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Yao R, Xie C, Xia X. Recent progress in mRNA cancer vaccines. Hum Vaccin Immunother 2024; 20:2307187. [PMID: 38282471 PMCID: PMC10826636 DOI: 10.1080/21645515.2024.2307187] [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: 09/28/2023] [Accepted: 01/16/2024] [Indexed: 01/30/2024] Open
Abstract
The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens, structural optimization of mRNA, and the development of alternative RNA-based vectors and efficient targeted delivery vectors. Clinical trials are currently underway for various cancer vaccines that encode tumor-associated antigens (TAAs), tumor-specific antigens (TSAs), or immunomodulators. In this paper, we summarize the optimization of mRNA and the emergence of RNA-based expression vectors in cancer vaccines. We begin by reviewing the advancement and utilization of state-of-the-art targeted lipid nanoparticles (LNPs), followed by presenting the primary classifications and clinical applications of mRNA cancer vaccines. Collectively, mRNA vaccines are emerging as a central focus in cancer immunotherapy, offering the potential to address multiple challenges in cancer treatment, either as standalone therapies or in combination with current cancer treatments.
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Affiliation(s)
- Ruhui Yao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunyuan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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2
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Kulkarni S, Morrissey A, Sebastian A, Keller CA, Giardine B, Smith C, Akinniyi OT, Arnaoutov A, Albert I, Mahony S, Reese JC. Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.612038. [PMID: 39314347 PMCID: PMC11419117 DOI: 10.1101/2024.09.10.612038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
CCR4-NOT regulates multiple steps in gene regulation, including transcription, mRNA decay, protein ubiquitylation, and translation. It has been well studied in budding yeast; however, relatively less is known about its regulation and functions in mammals. To characterize the functions of the human CCR4-NOT complex, we developed a rapid auxin-induced degron system to deplete CNOT1 (the scaffold of the complex) and CNOT4 (E3 ubiquitin ligase) in cell culture. Transcriptome-wide measurements of gene-expression revealed that depleting CNOT1 changed several thousand transcripts, wherein most mRNAs were increased and resulted in a global decrease in mRNA decay rates. In contrast to what was observed in CNOT1-depleted cells, CNOT4 depletion only modestly changed RNA steady-state levels and, surprisingly, led to a global acceleration in mRNA decay. To further investigate the role of CCR4-NOT in transcription, we used transient transcriptome sequencing (TT-seq) to measure ongoing RNA synthesis. Depletion of either subunit resulted in increased RNA synthesis of several thousand genes. In contrast to most of the genome, a rapid reduction in the synthesis of KRAB-Zinc-Finger-proteins (KZNFs) genes, especially those clustered on chromosome 19, was observed. KZNFs are transcriptional repressors of retro-transposable elements (rTEs), and consistent with the decreased KZNFs expression, we observed a significant and rapid activation of rTEs, mainly Long interspersed Nuclear Elements (LINEs). Our data reveal that CCR4-NOT regulates gene expression and silences retrotransposons across the genome by maintaining KZNF expression. These data establish CCR4-NOT as a global regulator of gene expression, and we have identified a novel mammalian-specific function of the complex, the suppression of rTEs.
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3
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Pereira CD, Espadas G, Martins F, Bertrand AT, Servais L, Sabidó E, Chevalier P, da Cruz e Silva OA, Rebelo S. Quantitative proteome analysis of LAP1-deficient human fibroblasts: A pilot approach for predicting the signaling pathways deregulated in LAP1-associated diseases. Biochem Biophys Rep 2024; 39:101757. [PMID: 39035020 PMCID: PMC11260385 DOI: 10.1016/j.bbrep.2024.101757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/23/2024] Open
Abstract
Lamina-associated polypeptide 1 (LAP1), a ubiquitously expressed nuclear envelope protein, appears to be essential for the maintenance of cell homeostasis. Although rare, mutations in the human LAP1-encoding TOR1AIP1 gene cause severe diseases and can culminate in the premature death of affected individuals. Despite there is increasing evidence of the pathogenicity of TOR1AIP1 mutations, the current knowledge on LAP1's physiological roles in humans is limited; hence, investigation is required to elucidate the critical functions of this protein, which can be achieved by uncovering the molecular consequences of LAP1 depletion, a topic that remains largely unexplored. In this work, the proteome of patient-derived LAP1-deficient fibroblasts carrying a pathological TOR1AIP1 mutation (LAP1 E482A) was quantitatively analyzed to identify global changes in protein abundance levels relatively to control fibroblasts. An in silico functional enrichment analysis of the mass spectrometry-identified differentially expressed proteins was also performed, along with additional in vitro functional assays, to unveil the biological processes that are potentially dysfunctional in LAP1 E482A fibroblasts. Collectively, our findings suggest that LAP1 deficiency may induce significant alterations in various cellular activities, including DNA repair, messenger RNA degradation/translation, proteostasis and glutathione metabolism/antioxidant response. This study sheds light on possible new functions of human LAP1 and could set the basis for subsequent in-depth mechanistic investigations. Moreover, by identifying deregulated signaling pathways in LAP1-deficient cells, our work may offer valuable molecular targets for future disease-modifying therapies for TOR1AIP1-associated nuclear envelopathies.
