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Bao J, Su B, Chen Z, Sun Z, Peng J, Zhao S. A UTP3-dependent nucleolar translocation pathway facilitates pre-rRNA 5'ETS processing. Nucleic Acids Res 2024:gkae631. [PMID: 39036955 DOI: 10.1093/nar/gkae631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
The ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. Whilst the biochemical mechanisms of the SSU processome in 18S rRNA processing and maturation have been extensively studied, how SSU processome components enter the nucleolus has yet to be systematically investigated. Here, in examining the nucleolar localization of 50 human SSU processome components, we found that UTP3, together with another 24 proteins, enter the nucleolus autonomously. For the remaining 25 proteins we found that UTP3/SAS10 assists the nucleolar localization of five proteins (MPP10, UTP25, EMG1 and the two UTP-B components UTP12 and UTP13), likely through its interaction with nuclear importin α. This 'ferrying' function of UTP3 was then confirmed as conserved in the zebrafish. We also found that knockdown of human UTP3 impairs cleavage at the A0-site while loss-of-function of either utp3/sas10 or utp13/tbl3 in zebrafish causes the accumulation of aberrantly processed 5'ETS products, which highlights the crucial role of UTP3 in mediating 5'ETS processing. Mechanistically, we found that UTP3 facilitates the degradation of processed 5'ETS by recruiting the RNA exosome component EXOSC10 to the nucleolus. These findings lay the groundwork for studying the mechanism of cytoplasm-to-nucleolus trafficking of SSU processome components.
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Affiliation(s)
- Jiayang Bao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baochun Su
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zheyan Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhaoxiang Sun
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuyi Zhao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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2
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Fasken MB, Leung SW, Cureton LA, Al-Awadi M, Al-Kindy A, van Hoof A, Khoshnevis S, Ghalei H, Al-Maawali A, Corbett AH. A Biallelic Variant of the RNA Exosome Gene, EXOSC4, Associated with Neurodevelopmental Defects Impairs RNA Exosome Function and Translation. J Biol Chem 2024:107571. [PMID: 39009343 DOI: 10.1016/j.jbc.2024.107571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/15/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
The RNA exosome is an evolutionarily conserved complex required for both precise RNA processing and decay. Pathogenic variants in EXOSC genes, which encode structural subunits of this complex, are linked to several autosomal recessive disorders. Here, we describe a missense allele of the EXOSC4 gene that causes a collection of clinical features in two affected siblings. This missense variant (NM_019037.3: exon3:c.560T>C), changes a leucine residue within a conserved region of EXOSC4 to proline (p.Leu187Pro). The two affected individuals show prenatal growth restriction, failure to thrive, global developmental delay, intracerebral and basal ganglia calcifications, and kidney failure. Homozygosity for the damaging variant was identified by exome sequencing with Sanger sequencing to confirm segregation. To explore the functional consequences of this amino acid change, we modeled EXOSC4-L187P in the corresponding budding yeast protein, Rrp41 (Rrp41-L187P). Cells that express Rrp41-L187P as the sole copy of the essential Rrp41 protein show growth defects. Steady-state levels of both Rrp41-L187P and EXOSC4-L187P are decreased compared to controls and EXOSC4-L187P shows decreased co-purification with other RNA exosome subunits. RNA exosome target transcripts accumulate in rrp41-L187P cells, including the 7S precursor of 5.8S rRNA. Polysome profiles show a decrease in actively translating ribosomes in rrp41-L187P cells as compared to control cells with incorporation of 7S pre-rRNA into polysomes. This work adds EXOSC4 to the structural subunits of the RNA exosome that have been linked to human disease and defines foundational molecular defects that could contribute to the adverse phenotypes caused by EXOSC pathogenic variants.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA USA 30322;.
| | - Sara W Leung
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA USA 30322
| | - Lauryn A Cureton
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA USA 30322;; Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322
| | - Maha Al-Awadi
- Sultan Qaboos Hospital, Ministry of Health, Salalah, Oman
| | - Adila Al-Kindy
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA 77030
| | - Sohail Khoshnevis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA USA 30322
| | - Homa Ghalei
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA USA 30322;.
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman;; Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman.
| | - Anita H Corbett
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA USA 30322;.
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3
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Wijnsma KL, Schijvens AM, Bouwmeester RN, Aarts LAM, van den Heuvel L(BP, Haaxma CA, van de Kar NCAJ. Mutations in Genes Encoding Subunits of the RNA Exosome as a Potential Novel Cause of Thrombotic Microangiopathy. Int J Mol Sci 2024; 25:7604. [PMID: 39062862 PMCID: PMC11277116 DOI: 10.3390/ijms25147604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Thrombotic microangiopathy (TMA) in association with RNA exosome encoding mutations has only recently been recognized. Here, we present an infant (female) with an EXOSC5 mutation (c.230_232del p.Glu77del) associated with the clinical phenotype known as CABAC syndrome (cerebellar ataxia, brain abnormalities, and cardiac conduction defects), including pontocerebellar hypoplasia, who developed renal TMA. At the age of four months, she presented with signs of septic illness, after which she developed TMA. A stool culture showed rotavirus as a potential trigger. The patient received eculizumab once, alongside supportive treatment, while awaiting diagnostic analysis of TMA, including genetic complement analysis, all of which were negative. Eculizumab was withdrawn and the patient's TMA recovered quickly. A review of the literature identified an additional four patients (age < 1 year) who developed TMA after a viral trigger in the presence of mutations in EXOSC3. The recurrence of TMA in one of these patients with an EXOSC3 mutation while on eculizumab treatment underscores the apparent lack of responsiveness to C5 inhibition. In conclusion, mutations in genes influencing the RNA exosome, like EXOSC3 and EXOSC5, characterized by neurodevelopment and neurodegenerative disorders could potentially lead to TMA in the absence of complement dysregulation. Hence, these patients were likely non-responsive to eculizumab.
