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Zhang X, Joseph S, Wu D, Bowser JL, Vaziri C. The DNA Damage Response (DDR) landscape of endometrial cancer defines discrete disease subtypes and reveals therapeutic opportunities. NAR Cancer 2024; 6:zcae015. [PMID: 38596432 PMCID: PMC11000323 DOI: 10.1093/narcan/zcae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/12/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024] Open
Abstract
Genome maintenance is an enabling characteristic that allows neoplastic cells to tolerate the inherent stresses of tumorigenesis and evade therapy-induced genotoxicity. Neoplastic cells also deploy many mis-expressed germ cell proteins termed Cancer Testes Antigens (CTAs) to promote genome maintenance and survival. Here, we present the first comprehensive characterization of the DNA Damage Response (DDR) and CTA transcriptional landscapes of endometrial cancer in relation to conventional histological and molecular subtypes. We show endometrial serous carcinoma (ESC), an aggressive endometrial cancer subtype, is defined by gene expression signatures comprising members of the Replication Fork Protection Complex (RFPC) and Fanconi Anemia (FA) pathway and CTAs with mitotic functions. DDR and CTA-based profiling also defines a subset of highly aggressive endometrioid endometrial carcinomas (EEC) with poor clinical outcomes that share similar profiles to ESC yet have distinct characteristics based on conventional histological and genomic features. Using an unbiased CRISPR-based genetic screen and a candidate gene approach, we confirm that DDR and CTA genes that constitute the ESC and related EEC gene signatures are required for proliferation and therapy-resistance of cultured endometrial cancer cells. Our study validates the use of DDR and CTA-based tumor classifiers and reveals new vulnerabilities of aggressive endometrial cancer where none currently exist.
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Affiliation(s)
- Xingyuan Zhang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC - 27599, USA
| | - Sayali Joseph
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC - 27599, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, School of Dentistry, Chapel Hill, NC - 27599, USA
| | - Jessica L Bowser
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC - 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC - 27599, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC - 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC - 27599, USA
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2
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Wu T, Chen X, Zhang X. Vissers-Bodmer syndrome caused by a novel de novo CNOT1 frameshift variant. Am J Med Genet A 2024; 194:363-367. [PMID: 37818768 DOI: 10.1002/ajmg.a.63439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/24/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023]
Abstract
Vissers-Bodmer Syndrome (VIBOS) is an autosomal dominant disorder caused by variants in the CNOT1 gene. It is characterized by systemic developmental and language-motor delay, intellectual disabilities, growth and behavioral abnormalities, hypotonia, and distal skeletal defects, such as deformities of the hands and feet. This syndrome becomes evident during infancy and can display a highly variable phenotype. Thirty-nine individuals with heterozygous de novo CNOT1 variants were first reported in 2019. Herein, we report a child with VIBOS who exhibited delayed motor development for over 4 years, along with hypotonia and atypical facial features. Notably, the patient developed short stature as the primary characteristic without any intellectual disability or organic nervous system lesions. Genetic testing revealed a de novo base duplication variant in exon 5 of the CNOT1 gene, NM_016284.5(CNOT1):c.316_317dup(p.Pro107Serfs*10). Importantly, the pathogenicity of this specific variant has not been reported in relevant literature. This study reports a new variant, thereby enriching the variant spectrum of CNOT1 associated with VIBOS, and contributes to the genetic counseling of affected families.
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Affiliation(s)
- Tingting Wu
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xi Chen
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xingxing Zhang
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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3
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Airhihen B, Pavanello L, Maryati M, Winkler GS. Quantitative Biochemical Analysis of Deadenylase Enzymes Using Fluorescence and Chemiluminescence-Based Assays. Methods Mol Biol 2024; 2723:55-68. [PMID: 37824064 DOI: 10.1007/978-1-0716-3481-3_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] [Indexed: 10/13/2023]
Abstract
Deadenylase enzymes play a key role in mRNA degradation and RNA processing. In this chapter, we describe two activity assays for the quantitative biochemical analysis of deadenylase enzymes, which can easily be adapted for other nuclease enzymes. The assays use distinct principles of detection, which are based on differential annealing of a probe complementary to the substrate RNA or detection of adenosine monophosphate (AMP). The assays are sensitive, flexible, and can be used in low-throughput tube-based formats and 96-well or 384-well plate formats. The assays rely on plate reader detection and can be carried out using manual pipetting or robotic liquid handling equipment. In addition to two activity assays, we describe differential scanning fluorimetry (thermal shift assay) as a complementary assay that allows the direct characterization of ligand binding to deadenylase enzymes. The assays can be useful for the characterization of deadenylase variants and are particularly suitable for the discovery and development of small-molecule inhibitors of deadenylase enzymes.