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Affiliation(s)
- Cátia D. Pereira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Guadalupe Espadas
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Filipa Martins
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Anne T. Bertrand
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Laurent Servais
- MDUK Oxford Neuromuscular Center, Department of Paediatrics, University of Oxford and NIHR Oxford Biomedical Research Center, Oxford, OX3 9DU, United Kingdom
- Neuromuscular Center, Division of Paediatrics, University Hospital of Liège and University of Liège, 4000, Liège, Belgium
| | - Eduard Sabidó
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Philippe Chevalier
- Université Claude Bernard Lyon 1, Lyon, France
- Hospices Civils de Lyon, Lyon, France
| | - Odete A.B. da Cruz e Silva
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Sandra Rebelo
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
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Shi X, Gekas C, Verduzco D, Petiwala S, Jeffries C, Lu C, Murphy E, Anton T, Vo AH, Xiao Z, Narayanan P, Sun BC, D'Souza AL, Barnes JM, Roy S, Ramathal C, Flister MJ, Dezso Z. Building a translational cancer dependency map for The Cancer Genome Atlas. NATURE CANCER 2024; 5:1176-1194. [PMID: 39009815 PMCID: PMC11358024 DOI: 10.1038/s43018-024-00789-y] [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: 12/21/2022] [Accepted: 05/31/2024] [Indexed: 07/17/2024]
Abstract
Cancer dependency maps have accelerated the discovery of tumor vulnerabilities that can be exploited as drug targets when translatable to patients. The Cancer Genome Atlas (TCGA) is a compendium of 'maps' detailing the genetic, epigenetic and molecular changes that occur during the pathogenesis of cancer, yet it lacks a dependency map to translate gene essentiality in patient tumors. Here, we used machine learning to build translational dependency maps for patient tumors, which identified tumor vulnerabilities that predict drug responses and disease outcomes. A similar approach was used to map gene tolerability in healthy tissues to prioritize tumor vulnerabilities with the best therapeutic windows. A subset of patient-translatable synthetic lethalities were experimentally tested, including PAPSS1/PAPSS12 and CNOT7/CNOT78, which were validated in vitro and in vivo. Notably, PAPSS1 synthetic lethality was driven by collateral deletion of PAPSS2 with PTEN and was correlated with patient survival. Finally, the translational dependency map is provided as a web-based application for exploring tumor vulnerabilities.
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Affiliation(s)
- Xu Shi
- AbbVie Bay Area, South San Francisco, CA, USA
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Zhao Q, Pavanello L, Bartlam M, Winkler GS. Structure and function of molecular machines involved in deadenylation-dependent 5'-3' mRNA degradation. Front Genet 2023; 14:1233842. [PMID: 37876592 PMCID: PMC10590902 DOI: 10.3389/fgene.2023.1233842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
In eukaryotic cells, the synthesis, processing, and degradation of mRNA are important processes required for the accurate execution of gene expression programmes. Fully processed cytoplasmic mRNA is characterised by the presence of a 5'cap structure and 3'poly(A) tail. These elements promote translation and prevent non-specific degradation. Degradation via the deadenylation-dependent 5'-3' degradation pathway can be induced by trans-acting factors binding the mRNA, such as RNA-binding proteins recognising sequence elements and the miRNA-induced repression complex. These factors recruit the core mRNA degradation machinery that carries out the following steps: i) shortening of the poly(A) tail by the Ccr4-Not and Pan2-Pan3 poly (A)-specific nucleases (deadenylases); ii) removal of the 5'cap structure by the Dcp1-Dcp2 decapping complex that is recruited by the Lsm1-7-Pat1 complex; and iii) degradation of the mRNA body by the 5'-3' exoribonuclease Xrn1. In this review, the biochemical function of the nucleases and accessory proteins involved in deadenylation-dependent mRNA degradation will be reviewed with a particular focus on structural aspects of the proteins and enzymes involved.
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Affiliation(s)
- Qi Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Lorenzo Pavanello
- School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
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Patel LR, Stratton SA, McLaughlin M, Krause P, Allton K, Rivas AL, Barbosa D, Hart T, Barton MC. Genome-wide CRISPR-Cas9 screen analyzed by SLIDER identifies network of repressor complexes that regulate TRIM24. iScience 2023; 26:107126. [PMID: 37426340 PMCID: PMC10329041 DOI: 10.1016/j.isci.2023.107126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/12/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
TRIM24 is an oncogenic chromatin reader that is frequently overexpressed in human tumors and associated with poor prognosis. However, TRIM24 is rarely mutated, duplicated, or rearranged in cancer. This raises questions about how TRIM24 is regulated and what changes in its regulation are responsible for its overexpression. Here, we perform a genome-wide CRISPR-Cas9 screen by fluorescence-activated cell sorting (FACS) that nominated 220 negative regulators and elucidated a regulatory network that includes the KAP1 corepressor, CNOT deadenylase, and GID/CTLH E3 ligase. Knocking out required components of these three complexes caused TRIM24 overexpression, confirming their negative regulation of TRIM24. Our findings identify regulators of TRIM24 that nominate previously unexplored contexts for this oncoprotein in biology and disease. These findings were enabled by SLIDER, a new scoring system designed and vetted in our study as a broadly applicable tool for analysis of CRISPR screens performed by FACS.
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Affiliation(s)
- Lalit R. Patel
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX, USA
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sabrina A. Stratton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Megan McLaughlin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Krause
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | - Kendra Allton
- The Neurodegeneration Consortium, Therapeutics Discovery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrés López Rivas
- School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA
| | - Daniela Barbosa
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle C. Barton
- Division of Oncological Sciences, Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, US
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Pekovic F, Rammelt C, Kubíková J, Metz J, Jeske M, Wahle E. RNA binding proteins Smaug and Cup induce CCR4-NOT-dependent deadenylation of the nanos mRNA in a reconstituted system. Nucleic Acids Res 2023; 51:3950-3970. [PMID: 36951092 PMCID: PMC10164591 DOI: 10.1093/nar/gkad159] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 01/22/2023] [Accepted: 02/22/2023] [Indexed: 03/24/2023] Open
Abstract
Posttranscriptional regulation of the maternal nanos mRNA is essential for the development of the anterior - posterior axis of the Drosophila embryo. The nanos RNA is regulated by the protein Smaug, which binds to Smaug recognition elements (SREs) in the nanos 3'-UTR and nucleates the assembly of a larger repressor complex including the eIF4E-T paralog Cup and five additional proteins. The Smaug-dependent complex represses translation of nanos and induces its deadenylation by the CCR4-NOT deadenylase. Here we report an in vitro reconstitution of the Drosophila CCR4-NOT complex and Smaug-dependent deadenylation. We find that Smaug by itself is sufficient to cause deadenylation by the Drosophila or human CCR4-NOT complexes in an SRE-dependent manner. CCR4-NOT subunits NOT10 and NOT11 are dispensable, but the NOT module, consisting of NOT2, NOT3 and the C-terminal part of NOT1, is required. Smaug interacts with the C-terminal domain of NOT3. Both catalytic subunits of CCR4-NOT contribute to Smaug-dependent deadenylation. Whereas the CCR4-NOT complex itself acts distributively, Smaug induces a processive behavior. The cytoplasmic poly(A) binding protein (PABPC) has a minor inhibitory effect on Smaug-dependent deadenylation. Among the additional constituents of the Smaug-dependent repressor complex, Cup also facilitates CCR4-NOT-dependent deadenylation, both independently and in cooperation with Smaug.