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Affiliation(s)
- Kioa L. Wijnsma
- Department of Pediatric Nephrology, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands (R.N.B.); (L.P.v.d.H.); (N.C.A.J.v.d.K.)
| | - Anne M. Schijvens
- Department of Pediatric Nephrology, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands (R.N.B.); (L.P.v.d.H.); (N.C.A.J.v.d.K.)
| | - Romy N. Bouwmeester
- Department of Pediatric Nephrology, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands (R.N.B.); (L.P.v.d.H.); (N.C.A.J.v.d.K.)
| | - Lonneke A. M. Aarts
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Lambertus (Bert) P. van den Heuvel
- Department of Pediatric Nephrology, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands (R.N.B.); (L.P.v.d.H.); (N.C.A.J.v.d.K.)
| | - Charlotte A. Haaxma
- Department of Pediatric Neurology, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Nicole C. A. J. van de Kar
- Department of Pediatric Nephrology, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands (R.N.B.); (L.P.v.d.H.); (N.C.A.J.v.d.K.)
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4
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Cavusoglu D, Ozturk G, Turkdogan D, Kurul SH, Yis U, Komur M, Incecik F, Kara B, Sahin T, Unver O, Dilber C, Mert GG, Gunay C, Uzan GS, Ersoy O, Oktay Y, Mermer S, Tuncer GO, Gungor O, Ozcora GDK, Gumus U, Sezer O, Cetin GO, Demir F, Yilmaz A, Gurbuz G, Topcu M, Topaloglu H, Ceylan AC, Ceylaner S, Gleeson JG, Icagasioglu DF, Sonmez FM. Evaluation of the Patients with the Diagnosis of Pontocerebellar Hypoplasia: A Multicenter National Study. CEREBELLUM (LONDON, ENGLAND) 2024:10.1007/s12311-024-01690-1. [PMID: 38622473 DOI: 10.1007/s12311-024-01690-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/17/2024]
Abstract
Pontocerebellar hypoplasia (PCH) is a heterogeneous group of neurodegenerative disorders characterized by hypoplasia and degeneration of the cerebellum and pons. We aimed to identify the clinical, laboratory, and imaging findings of the patients with diagnosed PCH with confirmed genetic analysis. We collected available clinical data, laboratory, and imaging findings in our retrospective multicenter national study of 64 patients with PCH in Turkey. The genetic analysis included the whole-exome sequencing (WES), targeted next-generation sequencing (NGS), or single gene analysis. Sixty-four patients with PCH were 28 female (43.8%) and 36 (56.3%) male. The patients revealed homozygous mutation in 89.1%, consanguinity in 79.7%, pregnancy at term in 85.2%, microcephaly in 91.3%, psychomotor retardation in 98.4%, abnormal neurological findings in 100%, seizure in 63.8%, normal biochemistry and metabolic investigations in 92.2%, and dysmorphic findings in 51.2%. The missense mutation was found to be the most common variant type in all patients with PCH. It was detected as CLP1 (n = 17) was the most common PCH related gene. The homozygous missense variant c.419G > A (p.Arg140His) was identified in all patients with CLP1. Moreover, all patients showed the same homozygous missense variant c.919G > T (p.A307S) in TSEN54 group (n = 6). In Turkey, CLP1 was identified as the most common causative gene with the identical variant c.419G > A; p.Arg140His. The current study supports that genotype data on PCH leads to phenotypic variability over a wide phenotypic spectrum.
