1
|
Philippot Q, Kannengiesser C, Debray MP, Gauvain C, Ba I, Vieri M, Gondouin A, Naccache JM, Reynaud-Gaubert M, Uzunhan Y, Bondue B, Israël-Biet D, Dieudé P, Fourrage C, Lainey E, Manali E, Papiris S, Wemeau L, Hirschi S, Mal H, Nunes H, Schlemmer F, Blanchard E, Beier F, Cottin V, Crestani B, Borie R. Interstitial lung diseases associated with mutations of poly(A)-specific ribonuclease: A multicentre retrospective study. Respirology 2022; 27:226-235. [PMID: 34981600 DOI: 10.1111/resp.14195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/21/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Poly(A)-specific ribonuclease (PARN) mutations have been associated with familial pulmonary fibrosis. This study aims to describe the phenotype of patients with interstitial lung disease (ILD) and heterozygous PARN mutations. METHODS We performed a retrospective, observational, non-interventional study of patients with an ILD diagnosis and a pathogenic heterozygous PARN mutation followed up in a centre of the OrphaLung network. RESULTS We included 31 patients (29 from 16 kindreds and two sporadic patients). The median age at ILD diagnosis was 59 years (range 54 to 63). In total, 23 (74%) patients had a smoking history and/or fibrogenic exposure. The pulmonary phenotypes were heterogenous, but the most frequent diagnosis was idiopathic pulmonary fibrosis (n = 12, 39%). Haematological abnormalities were identified in three patients and liver disease in two. In total, 21 patients received a specific treatment for ILD: steroids (n = 13), antifibrotic agents (n = 11), immunosuppressants (n = 5) and N-acetyl cysteine (n = 2). The median forced vital capacity decline for the whole sample was 256 ml/year (range -363 to -148). After a median follow-up of 32 months (range 18 to 66), 10 patients had died and six had undergone lung transplantation. The median transplantation-free survival was 54 months (95% CI 29 to ∞). Extra-pulmonary features were less frequent with PARN mutation than telomerase reverse transcriptase (TERT) or telomerase RNA component (TERC) mutation. CONCLUSION IPF is common among individuals with PARN mutation, but other ILD subtypes may be observed.
Collapse
Affiliation(s)
| | - Caroline Kannengiesser
- INSERM, Unité 1152, Université de Paris, Paris, France.,Laboratoire de Génétique, Hôpital Bichat, APHP, Paris, France
| | - Marie Pierre Debray
- INSERM, Unité 1152, Université de Paris, Paris, France.,Service de Radiologie, Hôpital Bichat, APHP, Paris, France
| | | | - Ibrahima Ba
- Laboratoire de Génétique, Hôpital Bichat, APHP, Paris, France
| | - Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Anne Gondouin
- Service de Pneumologie, CHU de Besançon, Besancon, France
| | | | | | | | | | | | - Philippe Dieudé
- INSERM, Unité 1152, Université de Paris, Paris, France.,Service de Rhumatologie, Hôpital Bichat, APHP, Paris, France
| | - Cécile Fourrage
- Service de Génétique Hôpital Necker Enfants Malades, APHP, Paris, France.,Plateforme de Bio-informatique, Institut Imagine, Université de Paris, Paris, France
| | - Elodie Lainey
- Laboratoire d'Hématologie Hôpital Robert Debré, APHP, Paris, France
| | - Effrosyne Manali
- 2nd Pulmonary department, Attikon University Hospital, Athens, Greece
| | - Spyros Papiris
- 2nd Pulmonary department, Attikon University Hospital, Athens, Greece
| | | | | | - Hervé Mal
- INSERM, Unité 1152, Université de Paris, Paris, France.,Service de Pneumologie B, Hôpital Bichat, APHP, Paris, France
| | - Hilario Nunes
- Service de Pneumologie, Hôpital Avicenne, APHP, Bobigny, France
| | - Frédéric Schlemmer
- Unité de Pneumologie, Université Paris-Est Créteil, APHP, Hôpitaux Universitaires Henri Mondor, Créteil, France
| | | | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Vincent Cottin
- Coordonnateur OrphaLung, Centre coordonnateur national de référence des maladies pulmonaires rares, Service de Pneumologie, Hôpital Louis Pradel, Université de Lyon, INRAE, member of Radico-ILD, Lyon, France.,RespiFil, ERN-LUNG, Lyon, France
| | - Bruno Crestani
- Service de Pneumologie A, Hôpital Bichat, APHP, Paris, France.,INSERM, Unité 1152, Université de Paris, Paris, France
| | - Raphaël Borie
- Service de Pneumologie A, Hôpital Bichat, APHP, Paris, France.,INSERM, Unité 1152, Université de Paris, Paris, France
| | | |
Collapse
|
2
|
Hirayama T. PARN-like Proteins Regulate Gene Expression in Land Plant Mitochondria by Modulating mRNA Polyadenylation. Int J Mol Sci 2021; 22:ijms221910776. [PMID: 34639116 PMCID: PMC8509313 DOI: 10.3390/ijms221910776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 10/02/2021] [Indexed: 11/20/2022] Open
Abstract
Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mRNA processing, and translation. These systems differ from those operating in the host cell, and among eukaryotes. In recent decades, studies have revealed several plant-specific features of mitochondrial gene regulation. The polyadenylation status of mRNA is critical for its stability and translation in mitochondria. In this short review, I focus on recent advances in understanding the mechanisms regulating mRNA polyadenylation in plant mitochondria, including the role of poly(A)-specific ribonuclease-like proteins (PARNs). Accumulating evidence suggests that plant mitochondria have unique regulatory systems for mRNA poly(A) status and that PARNs play pivotal roles in these systems.