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Affiliation(s)
- Filip Pekovic
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle, Germany
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Frederick, MD 21702, USA
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle, Germany
| | - Jana Kubíková
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jutta Metz
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Mandy Jeske
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle, Germany
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Pavanello L, Hall M, Winkler GS. Regulation of eukaryotic mRNA deadenylation and degradation by the Ccr4-Not complex. Front Cell Dev Biol 2023; 11:1153624. [PMID: 37152278 PMCID: PMC10157403 DOI: 10.3389/fcell.2023.1153624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Accurate and precise regulation of gene expression programmes in eukaryotes involves the coordinated control of transcription, mRNA stability and translation. In recent years, significant progress has been made about the role of sequence elements in the 3' untranslated region for the regulation of mRNA degradation, and a model has emerged in which recruitment of the Ccr4-Not complex is the critical step in the regulation of mRNA decay. Recruitment of the Ccr4-Not complex to a target mRNA results in deadenylation mediated by the Caf1 and Ccr4 catalytic subunits of the complex. Following deadenylation, the 5' cap structure is removed, and the mRNA subjected to 5'-3' degradation. Here, the role of the human Ccr4-Not complex in cytoplasmic deadenylation of mRNA is reviewed, with a particular focus on mechanisms of its recruitment to mRNA by sequence motifs in the 3' untranslated region, codon usage, as well as general mechanisms involving the poly(A) tail.
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Affiliation(s)
- Lorenzo Pavanello
- School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Michael Hall
- School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
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Niceta M, Pizzi S, Inzana F, Peron A, Bakhtiari S, Nizon M, Levy J, Mancini C, Cogné B, Radio FC, Agolini E, Cocciadiferro D, Novelli A, Salih MA, Recalcati MP, Arancio R, Besnard M, Tabet A, Kruer MC, Priolo M, Dallapiccola B, Tartaglia M. Delineation of the clinical profile of CNOT2 haploinsufficiency and overview of the IDNADFS phenotype. Clin Genet 2023; 103:156-166. [PMID: 36224108 PMCID: PMC9939052 DOI: 10.1111/cge.14247] [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: 07/19/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 01/07/2023]
Abstract
CNOT2 haploinsufficiency underlies a rare neurodevelopmental disorder named Intellectual Developmental disorder with NAsal speech, Dysmorphic Facies, and variable Skeletal anomalies (IDNADFS, OMIM 618608). The condition clinically overlaps with chromosome 12q15 deletion syndrome, suggesting a major contribution of CNOT2 haploinsufficiency to the latter. CNOT2 is a member of the CCR4-NOT complex, which is a master regulator of multiple cellular processes, including gene expression, RNA deadenylation, and protein ubiquitination. To date, less than 20 pathogenic 12q15 microdeletions encompassing CNOT2, together with a single truncating variant of the gene, and two large intragenic deletions have been reported. Due to the small number of affected subjects described so far, the clinical profile of IDNADFS has not been fully delineated. Here we report five unrelated individuals, three of which carrying de novo intragenic CNOT2 variants, one presenting with a multiexon intragenic deletion, and an additional case of 12q15 microdeletion syndrome. Finally, we assess the features of IDNADFS by reviewing published and present affected individuals and reevaluate the clinical phenotype of this neurodevelopmental disorder.