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Affiliation(s)
- Dilek Cavusoglu
- Departments of Pediatric Neurology, Afyonkarahisar Health Sciences University, Afyon, Turkey
| | - Gulten Ozturk
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Dilsad Turkdogan
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Semra Hiz Kurul
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | - Uluc Yis
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | - Mustafa Komur
- Departments of Pediatric Neurology, Mersin University, Mersin, Turkey
| | - Faruk Incecik
- Departments of Pediatric Neurology, Cukurova University, Adana, Turkey
| | - Bulent Kara
- Departments of Pediatric Neurology, Kocaeli University, Kocaeli, Turkey
| | - Turkan Sahin
- Departments of Pediatric Neurology, Bezmialem Vakif University, Istanbul, Turkey
| | - Olcay Unver
- Departments of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Cengiz Dilber
- Departments of Pediatric Neurology, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
| | - Gulen Gul Mert
- Departments of Pediatric Neurology, Cukurova University, Adana, Turkey
| | - Cagatay Gunay
- Departments of Pediatric Neurology, Dokuz Eylul University, Izmir, Turkey
| | | | - Ozlem Ersoy
- Departments of Pediatric Neurology, Mersin University, Mersin, Turkey
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Serdar Mermer
- Departments of Medical Genetics, Mersin University, Mersin, Turkey
| | - Gokcen Oz Tuncer
- Departments of Pediatric Neurology, Ondokuz Mayıs University, Samsun, Turkey
| | - Olcay Gungor
- Departments of Pediatric Neurology, Pamukkale University, Denizli, Turkey
| | | | - Ugur Gumus
- Departments of Medical Genetics, Dr Ersin Arslan Training and Research Hospital, Gaziantep, Turkey
| | - Ozlem Sezer
- Departments of Medical Genetics, Samsun Training and Research Hospital, Samsun, Turkey
| | - Gokhan Ozan Cetin
- Departments of Medical Genetics, Pamukkale University, Denizli, Turkey
| | - Fatma Demir
- Departments of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Arzu Yilmaz
- Departments of Pediatric Neurology, Ankara Training and Research Hospital, Ankara, Turkey
| | - Gurkan Gurbuz
- Departments of Pediatric Neurology, Tekirdag Namik Kemal University, Tekirdag, Turkey
| | - Meral Topcu
- Departments of Pediatric Neurology, Hacettepe University,Retired Lecturer, Ankara, Turkey
| | - Haluk Topaloglu
- Departments of Pediatric Neurology, Yeditepe University, Istanbul, Turkey
| | - Ahmet Cevdet Ceylan
- Departments of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | | | - Joseph G Gleeson
- Department of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, La Jolla, San Diego, CA, USA
| | | | - F Mujgan Sonmez
- Departments of Pediatric Neurology, Department of Child Neurology, Karadeniz Technical University Medical Faculty, Retired Lecturer, Trabzon, Turkey.
- Yuksek Ihtisas University, Faculty of Medicine, Ankara, Turkey.
- , Aziziye Mah. Cinnah Cad. 102/3, Cankaya, Ankara, Türkiye.
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5
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Zaki MS, Abdel-Ghafar SF, Abdel-Hamid MS. A missense variant in EXOSC8 causes exon skipping and expands the phenotypic spectrum of pontocerebellar hypoplasia type 1C. J Hum Genet 2024; 69:79-84. [PMID: 38017281 PMCID: PMC10810757 DOI: 10.1038/s10038-023-01207-4] [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: 07/10/2023] [Revised: 08/29/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
Pontocerebellar hypoplasia (PCH) is a rare heterogeneous neurodegenerative disorder affecting the pons and cerebellum and is currently classified into 17 types (PCH1-PCH17). PCH1 is distinguishable from other types by the association of spinal motor neuron dysfunction. Based on the underlying genetic etiology, PCH1 is further classified into 6 different subtypes (PCH1 A-F). Of them, PCH type 1C is caused by pathogenic variants in EXOSC8 gene and so far, only four families have been described in the literature. In this study, we report a new patient with PCH1 who proved by whole-exome sequencing to harbor a novel homozygous missense variant in the splice region of EXOSC8 gene (c.238 G > A; p.Val80Ile). Studying mRNA of the patient confirmed that this variant results in skipping of exon 5 of the gene and early protein truncation. Our patient presented with the main clinical findings of PCH type 1C including psychomotor retardation, spasticity, spinal muscle atrophy, and respiratory problems. However, unlike most of the reported cases, he did not develop hearing or visual impairment and displayed a longer survival. In addition, our patient had dysmorphic facies, nystagmus, congenital esotropia and contractures which were infrequently described in patients with EXOSC8. Diaphragmatic hernia, dilated lateral ventricles, hypoplastic temporal lobes, and thinning of the brain stem were additional new findings noted in our patient. This study presents the fifth family with this extremely rare type of PCH and expands the associated clinical and brain imaging findings.
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Affiliation(s)
- Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.
| | - Sherif F Abdel-Ghafar
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.
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6
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Brocklebank V, Walsh PR, Smith-Jackson K, Hallam TM, Marchbank KJ, Wilson V, Bigirumurame T, Dutt T, Montgomery EK, Malina M, Wong EKS, Johnson S, Sheerin NS, Kavanagh D. Atypical hemolytic uremic syndrome in the era of terminal complement inhibition: an observational cohort study. Blood 2023; 142:1371-1386. [PMID: 37369098 PMCID: PMC10651868 DOI: 10.1182/blood.2022018833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 05/11/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Historically, the majority of patients with complement-mediated atypical hemolytic uremic syndrome (CaHUS) progress to end-stage kidney disease (ESKD). Single-arm trials of eculizumab with a short follow-up suggested efficacy. We prove, for the first time to our knowledge, in a genotype matched CaHUS cohort that the 5-year cumulative estimate of ESKD-free survival improved from 39.5% in a control cohort to 85.5% in the eculizumab-treated cohort (hazard ratio, 4.95; 95% confidence interval [CI], 2.75-8.90; P = .000; number needed to treat, 2.17 [95% CI, 1.81-2.73]). The outcome of eculizumab treatment is associated with the underlying genotype. Lower serum creatinine, lower platelet count, lower blood pressure, and younger age at presentation as well as shorter time between presentation and the first dose of eculizumab were associated with estimated glomerular filtration rate >60 ml/min at 6 months in multivariate analysis. The rate of meningococcal infection in the treated cohort was 550 times greater than the background rate in the general population. The relapse rate upon eculizumab withdrawal was 1 per 9.5 person years for patients with a pathogenic mutation and 1 per 10.8 person years for those with a variant of uncertain significance. No relapses were recorded in 67.3 person years off eculizumab in those with no rare genetic variants. Eculizumab was restarted in 6 individuals with functioning kidneys in whom it had been stopped, with no individual progressing to ESKD. We demonstrated that biallelic pathogenic mutations in RNA-processing genes, including EXOSC3, encoding an essential part of the RNA exosome, cause eculizumab nonresponsive aHUS. Recessive HSD11B2 mutations causing apparent mineralocorticoid excess may also present with thrombotic microangiopathy.