Collapse
Affiliation(s)
- Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurahiki 710-0046, Okayama, Japan
| |
Collapse
|
3
|
Otsuka K, Mamiya A, Konishi M, Nozaki M, Kinoshita A, Tamaki H, Arita M, Saito M, Yamamoto K, Hachiya T, Noguchi K, Ueda T, Yagi Y, Kobayashi T, Nakamura T, Sato Y, Hirayama T, Sugiyama M. Temperature-dependent fasciation mutants provide a link between mitochondrial RNA processing and lateral root morphogenesis. eLife 2021; 10:61611. [PMID: 33443014 PMCID: PMC7846275 DOI: 10.7554/elife.61611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/13/2021] [Indexed: 12/18/2022] Open
Abstract
Although mechanisms that activate organogenesis in plants are well established, much less is known about the subsequent fine-tuning of cell proliferation, which is crucial for creating properly structured and sized organs. Here we show, through analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), that mitochondrial RNA processing is required for limiting cell division during early lateral root (LR) organogenesis. These mutants formed abnormally broadened (i.e. fasciated) LRs under high-temperature conditions due to extra cell division. All TDF proteins localized to mitochondria, where they were found to participate in RNA processing: RRD1 in mRNA deadenylation, and RRD2 and RID4 in mRNA editing. Further analysis suggested that LR fasciation in the TDF mutants is triggered by reactive oxygen species generation caused by defective mitochondrial respiration. Our findings provide novel clues for the physiological significance of mitochondrial activities in plant organogenesis.
Collapse
Affiliation(s)
- Kurataka Otsuka
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Akihito Mamiya
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mineko Konishi
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mamoru Nozaki
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuko Kinoshita
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Tamaki
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masaki Arita
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masato Saito
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kayoko Yamamoto
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takushi Hachiya
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Shimane, Japan
| | - Ko Noguchi
- Department of Applied Life Science, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Aichi, Japan
| | - Yusuke Yagi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Takehito Kobayashi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Takahiro Nakamura
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yasushi Sato
- Biology and Environmental Science, Graduate School of Science and Engineering, Ehime University, Ehime, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
4
|
Yan YB. Diverse functions of deadenylases in DNA damage response and genomic integrity. Wiley Interdiscip Rev 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
| |
Collapse
|
5
|
Duan TL, Jiao H, He GJ, Yan YB. Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN). Cells 2020; 9:E162. [PMID: 31936572 DOI: 10.3390/cells9010162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
|
6
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
7
|
van Batenburg AA, Kazemier KM, Peeters T, van Oosterhout MFM, van der Vis JJ, Grutters JC, Goldschmeding R, van Moorsel CHM. Cell Type-Specific Quantification of Telomere Length and DNA Double-strand Breaks in Individual Lung Cells by Fluorescence In Situ Hybridization and Fluorescent Immunohistochemistry. J Histochem Cytochem 2018. [PMID: 29529386 DOI: 10.1369/0022155418761351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Telomeres are small repetitive DNA sequences at the ends of chromosomes which act as a buffer in age-dependent DNA shortening. Insufficient telomere repeats will be recognized as double-strand breaks. Presently, it is becoming more evident that telomere attrition, whether or not caused by mutations in telomere maintenance genes, plays an important role in many inflammatory and age-associated diseases. In this report, a method to (semi)quantitatively assess telomere length and DNA double-strand breaks in formalin-fixed paraffin-embedded (FFPE) tissue is described. Therefore, a novel combination of quantitative fluorescence in situ hybridization, tissue elution, and immunofluorescence staining techniques was developed. Caveolin-1 (type 1 pneumocytes), pro-surfactant protein C (type 2 pneumocytes), club cell-10 (club cells), and alpha smooth muscle actin (smooth muscle cells) markers were used to identify cell types. To visualize all the different probes, restaining the tissue by heat-mediated slide elution is essential. Fluorescent signals of telomeres and DNA double-strand breaks were quantified using the Telometer plugin of ImageJ. As example, we analyzed lung tissue from a familial pulmonary fibrosis patient with a mutation in the telomere-associated gene poly(A)-specific ribonuclease ( PARN). The protocol displays a novel opportunity to directly quantitatively link DNA double-strand breaks to telomere length in specific FFPE cells.
Collapse
Affiliation(s)
- 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.,Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ton Peeters
- Department of Pathology, University Medical Center Utrecht, Utrecht, 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 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
| | - Roel Goldschmeding
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Coline H M van Moorsel
- 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
| |
Collapse
|