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Affiliation(s)
- Marcello Niceta
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
- Department of PediatricsSapienza UniversityRomeItaly
| | - Simone Pizzi
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Francesca Inzana
- Genetic Counseling ServiceRegional Hospital of BolzanoBolzanoItaly
| | - Angela Peron
- Medical GeneticsASST Santi Paolo e Carlo, Ospedale San PaoloMilanItaly
- Division of Medical Genetics, Department of PediatricsUniversity of UtahSalt Lake CityUtahUSA
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric NeurologyBarrow Neurological Institute, Phoenix Children's HospitalPhoenixArizonaUSA
- Departments of Child Health, Neurology, and Cellular and Molecular Medicine, and Program in GeneticsUniversity of Arizona College of Medicine – PhoenixPhoenixArizonaUSA
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique MédicaleL'institut du thorax, INSERM, CNRS, UNIV NantesNantesFrance
| | - Jonathan Levy
- Genetics DepartmentAP‐HP, Robert‐Debré University HospitalParisFrance
| | - Cecilia Mancini
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Benjamin Cogné
- Laboratoire de Génétique MoléculaireCHU de NantesNantesFrance
| | | | - Emanuele Agolini
- Translational Cytogenomics Research UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Dario Cocciadiferro
- Translational Cytogenomics Research UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Antonio Novelli
- Translational Cytogenomics Research UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Mustafa A. Salih
- Neurology Division, Department of PediatricsCollege of Medicine, King Saud UniversityRiyadhSaudi Arabia
- Department of PediatricsCollege of Medicine, Almughtaribeen UniversityKhartoumSudan
| | - Maria Paola Recalcati
- Medical Cytogenetics LaboratoryIstituto Auxologico Italiano IRCCSCusano MilaninoItaly
| | - Rosangela Arancio
- Clinica PediatricaOspedale San Paolo, ASST Santi Paolo CarloMilanItaly
| | - Marianne Besnard
- Service de NéonatologieCentre Hospitalier de Polynésie FrançaisePapeeteFrench Polynesia
| | - Anne‐Claude Tabet
- Human Genetics and Cognitive FunctionsInstitut Pasteur, UMR3571 CNRS, Université de ParisParisFrance
- Cytogenetic UnitRobert Debré Hospital, APHPParisFrance
| | - Michael C. Kruer
- Departments of Child Health, Neurology, and Cellular and Molecular Medicine, and Program in GeneticsUniversity of Arizona College of Medicine – PhoenixPhoenixArizonaUSA
| | - Manuela Priolo
- UOSD Genetica MedicaGrande Ospedale Metropolitano “Bianchi‐Melacrino‐Morelli”Reggio CalabriaItaly
| | - Bruno Dallapiccola
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Marco Tartaglia
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
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Liu J, Lu X, Zhang S, Yuan L, Sun Y. Molecular Insights into mRNA Polyadenylation and Deadenylation. Int J Mol Sci 2022; 23:ijms231910985. [PMID: 36232288 PMCID: PMC9570436 DOI: 10.3390/ijms231910985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Poly(A) tails are present on almost all eukaryotic mRNAs, and play critical roles in mRNA stability, nuclear export, and translation efficiency. The biosynthesis and shortening of a poly(A) tail are regulated by large multiprotein complexes. However, the molecular mechanisms of these protein machineries still remain unclear. Recent studies regarding the structural and biochemical characteristics of those protein complexes have shed light on the potential mechanisms of polyadenylation and deadenylation. This review summarizes the recent structural studies on pre-mRNA 3′-end processing complexes that initiate the polyadenylation and discusses the similarities and differences between yeast and human machineries. Specifically, we highlight recent biochemical efforts in the reconstitution of the active human canonical pre-mRNA 3′-end processing systems, as well as the roles of RBBP6/Mpe1 in activating the entire machinery. We also describe how poly(A) tails are removed by the PAN2-PAN3 and CCR4-NOT deadenylation complexes and discuss the emerging role of the cytoplasmic poly(A)-binding protein (PABPC) in promoting deadenylation. Together, these recent discoveries show that the dynamic features of these machineries play important roles in regulating polyadenylation and deadenylation.
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Effects of Extracellular Vesicles from Osteogenic Differentiated Human BMSCs on Osteogenic and Adipogenic Differentiation Capacity of Naïve Human BMSCs. Cells 2022; 11:cells11162491. [PMID: 36010568 PMCID: PMC9406723 DOI: 10.3390/cells11162491] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022] Open
Abstract
Osteoporosis, or steroid-induced osteonecrosis of the hip, is accompanied by increased bone marrow adipogenesis. Such a disorder of adipogenic/osteogenic differentiation, affecting bone-marrow-derived mesenchymal stem cells (BMSCs), contributes to bone loss during aging. Here, we investigated the effects of extracellular vesicles (EVs) isolated from human (h)BMSCs during different stages of osteogenic differentiation on the osteogenic and adipogenic differentiation capacity of naïve (undifferentiated) hBMSCs. We observed that all EV groups increased viability and proliferation capacity and suppressed the apoptosis of naïve hBMSCs. In particular, EVs derived from hBMSCs at late-stage osteogenic differentiation promoted the osteogenic potential of naïve hBMSCs more effectively than EVs derived from naïve hBMSCs (naïve EVs), as indicated by the increased gene expression of COL1A1 and OPN. In contrast, the adipogenic differentiation capacity of naïve hBMSCs was inhibited by treatment with EVs from osteogenic differentiated hBMSCs. Proteomic analysis revealed that osteogenic EVs and naïve EVs contained distinct protein profiles, with pro-osteogenic and anti-adipogenic proteins encapsulated in osteogenic EVs. We speculate that osteogenic EVs could serve as an intercellular communication system between bone- and bone-marrow adipose tissue, for transporting osteogenic factors and thus favoring pro-osteogenic processes. Our data may support the theory of an endocrine circuit with the skeleton functioning as a ductless gland.
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Perzanowska O, Smietanski M, Jemielity J, Kowalska J. Chemically Modified Poly(A) Analogs Targeting PABP: Structure Activity Relationship and Translation Inhibitory Properties. Chemistry 2022; 28:e202201115. [PMID: 35575378 PMCID: PMC9400960 DOI: 10.1002/chem.202201115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/13/2022]
Abstract
Poly(A)‐binding protein (PABP) is an essential element of cellular translational machinery. Recent studies have revealed that poly(A) tail modifications can modulate mRNA stability and translational potential, and that oligoadenylate‐derived PABP ligands can act as effective translational inhibitors with potential applications in pain management. Although extensive research has focused on protein‐RNA and protein‐protein interactions involving PABPs, further studies are required to examine the ligand specificity of PABP. In this study, we developed a microscale thermophoresis‐based assay to probe the interactions between PABP and oligoadenylate analogs containing different chemical modifications. Using this method, we evaluated oligoadenylate analogs modified with nucleobase, ribose, and phosphate moieties to identify modification hotspots. In addition, we determined the susceptibility of the modified oligos to CNOT7 to identify those with the potential for increased cellular stability. Consequently, we selected two enzymatically stable oligoadenylate analogs that inhibit translation in rabbit reticulocyte lysates with a higher potency than a previously reported PABP ligand. We believe that the results presented in this study and the implemented methodology can be capitalized upon in the future development of RNA‐based biological tools.