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Affiliation(s)
- Vicky Brocklebank
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Complement Therapeutics Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Patrick R. Walsh
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Complement Therapeutics Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kate Smith-Jackson
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Complement Therapeutics Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas M. Hallam
- Complement Therapeutics Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kevin J. Marchbank
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Complement Therapeutics Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Valerie Wilson
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Theophile Bigirumurame
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tina Dutt
- Department of Haematology, Royal Liverpool University Hospital, Liverpool, United Kingdom
| | - Emma K. Montgomery
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Michal Malina
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Complement Therapeutics Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Great North Children's Hospital, Sir James Spence Institute, Royal Victoria Infirmary, Newcastle, United Kingdom
| | - Edwin K. S. Wong
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Sally Johnson
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Great North Children's Hospital, Sir James Spence Institute, Royal Victoria Infirmary, Newcastle, United Kingdom
| | - Neil S. Sheerin
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Complement Therapeutics Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Kavanagh
- National Renal Complement Therapeutics Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Complement Therapeutics Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- National Institute for Health and Care Research Newcastle Biomedical Research Centre, Biomedical Research Building, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
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7
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Eastham MJ, Pelava A, Wells GR, Watkins NJ, Schneider C. RPS27a and RPL40, Which Are Produced as Ubiquitin Fusion Proteins, Are Not Essential for p53 Signalling. Biomolecules 2023; 13:898. [PMID: 37371478 DOI: 10.3390/biom13060898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Two of the four human ubiquitin-encoding genes express ubiquitin as an N-terminal fusion precursor polypeptide, with either ribosomal protein (RP) RPS27a or RPL40 at the C-terminus. RPS27a and RPL40 have been proposed to be important for the induction of the tumour suppressor p53 in response to defects in ribosome biogenesis, suggesting that they may play a role in the coordination of ribosome production, ubiquitin levels and p53 signalling. Here, we report that RPS27a is cleaved from the ubiquitin-RP precursor in a process that appears independent of ribosome biogenesis. In contrast to other RPs, the knockdown of either RPS27a or RPL40 did not stabilise the tumour suppressor p53 in U2OS cells. Knockdown of neither protein blocked p53 stabilisation following inhibition of ribosome biogenesis by actinomycin D, indicating that they are not needed for p53 signalling in these cells. However, the knockdown of both RPS27a and RPL40 in MCF7 and LNCaP cells robustly induced p53, consistent with observations made with the majority of other RPs. Importantly, RPS27a and RPL40 are needed for rRNA production in all cell lines tested. Our data suggest that the role of RPS27a and RPL40 in p53 signalling, but not their importance in ribosome biogenesis, differs between cell types.
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Affiliation(s)
- Matthew John Eastham
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andria Pelava
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Graeme Raymond Wells
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Nicholas James Watkins
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Claudia Schneider
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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8
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LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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9
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Cui K, Gong L, Zhang H, Chen Y, Liu B, Gong Z, Li J, Wang Y, Sun S, Li Y, Zhang Q, Cao Y, Li Q, Fei B, Huang Z. EXOSC8 promotes colorectal cancer tumorigenesis via regulating ribosome biogenesis-related processes. Oncogene 2022; 41:5397-5410. [PMID: 36348012 DOI: 10.1038/s41388-022-02530-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Extensive protein synthesis is necessary for uncontrolled cancer cell proliferation, requiring hyperactive ribosome biogenesis. Our previous Pan-cancer study has identified EXOSC8 as a potential copy number variation (CNV)-driven rRNA metabolism-related oncogene in colorectal cancer (CRC). Herein, we further investigated proliferation-prompting functions and mechanisms of EXOSC8 in CRC by performing in silico analyses and wet-lab experiments. We uncovered that increased EXOSC8 expression and CNV levels are strongly associated with ribosome biogenesis-related factor levels in CRC, including ribosome proteins (RPs), eukaryotic translation initiation factors and RNA polymerase I/III. EXOSC8 silence decreases nucleolar protein and proliferation marker levels, as well as rRNA/DNA and global protein syntheses. Clinically, EXOSC8 is upregulated across human cancers, particularly CNV-driven upregulation in CRC was markedly associated with poor clinical outcomes. Mechanistically, EXOSC8 knockdown increased p53 levels in CRC, and the oncogenic proliferation phenotypes of EXOSC8 depended on p53 in vitro and in vivo. We discovered that EXOSC8 knockdown in CRC cells triggers ribosomal stress, nucleolar RPL5/11 being released into the nucleoplasm and "hijacking" Mdm2 to block its E3 ubiquitin ligase function, thus releasing and activating p53. Furthermore, our therapeutic experiments provided initial evidence that EXOSC8 might serve as a potential therapeutic target in CRC. Our findings revealed, for the first time, that the RNA exosome gene (EXOSC8) promotes CRC tumorigenesis by regulating cancer-related ribosome biogenesis in CRC. This study further extends our previous Pan-cancer study of the rRNA metabolism-related genes. The inhibition of EXOSC8 is a novel therapeutic strategy for the RPs-Mdm2-p53 ribosome biogenesis surveillance pathway in CRC.