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Affiliation(s)
- Blessing Airhihen
- School of Pharmacy, University of Nottingham, Nottingham, UK
- School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | | | - Maryati Maryati
- School of Pharmacy, University of Nottingham, Nottingham, UK
- Faculty of Pharmacy, Universitas Muhammadiyah Surakarta, Surakarta, Indonesia
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4
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Zhang X, Joseph S, Wu D, Bowser JL, Vaziri C. The DNA Damage Response (DDR) landscape of endometrial cancer defines discrete disease subtypes and reveals therapeutic opportunities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567919. [PMID: 38045328 PMCID: PMC10690150 DOI: 10.1101/2023.11.20.567919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genome maintenance is an enabling characteristic that allows neoplastic cells to tolerate the inherent stresses of tumorigenesis and evade therapy-induced genotoxicity. Neoplastic cells also deploy mis-expressed germ cell proteins termed Cancer Testes Antigens (CTAs) to promote genome maintenance and survival. Here, we present the first comprehensive characterization of the DNA Damage Response (DDR) and CTA transcriptional landscapes of endometrial cancer in relation to conventional histological and molecular subtypes. We show endometrial serous carcinoma (ESC), an aggressive endometrial cancer subtype, is defined by gene expression signatures comprising members of the Replication Fork Protection Complex (RFPC) and Fanconi Anemia (FA) pathway and CTAs with mitotic functions. DDR and CTA- based profiling also defines a subset of highly aggressive endometrioid endometrial carcinomas (EEC) with poor clinical outcomes that share similar profiles to ESC yet have distinct characteristics based on conventional histological and genomic features. Using an unbiased CRISPR-based genetic screen and a candidate gene approach, we confirm that DDR and CTA genes that constitute the ESC and related EEC gene signatures are required for proliferation and therapy-resistance of cultured endometrial cancer cells. Our study validates the use of DDR and CTA-based tumor classifiers and reveals new vulnerabilities of aggressive endometrial cancer where none currently exist.
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5
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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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von Wintzingerode L, Ben-Zeev B, Cesario C, Chan KM, Depienne C, Elpeleg O, Iascone M, Kelley WV, Nassogne MC, Niceta M, Pezzani L, Rahner N, Revencu N, Bekheirnia MR, Santiago-Sim T, Tartaglia M, Thompson ML, Trivisano M, Hentschel J, Sticht H, Abou Jamra R, Oppermann H. De novo variants in CNOT9 cause a neurodevelopmental disorder with or without epilepsy. Genet Med 2023; 25:100859. [PMID: 37092538 DOI: 10.1016/j.gim.2023.100859] [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: 11/20/2022] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023] Open
Abstract
PURPOSE The study aimed to clinically and molecularly characterize the neurodevelopmental disorder associated with heterozygous de novo variants in CNOT9. METHODS Individuals were clinically examined. Variants were identified using exome or genome sequencing. These variants were evaluated using in silico predictions, and their functional relevance was further assessed by molecular models and research in the literature. The variants have been classified according to the criteria of the American College of Medical Genetics. RESULTS We report on 7 individuals carrying de novo missense variants in CNOT9, p.(Arg46Gly), p.(Pro131Leu), and p.(Arg227His), and, recurrent in 4 unrelated individuals, p.(Arg292Trp). All affected persons have developmental delay/intellectual disability, with 5 of them showing seizures. Other symptoms include muscular hypotonia, facial dysmorphism, and behavioral abnormalities. Molecular modeling predicted that the variants are damaging and would lead to reduced protein stability or impaired recognition of interaction partners. Functional analyses in previous studies showed a pathogenic effect of p.(Pro131Leu) and p.(Arg227His). CONCLUSION We propose CNOT9 as a novel gene for neurodevelopmental disorder and epilepsy.
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Affiliation(s)
| | - Bruria Ben-Zeev
- Pediatric Neurology Institute, Sheba Medical Center, Ramat Gan, Israel
| | - Claudia Cesario
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Katie M Chan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Maria Iascone
- Laboratory of Medical Genetics, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | | | - Marie-Cécile Nassogne
- Reference Centre for refractory Epilepsy, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - Marcello Niceta
- Molecular Genetics and Functional Genomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Lidia Pezzani
- Paediatric Department, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Nils Rahner
- MVZ Institute for Clinical Genetics and Tumor Genetics, Bonn, Germany
| | - Nicole Revencu
- Center for Human Genetics, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - Mir Reza Bekheirnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Marina Trivisano
- Clinical and Experimental Neurology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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7
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Raisch T, Valkov E. Regulation of the multisubunit CCR4-NOT deadenylase in the initiation of mRNA degradation. Curr Opin Struct Biol 2022; 77:102460. [PMID: 36116370 PMCID: PMC9771892 DOI: 10.1016/j.sbi.2022.102460] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/19/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022]
Abstract
The conserved CCR4-NOT complex initiates the decay of mRNAs by catalyzing the shortening of their poly(A) tails in a process known as deadenylation. Recent studies have provided mechanistic insights into the action and regulation of this molecular machine. The two catalytic enzymatic subunits of the complex hydrolyze polyadenosine RNA. Notably, the non-catalytic subunits substantially enhance the complex's affinity and sequence selectivity for polyadenosine by directly contacting the RNA. An additional regulatory mechanism is the active recruitment of the CCR4-NOT to transcripts targeted for decay by RNA-binding proteins that recognize motifs or sequences residing predominantly in untranslated regions. This targeting and strict control of the mRNA deadenylation process emerges as a crucial nexus during post-transcriptional regulation of gene expression.