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Affiliation(s)
- Olga Perzanowska
- Division of Biophysics Faculty of Physics University of Warsaw Ludwika Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Miroslaw Smietanski
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Jacek Jemielity
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Joanna Kowalska
- Division of Biophysics Faculty of Physics University of Warsaw Ludwika Pasteura 5 02-093 Warsaw Poland
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13
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Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development. Nat Cell Biol 2022; 24:968-980. [PMID: 35697785 DOI: 10.1038/s41556-022-00928-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/27/2022] [Indexed: 12/12/2022]
Abstract
In mammals, translational control plays critical roles during oocyte-to-embryo transition (OET) when transcription ceases. However, the underlying regulatory mechanisms remain challenging to study. Here, using low-input Ribo-seq (Ribo-lite), we investigated translational landscapes during OET using 30-150 mouse oocytes or embryos per stage. Ribo-lite can also accommodate single oocytes. Combining PAIso-seq to interrogate poly(A) tail lengths, we found a global switch of translatome that closely parallels changes of poly(A) tails upon meiotic resumption. Translation activation correlates with polyadenylation and is supported by polyadenylation signal proximal cytoplasmic polyadenylation elements (papCPEs) in 3' untranslated regions. By contrast, translation repression parallels global de-adenylation. The latter includes transcripts containing no CPEs or non-papCPEs, which encode many transcription regulators that are preferentially re-activated before zygotic genome activation. CCR4-NOT, the major de-adenylation complex, and its key adaptor protein BTG4 regulate translation downregulation often independent of RNA decay. BTG4 is not essential for global de-adenylation but is required for selective gene de-adenylation and production of very short-tailed transcripts. In sum, our data reveal intimate interplays among translation, RNA stability and poly(A) tail length regulation underlying mammalian OET.
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14
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Quan Y, Wang M, Xu C, Wang X, Wu Y, Qin D, Lin Y, Lu X, Lu F, Li L. Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition. Nucleic Acids Res 2022; 50:4414-4435. [PMID: 35390160 PMCID: PMC9071485 DOI: 10.1093/nar/gkac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/11/2022] [Accepted: 03/26/2022] [Indexed: 11/14/2022] Open
Abstract
Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
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Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meijiao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengpeng Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxuan Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Zhang Q, Pavanello L, Potapov A, Bartlam M, Winkler GS. Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements. Protein Sci 2022; 31:758-764. [PMID: 34923703 PMCID: PMC8862426 DOI: 10.1002/pro.4262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 11/11/2022]
Abstract
Regulated degradation of mature, cytoplasmic mRNA is a key step in eukaryotic gene regulation. This process is typically initiated by the recruitment of deadenylase enzymes by cis-acting elements in the 3' untranslated region resulting in the shortening and removal of the 3' poly(A) tail of the target mRNA. The Ccr4-Not complex, a major eukaryotic deadenylase, contains two exoribonuclease subunits with selectivity toward poly(A): Caf1 and Ccr4. The Caf1 deadenylase subunit binds the MIF4G domain of the large subunit CNOT1 (Not1) that is the scaffold of the complex. The Ccr4 nuclease is connected to the complex via its leucine-rich repeat (LRR) domain, which binds Caf1, whereas the catalytic activity of Ccr4 is provided by its EEP domain. While the relative positions of the MIF4G domain of CNOT1, the Caf1 subunit, and the LRR domain of Ccr4 are clearly defined in current models, the position of the EEP nuclease domain of Ccr4 is ambiguous. Here, we use X-ray crystallography, the AlphaFold resource of predicted protein structures, and pulse electron paramagnetic resonance spectroscopy to determine and validate the position of the EEP nuclease domain of Ccr4 resulting in an improved model of the human Ccr4-Not nuclease module.
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Affiliation(s)
- Qionglin Zhang
- Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Lorenzo Pavanello
- School of PharmacyUniversity of NottinghamNottinghamUK,Present address:
LifeArcStevenage Bioscience Catalyst Open Innovation CampusStevenageUK
| | - Alexey Potapov
- School of Physics and Astronomy, Sir Peter Mansfield Imaging CentreUniversity of NottinghamNottinghamUK
| | - Mark Bartlam
- Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
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16
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Stoney PN, Yanagiya A, Nishijima S, Yamamoto T. CNOT7 outcompetes its paralog CNOT8 for integration into the CCR4-NOT complex. J Mol Biol 2022; 434:167523. [DOI: 10.1016/j.jmb.2022.167523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/08/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
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17
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Suzuki T, Hoshina M, Nishijima S, Hoshina N, Kikuguchi C, Tomohiro T, Fukao A, Fujiwara T, Yamamoto T. Regulation of CCR4-NOT complex deadenylase activity and cellular responses by MK2-dependent phosphorylation of CNOT2. RNA Biol 2022; 19:234-246. [PMID: 35129087 PMCID: PMC8820811 DOI: 10.1080/15476286.2021.2021676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
CCR4-NOT complex-mediated mRNA deadenylation serves critical functions in multiple biological processes, yet how this activity is regulated is not fully understood. Here, we show that osmotic stress induces MAPKAPK-2 (MK2)-mediated phosphorylation of CNOT2. Programmed cell death is greatly enhanced by osmotic stress in CNOT2-depleted cells, indicating that CNOT2 is responsible for stress resistance of cells. Although wild-type (WT) and non-phosphorylatable CNOT2 mutants reverse this sensitivity, a phosphomimetic form of CNOT2, in which serine at the phosphorylation site is replaced with glutamate, does not have this function. We also show that mRNAs have elongated poly(A) tails in CNOT2-depleted cells and that introduction of CNOT2 WT or a non-phosphorylatable mutant, but not phosphomimetic CNOT2, renders their poly(A) tail lengths comparable to those in control HeLa cells. Consistent with this, the CCR4-NOT complex containing phosphomimetic CNOT2 exhibits less deadenylase activity than that containing CNOT2 WT. These data suggest that CCR4-NOT complex deadenylase activity is regulated by post-translational modification, yielding dynamic control of mRNA deadenylation.