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Affiliation(s)
- Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China.
| | - Liang Gong
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Han Zhang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Ying Chen
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Bingxin Liu
- The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Zhicheng Gong
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Jiuming Li
- Key Laboratory of Environment Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Yuanben Wang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Shengbai Sun
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Yajun Li
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Outstanding Overseas Scientists Center for Pulmonary Fibrosis of Henan Province, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan, 453000, China
| | - Qiang Zhang
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Yulin Cao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Qilin Li
- Computer Vision Lab, Department of Electrical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bojian Fei
- Department of Surgical Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China.
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10
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Hayne CK, Lewis TA, Stanley RE. Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1717. [PMID: 35156311 PMCID: PMC9465713 DOI: 10.1002/wrna.1717] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 04/30/2023]
Abstract
The splicing of transfer RNA (tRNA) introns is a critical step of tRNA maturation, for intron-containing tRNAs. In eukaryotes, tRNA splicing is a multi-step process that relies on several RNA processing enzymes to facilitate intron removal and exon ligation. Splicing is initiated by the tRNA splicing endonuclease (TSEN) complex which catalyzes the excision of the intron through its two nuclease subunits. Mutations in all four subunits of the TSEN complex are linked to a family of neurodegenerative and neurodevelopmental diseases known as pontocerebellar hypoplasia (PCH). Recent studies provide molecular insights into the structure, function, and regulation of the eukaryotic TSEN complex and are beginning to illuminate how mutations in the TSEN complex lead to neurodegenerative disease. Using new advancements in the prediction of protein structure, we created a three-dimensional model of the human TSEN complex. We review functions of the TSEN complex beyond tRNA splicing by highlighting recently identified substrates of the eukaryotic TSEN complex and discuss mechanisms for the regulation of tRNA splicing, by enzymes that modify cleaved tRNA exons and introns. Finally, we review recent biochemical and animal models that have worked to address the mechanisms that drive PCH and synthesize these studies with previous studies to try to better understand PCH pathogenesis. This article is categorized under: RNA Processing > tRNA Processing RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Cassandra K Hayne
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Tanae A Lewis
- Department of Chemistry, North Carolina Agricultural and Technical State University, Greensboro, North Carolina, USA
| | - Robin E Stanley
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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11
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Pontocerebellar Hypoplasia Type 1D: A Case Report and Comprehensive Literature Review. J Clin Med 2022; 11:jcm11154335. [PMID: 35893425 PMCID: PMC9368788 DOI: 10.3390/jcm11154335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/09/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
Pontocerebellar hypoplasia (PCH) is an autosomal recessive, neurodegenerative disorder with multiple subtypes leading to severe neurodevelopmental disabilities. PCH type 1 D is linked to alterations in the EXOSC9 gene. EXOSC9 is a component of the RNA exosome, an evolutionarily conserved ribonuclease complex essential for RNA degradation and processing. The clinical phenotype is characterized by cerebellar and pontine hypoplasia associated with motor neuronopathy. To date, nine patients have been reported in the literature with PCH1D. We report the case of an infant with PCH type 1D due to two variants in the EXOCS9 gene (NM_001034194.1: c.41T>C-p.Leu14Pro) and a novel variant (c.643C>T-p.Arg212*). This report thoroughly reviews the literature PCH1D and highlights the crucial role of the exosome in cellular homeostasis.
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12
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Bashirzade AA, Zabegalov KN, Volgin AD, Belova AS, Demin KA, de Abreu MS, Babchenko VY, Bashirzade KA, Yenkoyan KB, Tikhonova MA, Amstislavskaya TG, Kalueff AV. Modeling neurodegenerative disorders in zebrafish. Neurosci Biobehav Rev 2022; 138:104679. [PMID: 35490912 DOI: 10.1016/j.neubiorev.2022.104679] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/11/2022] [Accepted: 04/24/2022] [Indexed: 12/15/2022]
Abstract
Neurodegeneration is a major cause of Alzheimer's, Parkinson's, Huntington's, multiple and amyotrophic lateral sclerosis, pontocerebellar hypoplasia, dementia and other related brain disorders. Their complex pathogenesis commonly includes genetic and neurochemical deficits, misfolded protein toxicity, demyelination, apoptosis and mitochondrial dysfunctions. Albeit differing in specific underlying mechanisms, neurodegenerative disorders typically display evolutionarily conserved mechanisms across taxa. Here, we review the role of zebrafish models in recapitulating major human and rodent neurodegenerative conditions, demonstrating this species as a highly relevant experimental model for research on neurodegenerative diseases, and discussing how these fish models can further clarify the underlying genetic, neurochemical, neuroanatomical and behavioral pathogenic mechanisms.
