flow FISH), is diagnostic of DC. Androgens are a therapeutic option for DC/TBD-associated bone marrow failure (BMF). One report has shown an apparent increase in TL in patients while on treatment with the attenuated androgen danazol. The aim of this study was to compare TL over time in 10 androgen-treated and 16 untreated patients with DC. All subjects were enrolled in institutional review board-approved longitudinal cohort studies of inherited BMF. TL in 6-panel leukocyte subsets was measured by flow FISH. Generalized estimating equations (GEE) methodology was used to compare TL changes over time between groups. Unadjusted analyses showed annual median total lymphocyte TL attrition of -62 base pairs/year (bp/y) in androgen-treated patients with DC compared with -76 bp/y in untreated DC patients (P = .71). Longitudinal analysis using a GEE model, adjusted for age at sample collection, showed no statistically significant difference in TL change over time between treated and untreated patients (P = .24). The results were similar for each individual leukocyte subset evaluated. In summary, our data show the expected age-associated longitudinal telomere shortening in patients with DC, irrespective of androgen therapy. Caution is warranted when recommending androgen therapy for non-BMF manifestations of DC or TBDs until the biological mechanisms are better understood.
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19
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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: 48] [Impact Index Per Article: 9.6] [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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20
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Warren AJ. Molecular basis of the human ribosomopathy Shwachman-Diamond syndrome. Adv Biol Regul 2018; 67:109-127. [PMID: 28942353 PMCID: PMC6710477 DOI: 10.1016/j.jbior.2017.09.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [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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21
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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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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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Telomere-associated aging disorders. Ageing Res Rev 2017; 33:52-66. [PMID: 27215853 PMCID: PMC9926533 DOI: 10.1016/j.arr.2016.05.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 01/25/2023]
Abstract
Telomeres are dynamic nucleoprotein-DNA structures that cap and protect linear chromosome ends. Several monogenic inherited diseases that display features of human premature aging correlate with shortened telomeres, and are referred to collectively as telomeropathies. These disorders have overlapping symptoms and a common underlying mechanism of telomere dysfunction, but also exhibit variable symptoms and age of onset, suggesting they fall along a spectrum of disorders. Primary telomeropathies are caused by defects in the telomere maintenance machinery, whereas secondary telomeropathies have some overlapping symptoms with primary telomeropathies, but are generally caused by mutations in DNA repair proteins that contribute to telomere preservation. Here we review both the primary and secondary telomeropathies, discuss potential mechanisms for tissue specificity and age of onset, and highlight outstanding questions in the field and future directions toward elucidating disease etiology and developing therapeutic strategies.
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