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Affiliation(s)
- Toru Suzuki
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, Riken, Yokohama, Japan
| | - Miyuki Hoshina
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Saori Nishijima
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Naosuke Hoshina
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Chisato Kikuguchi
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, Riken, Yokohama, Japan
| | - Takumi Tomohiro
- Laboratory of Biochemistry, Kindai University, Higashi-Osaka, Japan
| | - Akira Fukao
- Laboratory of Biochemistry, Kindai University, Higashi-Osaka, Japan
| | | | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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18
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Jiang ZY, Fan HY. Five questions toward mRNA degradation in oocytes and preimplantation embryos: When, who, to whom, how, and why? Biol Reprod 2022; 107:62-75. [DOI: 10.1093/biolre/ioac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
RNA, the primary product of the genome, is subject to various biological events during its lifetime. During mammalian gametogenesis and early embryogenesis, germ cells and preimplantation embryos undergo marked changes in the transcriptome, including mRNA turnover. Various factors, including specialized proteins, RNAs, and organelles, function in an intricate degradation system, and the degradation selectivity is determined by effectors and their target mRNAs. RNA homeostasis regulators and surveillance factors function in the global transcriptome of oocytes and somatic cells. Other factors, including BTG4, PABPN1L, the CCR4-NOT subunits, CNOT6L and CNOT7, and TUTs, are responsible for two maternal mRNA avalanches: M- and Z-decay. In this review, we discuss recent advances in mRNA degradation mechanisms in mammalian oocytes and preimplantation embryos. We focused on the studies in mice, as a model mammalian species, and on RNA turnover effectors and the cis-elements in targeting RNAs.
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Affiliation(s)
- Zhi-Yan Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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19
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Loscalzo G, Scheel J, Ibañez-Cabellos JS, García-Lopez E, Gupta S, García-Gimenez JL, Mena-Mollá S, Perales-Marín A, Morales-Roselló J. Overexpression of microRNAs miR-25-3p, miR-185-5p and miR-132-3p in Late Onset Fetal Growth Restriction, Validation of Results and Study of the Biochemical Pathways Involved. Int J Mol Sci 2021; 23:ijms23010293. [PMID: 35008715 PMCID: PMC8745308 DOI: 10.3390/ijms23010293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/27/2022] Open
Abstract
In a prospective study, 48 fetuses were evaluated with Doppler ultrasound after 34 weeks and classified, according to the cerebroplacental ratio (CPR) and estimated fetal weight (EFW), into fetuses with normal growth and fetuses with late-onset fetal growth restriction (LO-FGR). Overexpression of miRNAs from neonatal cord blood belonging to LO-FGR fetuses, was validated by real-time PCR. In addition, functional characterization of overexpressed miRNAs was performed by analyzing overrepresented pathways, gene ontologies, and prioritization of synergistically working miRNAs. Three miRNAs: miR-25-3p, miR-185-5p and miR-132-3p, were significantly overexpressed in cord blood of LO-FGR fetuses. Pathway and gene ontology analysis revealed over-representation of certain molecular pathways associated with cardiac development and neuron death. In addition, prioritization of synergistically working miRNAs highlighted the importance of miR-185-5p and miR-25-3p in cholesterol efflux and starvation responses associated with LO-FGR phenotypes. Evaluation of miR-25-3p; miR-132-3p and miR-185-5p might serve as molecular biomarkers for the diagnosis and management of LO-FGR; improving the understanding of its influence on adult disease.
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Affiliation(s)
- Gabriela Loscalzo
- Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.P.-M.); (J.M.-R.)
- Department of Obstetrics and Gynecology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Correspondence: (G.L.); (J.S.)
| | - Julia Scheel
- Department of Systems Biology and Bioinformatics, University Rostock, 18055 Rostock, Germany;
- Correspondence: (G.L.); (J.S.)
| | - José Santiago Ibañez-Cabellos
- EpiDisease S.L, Parc Científic, University of Valencia, 46980 Paterna, Spain; (J.S.I.-C.); (E.G.-L.); (J.L.G.-G.); (S.M.-M.)
- Consortium Center for Biomedical Network Research on Rare Diseases (CIBERER), Carrer d’Alvaro de Bazan, 10, 46010 Valencia, Spain
| | - Eva García-Lopez
- EpiDisease S.L, Parc Científic, University of Valencia, 46980 Paterna, Spain; (J.S.I.-C.); (E.G.-L.); (J.L.G.-G.); (S.M.-M.)
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University Rostock, 18055 Rostock, Germany;
| | - José Luis García-Gimenez
- EpiDisease S.L, Parc Científic, University of Valencia, 46980 Paterna, Spain; (J.S.I.-C.); (E.G.-L.); (J.L.G.-G.); (S.M.-M.)
- Consortium Center for Biomedical Network Research on Rare Diseases (CIBERER), Carrer d’Alvaro de Bazan, 10, 46010 Valencia, Spain
- Institute of Health Carlos III, Biomedical Research Institute INCLIVA, 46010 Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - Salvador Mena-Mollá
- EpiDisease S.L, Parc Científic, University of Valencia, 46980 Paterna, Spain; (J.S.I.-C.); (E.G.-L.); (J.L.G.-G.); (S.M.-M.)
- Institute of Health Carlos III, Biomedical Research Institute INCLIVA, 46010 Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - Alfredo Perales-Marín
- Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.P.-M.); (J.M.-R.)
- Department of Obstetrics and Gynecology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - José Morales-Roselló
- Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.P.-M.); (J.M.-R.)