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Affiliation(s)
- Alim A Bashirzade
- Novosibirsk State University, Institute of Medicine and Psychology, Novosibirsk, Russia; Scientific Research Institute of Neuroscience and Medicine, Novosibirsk, Russia
| | | | - Andrey D Volgin
- Novosibirsk State University, Institute of Medicine and Psychology, Novosibirsk, Russia; Scientific Research Institute of Neuroscience and Medicine, Novosibirsk, Russia
| | - Alisa S Belova
- Novosibirsk State University, Institute of Medicine and Psychology, Novosibirsk, Russia; Scientific Research Institute of Neuroscience and Medicine, Novosibirsk, Russia
| | - Konstantin A Demin
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Granov Scientific Research Center of Radiology and Surgical Technologies, St. Petersburg, Russia; Almazov Medical Research Center, St. Petersburg, Russia
| | | | - Vladislav Ya Babchenko
- Novosibirsk State University, Institute of Medicine and Psychology, Novosibirsk, Russia; Scientific Research Institute of Neuroscience and Medicine, Novosibirsk, Russia
| | - Kseniya A Bashirzade
- Novosibirsk State University, Institute of Medicine and Psychology, Novosibirsk, Russia
| | - Konstantin B Yenkoyan
- Neuroscience Laboratory, COBRAIN Center, M Heratsi Yerevan State Medical University, Yerevan, Armenia; COBRAIN Center - Scientific Educational Center for Fundamental Brain Research, Yerevan, Armenia
| | - Maria A Tikhonova
- Novosibirsk State University, Institute of Medicine and Psychology, Novosibirsk, Russia; Scientific Research Institute of Neuroscience and Medicine, Novosibirsk, Russia
| | - Tamara G Amstislavskaya
- Novosibirsk State University, Institute of Medicine and Psychology, Novosibirsk, Russia; Scientific Research Institute of Neuroscience and Medicine, Novosibirsk, Russia
| | - Allan V Kalueff
- The Russian Academy of Sciences, Moscow, Russia; Ural Federal University, Yekaterinburg, Russia; COBRAIN Center - Scientific Educational Center for Fundamental Brain Research, Yerevan, Armenia.
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13
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Trehalose Treatment in Zebrafish Model of Lafora Disease. Int J Mol Sci 2022; 23:ijms23126874. [PMID: 35743315 PMCID: PMC9224929 DOI: 10.3390/ijms23126874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 01/18/2023] Open
Abstract
Mutations in the EPM2A gene encoding laforin cause Lafora disease (LD), a progressive myoclonic epilepsy characterized by drug-resistant seizures and progressive neurological impairment. To date, rodents are the only available models for studying LD; however, their use for drug screening is limited by regulatory restrictions and high breeding costs. To investigate the role of laforin loss of function in early neurodevelopment, and to screen for possible new compounds for treating the disorder, we developed a zebrafish model of LD. Our results showed the epm2a−/− zebrafish to be a faithful model of LD, exhibiting the main disease features, namely motor impairment and neuronal hyperexcitability with spontaneous seizures. The model also showed increased inflammatory response and apoptotic death, as well as an altered autophagy pathway that occurs early in development and likely contributes to the disease progression. Early administration of trehalose was found to be effective for rescuing motor impairment and neuronal hyperexcitability associated with seizures. Our study adds a new tool for investigating LD and might help to identify new treatment opportunities.
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14
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Taniue K, Tanu T, Shimoura Y, Mitsutomi S, Han H, Kakisaka R, Ono Y, Tamamura N, Takahashi K, Wada Y, Mizukami Y, Akimitsu N. RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival. Int J Mol Sci 2022; 23:496. [PMID: 35008922 PMCID: PMC8745236 DOI: 10.3390/ijms23010496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
The RNA exosome is a multi-subunit ribonuclease complex that is evolutionally conserved and the major cellular machinery for the surveillance, processing, degradation, and turnover of diverse RNAs essential for cell viability. Here we performed integrated genomic and clinicopathological analyses of 27 RNA exosome components across 32 tumor types using The Cancer Genome Atlas PanCancer Atlas Studies' datasets. We discovered that the EXOSC4 gene, which encodes a barrel component of the RNA exosome, was amplified across multiple cancer types. We further found that EXOSC4 alteration is associated with a poor prognosis of pancreatic cancer patients. Moreover, we demonstrated that EXOSC4 is required for the survival of pancreatic cancer cells. EXOSC4 also repressed BIK expression and destabilized SESN2 mRNA by promoting its degradation. Furthermore, knockdown of BIK and SESN2 could partially rescue pancreatic cells from the reduction in cell viability caused by EXOSC4 knockdown. Our study provides evidence for EXOSC4-mediated regulation of BIK and SESN2 mRNA in the survival of pancreatic tumor cells.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yuki Shimoura
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Shuhei Mitsutomi
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Nobue Tamamura
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Kenji Takahashi
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yusuke Mizukami
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
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15
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Bryant CJ, McCool MA, Abriola L, Surovtseva YV, Baserga SJ. A high-throughput assay for directly monitoring nucleolar rRNA biogenesis. Open Biol 2022; 12:210305. [PMID: 35078352 PMCID: PMC8790372 DOI: 10.1098/rsob.210305] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Studies of the regulation of nucleolar function are critical for ascertaining clearer insights into the basic biological underpinnings of ribosome biogenesis (RB), and for future development of therapeutics to treat cancer and ribosomopathies. A number of high-throughput primary assays based on morphological alterations of the nucleolus can indirectly identify hits affecting RB. However, there is a need for a more direct high-throughput assay for a nucleolar function to further evaluate hits. Previous reports have monitored nucleolar rRNA biogenesis using 5-ethynyl uridine (5-EU) in low-throughput. We report a miniaturized, high-throughput 5-EU assay that enables specific calculation of nucleolar rRNA biogenesis inhibition, based on co-staining of the nucleolar protein fibrillarin (FBL). The assay uses two siRNA controls: a negative non-targeting siRNA control and a positive siRNA control targeting RNA Polymerase 1 (RNAP1; POLR1A), and specifically quantifies median 5-EU signal within nucleoli. Maximum nuclear 5-EU signal can also be used to monitor the effects of putative small-molecule inhibitors of RNAP1, like BMH-21, or other treatment conditions that cause FBL dispersion. We validate the 5-EU assay on 68 predominately nucleolar hits from a high-throughput primary screen, showing that 58/68 hits significantly inhibit nucleolar rRNA biogenesis. Our new method establishes direct quantification of nucleolar function in high-throughput, facilitating closer study of RB in health and disease.
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Affiliation(s)
- Carson J. Bryant
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Mason A. McCool
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Susan J. Baserga
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA,Department of Genetics, Yale School of Medicine, New Haven, CT, USA,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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16
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Efficient Neuroprotective Rescue of Sacsin-Related Disease Phenotypes in Zebrafish. Int J Mol Sci 2021; 22:ijms22168401. [PMID: 34445111 PMCID: PMC8395086 DOI: 10.3390/ijms22168401] [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: 06/24/2021] [Revised: 07/24/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a multisystem hereditary ataxia associated with mutations in SACS, which encodes sacsin, a protein of still only partially understood function. Although mouse models of ARSACS mimic largely the disease progression seen in humans, their use in the validation of effective therapies has not yet been proposed. Recently, the teleost Danio rerio has attracted increasing attention as a vertebrate model that allows rapid and economical screening, of candidate molecules, and thus combines the advantages of whole-organism phenotypic assays and in vitro high-throughput screening assays. Through CRISPR/Cas9-based mutagenesis, we generated and characterized a zebrafish sacs-null mutant line that replicates the main features of ARSACS. The sacs-null fish showed motor impairment, hindbrain atrophy, mitochondrial dysfunction, and reactive oxygen species accumulation. As proof of principle for using these mutant fish in high-throughput screening studies, we showed that both acetyl-DL-leucine and tauroursodeoxycholic acid improved locomotor and biochemical phenotypes in sacs−/− larvae treated with these neuroprotective agents, by mediating significant rescue of the molecular functions altered by sacsin loss. Taken together, the evidence here reported shows the zebrafish to be a valuable model organism for the identification of novel molecular mechanisms and for efficient and rapid in vivo optimization and screening of potential therapeutic compounds. These findings may pave the way for new interventions targeting the earliest phases of Purkinje cell degeneration in ARSACS.
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17
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Rodríguez-García ME, Cotrina-Vinagre FJ, Bellusci M, Merino-López A, Chumilla-Calzada S, García-Silva MT, Martínez-Azorín F. New subtype of PCH1C caused by novel EXOSC8 variants in a 16-year-old Spanish patient. Neuromuscul Disord 2021; 31:773-782. [PMID: 34210538 DOI: 10.1016/j.nmd.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/05/2021] [Accepted: 05/20/2021] [Indexed: 10/21/2022]
Abstract
We report the case of a 16-year-old Spanish boy with cerebellar and spinal muscular atrophy, spasticity, psychomotor retardation, nystagmus, ophthalmoparesis, epilepsy, and mitochondrial respiratory chain (MRC) deficiency. Whole exome sequencing (WES) uncovered three variants (two of them novel) in a compound heterozygous in EXOSC8 gene (NM_181503.3:c.[390+1delG];[628C>T;815G>C]) that encodes the exosome complex component RRP43 protein (EXOSC8). In order to assess the pathogenicity of these variants, expression experiments of RNA and protein for EXOSC8 were carried out. The c.[390+1delG] variant produces the elimination of exon 7 (r.[345_390del]; p.[Ser116LysfsTer27]) and a decrease of the RNA expression in relation to the other allele (p.[Pro210Ser;Ser272Thr]). Furthermore, total mRNA expression is reduced by 30% and the protein level by 65%. EXOSC8 is an essential protein of the exosome core, a ubiquitously expressed complex responsible for RNA processing and degradation. Recessive mutations in EXOSC8 cause pontocerebellar hypoplasia type 1C (PCH1C), and currently, only two homozygous variants in this gene have been described. However, unlike PCH1C-affected individuals with EXOSC8 variants, our patient presents a normal supratentorial cerebral tissue (neither corpus callosum hypoplasia nor hypomyelination) with a less severe phenotype and longer survival. In conclusion, our data expand both genetic and phenotypic spectrum associated with EXOSC8 variants.