- Department of Obstetrics and Gynecology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
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20
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Dai XX, Jiang ZY, Wu YW, Sha QQ, Liu Y, Ding JY, Xi WD, Li J, Fan HY. CNOT6/6L-mediated mRNA degradation in ovarian granulosa cells is a key mechanism of gonadotropin-triggered follicle development. Cell Rep 2021; 37:110007. [PMID: 34788619 DOI: 10.1016/j.celrep.2021.110007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 07/27/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022] Open
Abstract
CCR4-NOT deadenylase is a major regulator of mRNA turnover. It contains two heterogeneous catalytic subunits CNOT7/8 and CNOT6/6L in vertebrates. The physiological function of each catalytic subunit is unclear due to the gene redundancy. In this study, Cnot6/6l double knockout mice are generated. Cnot6l-/- female mice are infertile, with poor ovarian responses to gonadotropins. Follicle-stimulating hormone (FSH) stimulates the transcription and translation of Cnot6 and Cnot6l in ovarian granulosa cells. CNOT6/6L function as key effectors of FSH in granulosa cells and trigger the clearance of specific transcripts in granulosa cells during preantral to antral follicle transition. These results demonstrate that FSH modulates granulosa cell function by stimulating selective translational activation and degradation of existing mRNAs, in addition to inducing de novo gene transcription. Meanwhile, this study provides in vivo evidence that CNOT6/6L-mediated mRNA deadenylation is dispensable in most somatic cell types, but is essential for female reproductive endocrine regulation.
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Affiliation(s)
- Xing-Xing Dai
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhi-Yan Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qian-Qian Sha
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Yang Liu
- Department of Assisted Reproduction, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong 226000, China
| | - Jia-Yi Ding
- Department of Assisted Reproduction, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong 226000, China
| | - Wen-Dong Xi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211100, China
| | - Jing Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211100, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
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21
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Morgan M, Kumar L, Li Y, Baptissart M. Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. Cell Mol Life Sci 2021; 78:8049-8071. [PMID: 34748024 DOI: 10.1007/s00018-021-04012-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/22/2023]
Abstract
Multiple RNA pathways are required to produce functional sperm. Here, we review RNA post-transcriptional regulation during spermatogenesis with particular emphasis on the role of 3' end modifications. From early studies in the 1970s, it became clear that spermiogenesis transcripts could be stored for days only to be translated at advanced stages of spermatid differentiation. The transition between the translationally repressed and active states was observed to correlate with the shortening of the transcripts' poly(A) tail, establishing a link between RNA 3' end metabolism and male germ cell differentiation. Since then, numerous RNA metabolic pathways have been implicated not only in the progression through spermatogenesis, but also in the maintenance of genomic integrity. Recent studies have characterized the elusive 3' biogenesis of Piwi-interacting RNAs (piRNAs), identified a critical role for messenger RNA (mRNA) 3' uridylation in meiotic progression, established the mechanisms that destabilize transcripts with long 3' untranslated regions (3'UTRs) in post-mitotic cells, and defined the physiological relevance of RNA exonucleases and deadenylases in male germ cells. In this review, we discuss RNA processing in the male germline in the light of the most recent findings. A brief recollection of different RNA-processing events will aid future studies exploring post-transcriptional regulation in spermatogenesis.
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Affiliation(s)
- Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA.
| | - Lokesh Kumar
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Marine Baptissart
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
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22
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Chen Y, Khazina E, Izaurralde E, Weichenrieder O. Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex. Nucleic Acids Res 2021; 49:6489-6510. [PMID: 34038562 PMCID: PMC8216464 DOI: 10.1093/nar/gkab414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 01/07/2023] Open
Abstract
The CCR4 and CAF1 deadenylases physically interact to form the CCR4-CAF1 complex and function as the catalytic core of the larger CCR4-NOT complex. Together, they are responsible for the eventual removal of the 3′-poly(A) tail from essentially all cellular mRNAs and consequently play a central role in the posttranscriptional regulation of gene expression. The individual properties of CCR4 and CAF1, however, and their respective contributions in different organisms and cellular environments are incompletely understood. Here, we determined the crystal structure of a human CCR4-CAF1 complex and characterized its enzymatic and substrate recognition properties. The structure reveals specific molecular details affecting RNA binding and hydrolysis, and confirms the CCR4 nuclease domain to be tethered flexibly with a considerable distance between both enzyme active sites. CCR4 and CAF1 sense nucleotide identity on both sides of the 3′-terminal phosphate, efficiently differentiating between single and consecutive non-A residues. In comparison to CCR4, CAF1 emerges as a surprisingly tunable enzyme, highly sensitive to pH, magnesium and zinc ions, and possibly allowing distinct reaction geometries. Our results support a picture of CAF1 as a primordial deadenylase, which gets assisted by CCR4 for better efficiency and by the assembled NOT proteins for selective mRNA targeting and regulation.
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Affiliation(s)
- Ying Chen
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elena Khazina
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
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23
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Yu J, Hu X, Chen X, Zhou Q, Jiang Q, Shi Z, Zhu H. CNOT7 modulates biological functions of ovarian cancer cells via AKT signaling pathway. Life Sci 2021; 268:118996. [PMID: 33412213 DOI: 10.1016/j.lfs.2020.118996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022]
Abstract
AIMS CNOT7 plays an important role in many biological processes, providing attractive opportunities for the treatment of malignant tumors. However, the functions and mechanism of CNOT7 in ovarian cancer (OC) have not been elucidated. The purpose of this study was to assess the role of CNOT7 in OC. MATERIALS AND METHODS SKOV3 and A2780 cells were chosen as the cell lines for the experiments of this manuscript via the analysis of the expression of CNOT7 protein and the mRNA level in ovarian surface epithelium (OSE) cells, SKOV3, HO8910 and A2780 cells. The expression of CNOT7 was detected by western blot assays and RT-PCR in A2780 and SKOV3 cells. The MTT assays, colony formation assays and EdU assays were used to measure cell proliferation when CNOT7 was knocked down or overexpressed in A2780 and SKOV3 cells. Furthermore, cell migration and invasion ability were achieved from transwell assays. Cell cycle and apoptosis rate after small interference RNA-CNOT7 (siRNA-CNOT7) were detected by flow cytometry assays. Finally, the cell proliferation, migration and invasion ability were detected when A2780 and SKOV3 cells with CNOT7 overexpression were treated with LY294002. KEY FINDINGS The expression of CNOT7 protein in OC cells, including SKOV3, HO8910 and A2780 cells were significantly higher than that in OSE cells (P < 0.05). The mRNA level of CNOT7 in HO8910 and A2780 cells were significantly higher than that in OSE cells (P < 0.01). However, the mRNA level of CNOT7 in SKOV3 cells was no significant difference compared with OSE cells (P > 0.05). The results suggested that knockdown of CNOT7 could inhibit the cell proliferation, migration and invasion ability in A2780 and SKOV3 cells, and increase cell apoptosis and autophagy. The expression of apoptosis-related molecules (PARP, Caspase3 and Caspase9) and autophagy-related protein (LC3B) were up-regulated after CNOT7 knockdown, while the expression of cycle-related protein (CDK6) and the anti-apoptotic gene (Bcl2) were downregulated. Meanwhile, the opposite results were observed when CNOT7 was overexpressed in A2780 and SKOV3 cells. It is worth noting that the effect of CNOT7 overexpression in A2780 and SKOV3 cells could be partially or completely eliminated by treatment with AKT inhibitor LY294002. SIGNIFICANCE CNOT7 has a carcinogenic effect in OC, and the carcinogenic effect may be achieved via the AKT signaling pathway.
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Affiliation(s)
- Jiangtao Yu
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, People's Republic of China
| | - Xiaoli Hu
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, People's Republic of China
| | - Xiuxiu Chen
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, People's Republic of China
| | - Qiangyong Zhou
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, People's Republic of China
| | - Qi Jiang
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, People's Republic of China
| | - Zhengzheng Shi
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, People's Republic of China.
| | - Haiyan Zhu
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, People's Republic of China; Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200126, People's Republic of China.
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Eskandarian S, Grand R, Irani S, Saeedi M, Mirfakhraie R. Importance of CNOT8 Deadenylase Subunit in DNA Damage Responses Following Ionizing Radiation (IR). Rep Biochem Mol Biol 2020; 9:163-170. [PMID: 33178865 DOI: 10.29252/rbmb.9.2.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Background The Ccr4-Not protein complex (CNOT complex) is a key regulator of gene expression in eukaryotic cells. Ccr4-Not Complex is composed of at least nine conserved subunits in mammalian cells with two main enzymatic activities. CNOT8 is a subunit of the complex with deadenylase activity that interacts transiently with the CNOT6 or CNOT6L subunits. Here, we focused on the role of the human CNOT8 subunit in the DNA damage response (DDR). Methods Cell viability was assessed to measure ATP level using a Cell Titer-Glo Luminescence reagent up to 4 days' post CNOT8 siRNA transfection. In addition, expression level of phosphorylated proteins in signalling pathways were detected by western blotting and immunofluorescence microscopy. CNOT8- depleted Hela cells post- 3 Gy ionizing radiation (IR) treatment were considered as a control. Results Our results from cell viability assays indicated a significant reduction at 72-hour post CNOT8 siRNA transfection (p= 0.04). Western blot analysis showed slightly alteration in the phosphorylation of DNA damage response (DDR) proteins in CNOT8-depleted HeLa cells following treatment with ionizing radiation (IR). Increased foci formation of γH2AX, RPA, 53BP1, and RAD51 foci was observed after IR in CNOT8-depleted cells compared to the control cells. Conclusion We conclude that CNOT8 deadenylase subunit is involved in the cellular response to DNA damage.
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Affiliation(s)
- Samira Eskandarian
- Department of Biology, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran.,Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK. B15 2TT
| | - Roger Grand
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK. B15 2TT
| | - Shiva Irani
- Department of Biology, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohsen Saeedi
- Stem Cell Research Center, Gorgan Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Golestan province, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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Takahashi A, Suzuki T, Soeda S, Takaoka S, Kobori S, Yamaguchi T, Mohamed HMA, Yanagiya A, Abe T, Shigeta M, Furuta Y, Kuba K, Yamamoto T. The CCR4-NOT complex maintains liver homeostasis through mRNA deadenylation. Life Sci Alliance 2020; 3:3/5/e201900494. [PMID: 32238456 PMCID: PMC7119370 DOI: 10.26508/lsa.201900494] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 03/11/2020] [Accepted: 03/14/2020] [Indexed: 12/12/2022] Open
Abstract
The biological significance of deadenylation in global gene expression is not fully understood. Here, we show that the CCR4-NOT deadenylase complex maintains expression of mRNAs, such as those encoding transcription factors, cell cycle regulators, DNA damage response-related proteins, and metabolic enzymes, at appropriate levels in the liver. Liver-specific disruption of Cnot1, encoding a scaffold subunit of the CCR4-NOT complex, leads to increased levels of mRNAs for transcription factors, cell cycle regulators, and DNA damage response-related proteins because of reduced deadenylation and stabilization of these mRNAs. CNOT1 suppression also results in an increase of immature, unspliced mRNAs (pre-mRNAs) for apoptosis-related and inflammation-related genes and promotes RNA polymerase II loading on their promoter regions. In contrast, mRNAs encoding metabolic enzymes become less abundant, concomitant with decreased levels of these pre-mRNAs. Lethal hepatitis develops concomitantly with abnormal mRNA expression. Mechanistically, the CCR4-NOT complex targets and destabilizes mRNAs mainly through its association with Argonaute 2 (AGO2) and butyrate response factor 1 (BRF1) in the liver. Therefore, the CCR4-NOT complex contributes to liver homeostasis by modulating the liver transcriptome through mRNA deadenylation.
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Affiliation(s)
- Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Toru Suzuki
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
| | - Shou Soeda
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shohei Takaoka
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shungo Kobori
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | | | - Akiko Yanagiya
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mayo Shigeta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yasuhide Furuta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan .,Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
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