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Affiliation(s)
- María Elena Rodríguez-García
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN). Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, E-28041 Madrid, Spain.
| | - Francisco Javier Cotrina-Vinagre
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN). Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041 Madrid, Spain
| | - Marcello Bellusci
- Unidad Pediátrica de Enfermedades Raras, Enfermedades Mitocondriales y Metabólicas Hereditarias, Hospital 12 de Octubre, E-28041, Madrid, Spain
| | - Abraham Merino-López
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN). Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041 Madrid, Spain
| | - Silvia Chumilla-Calzada
- Unidad Pediátrica de Enfermedades Raras, Enfermedades Mitocondriales y Metabólicas Hereditarias, Hospital 12 de Octubre, E-28041, Madrid, Spain
| | - María Teresa García-Silva
- Unidad Pediátrica de Enfermedades Raras, Enfermedades Mitocondriales y Metabólicas Hereditarias, Hospital 12 de Octubre, E-28041, Madrid, Spain
| | - Francisco Martínez-Azorín
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN). Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, E-28041 Madrid, Spain.
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18
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Zhu Q, Tao B, Chen H, Shi H, Huang L, Chen J, Hu M, Lo LJ, Peng J. Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish. Nucleic Acids Res 2021; 49:5743-5759. [PMID: 34019640 PMCID: PMC8191805 DOI: 10.1093/nar/gkab381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/24/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Yeast Rcl1 is a potential endonuclease that mediates pre-RNA cleavage at the A2-site to separate 18S rRNA from 5.8S and 25S rRNAs. However, the biological function of Rcl1 in opisthokonta is poorly defined. Moreover, there is no information regarding the exact positions of 18S pre-rRNA processing in zebrafish. Here, we report that zebrafish pre-rRNA harbours three major cleavage sites in the 5′ETS, namely –477nt (A′-site), –97nt (A0-site) and the 5′ETS and 18S rRNA link (A1-site), as well as two major cleavage regions within the ITS1, namely 208–218nt (site 2) and 20–33nt (site E). We also demonstrate that depletion of zebrafish Rcl1 mainly impairs cleavage at the A1-site. Phenotypically, rcl1–/– mutants exhibit a small liver and exocrine pancreas and die before 15 days post-fertilization. RNA-seq analysis revealed that the most significant event in rcl1–/– mutants is the up-regulated expression of a cohort of genes related to ribosome biogenesis and tRNA production. Our data demonstrate that Rcl1 is essential for 18S rRNA maturation at the A1-site and for digestive organogenesis in zebrafish. Rcl1 deficiency, similar to deficiencies in other ribosome biogenesis factors, might trigger a common mechanism to upregulate the expression of genes responsible for ribosome biogenesis.
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Affiliation(s)
- Qinfang Zhu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Boxiang Tao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Hong Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Ling Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Hu
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
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19
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Somashekar PH, Kaur P, Stephen J, Guleria VS, Kadavigere R, Girisha KM, Bielas S, Upadhyai P, Shukla A. Bi-allelic missense variant, p.Ser35Leu in EXOSC1 is associated with pontocerebellar hypoplasia. Clin Genet 2021; 99:594-600. [PMID: 33463720 PMCID: PMC9990822 DOI: 10.1111/cge.13928] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Abstract
RNA exosome is a highly conserved ribonuclease complex essential for RNA processing and degradation. Bi-allelic variants in exosome subunits EXOSC3, EXOSC8 and EXOSC9 have been reported to cause pontocerebellar hypoplasia type 1B, type 1C and type 1D, respectively, while those in EXOSC2 cause short stature, hearing loss, retinitis pigmentosa and distinctive facies. We ascertained an 8-months-old male with developmental delay, microcephaly, subtle dysmorphism and hypotonia. Pontocerebellar hypoplasia and delayed myelination were noted on neuroimaging. A similarly affected elder sibling succumbed at the age of 4-years 6-months. Chromosomal microarray returned normal results. Exome sequencing revealed a homozygous missense variant, c.104C > T p.(Ser35Leu) in EXOSC1 (NM_016046.5) as the possible candidate. In silico mutagenesis revealed loss of a polar contact with neighboring Leu37 residue. Quantitative real-time PCR indicated no appreciable differences in EXOSC1 transcript levels. Immunoblotting and blue native PAGE revealed reduction in the EXOSC1 protein levels and EXO9 complex in the proband, respectively. We herein report an individual with the bi-allelic variant c.104C>T p.(Ser35Leu) in EXOSC1 and clinical features of pontocerebellar hypoplasia type 1. Immunoblotting and blue native PAGE provide evidence for the pathogenicity of the variant. Thus, we propose EXOSC1 as a novel candidate gene for pontocerebellar hypoplasia.
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Affiliation(s)
- Puneeth H Somashekar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Joshi Stephen
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vishal Singh Guleria
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis and Imaging, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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