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Affiliation(s)
- Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
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8
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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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9
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Sun Z, Yin M, Ding Y, Zhu Z, Sun Y, Li K, Yan W. Integrative analysis of synovial sarcoma transcriptome reveals different types of transcriptomic changes. Front Genet 2022; 13:925564. [PMID: 36118864 PMCID: PMC9478865 DOI: 10.3389/fgene.2022.925564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Synovial sarcoma (SS) is a rare and aggressive cancer that can come from distinct soft tissue types including muscle and ligaments. However, the transcriptomic landscape of SS is still poorly understood. This study aimed to systematically dissect the changes in SS transcriptome from different perspectives.Methods: We performed deep total RNA sequencing on ten paired Synovial sarcoma and tumor-adjacent tissues to systematically dissect the transcriptomic profile of SS in terms of gene expression, alternative splicing, gene fusion, and circular RNAs.Results: A total of 2,309 upregulated and 1,977 downregulated genes were identified between SS and tumor-adjacent tissues. Those upregulated genes could lead to the upregulation of the cell cycle, ribosome, and DNA replication pathways, while the downregulated genes may result in the downregulation of a set of metabolic biological processes and signaling pathways. Moreover, 2,511 genes (including 21 splicing factors) were differentially alternative spliced, indicating that the deregulation of alternative splicing could be one important factor that contributes to tumorigenesis. Additionally, we identified the known gene fusions of SS18-SSX1/SSX2 as well as 11 potentially novel gene fusions. Interestingly, 49 circular RNAs were differentially expressed and their parental genes could function in muscle contraction and muscle system processes.Conclusions: Collectively, our comprehensive dissection of the transcriptomic changes of SS from both transcriptional and post-transcriptional levels provides novel insights into the biology and underlying molecular mechanism of SS.
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Affiliation(s)
- Zhengwang Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mengchen Yin
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Ding
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai, China
| | - Zixu Zhu
- No.2 High School of East China Normal University, Shanghai,200000, China
| | - Yangbai Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Kun Li
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
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10
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Ameerul A, Almasmoum H, Pavanello L, Dominguez C, Sebastiaan Winkler G. Structural model of the human BTG2–PABPC1 complex by combining mutagenesis, NMR chemical shift perturbation data and molecular docking. J Mol Biol 2022; 434:167662. [DOI: 10.1016/j.jmb.2022.167662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022]
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11
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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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12
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Al-Yhya N, Khan MF, Almeer RS, Alshehri MM, Aldughaim MS, Wadaan MA. Pharmacological inhibition of HDAC1/3-interacting proteins induced morphological changes, and hindered the cell proliferation and migration of hepatocellular carcinoma cells. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:49000-49013. [PMID: 33929667 DOI: 10.1007/s11356-021-13668-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Liver diseases are particularly severe health problems, but the options available for preventing and treating them remain limited. Accumulating evidence has shown that there is altered expression of individual histone deacetylase (HDAC) family members in hepatocellular carcinoma cells. In a previous study, we have identified a set of proteins which interact with histone deacetylase 1 and 3 (HDAC1/3) in hepatocellular carcinoma cell lines HepG2 by proteomic approach. This study was designed to investigate the therapeutic potential and expression of HDAC1/3-interacting genes in a human hepatocellular carcinoma cell line (HepG2). Pharmacological and transcriptional inhibition of HDAC1/3 resulted in the suppression of cancer cell proliferation, change of cell morphology, and downregulation of HDAC1/3 genes in HepG2 cells. The pharmacological inhibition also resulted in inhibition of liver cancer cell migration by wound scratch assay. Taken together, the results from this study show that the upregulation of HDAC1/3 in hepatocellular carcinoma resulted in the overexpression of CNOT1, PFDN2/6, and HMG20B, and that these genes could serve as novel molecular targets in liver cancer.
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Affiliation(s)
- Nouf Al-Yhya
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Muhammad Farooq Khan
- Bio-products Research Chair, Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Rafa Sharaf Almeer
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mana M Alshehri
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammed S Aldughaim
- Research Center, King Fahad Medical City, P.O.BOX:59046, Riyadh, 1152, Saudi Arabia
| | - Mohammad Ahmed Wadaan
- Bio-products Research Chair, Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
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13
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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: 7] [Impact Index Per Article: 2.3] [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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14
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Amine H, Ripin N, Sharma S, Stoecklin G, Allain FH, Séraphin B, Mauxion F. A conserved motif in human BTG1 and BTG2 proteins mediates interaction with the poly(A) binding protein PABPC1 to stimulate mRNA deadenylation. RNA Biol 2021; 18:2450-2465. [PMID: 34060423 PMCID: PMC8632095 DOI: 10.1080/15476286.2021.1925476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antiproliferative BTG/Tob proteins interact directly with the CAF1 deadenylase subunit of the CCR4-NOT complex. This binding requires the presence of two conserved motifs, boxA and boxB, characteristic of the BTG/Tob APRO domain. Consistently, these proteins were shown to stimulate mRNA deadenylation and decay in several instances. Two members of the family, BTG1 and BTG2, were reported further to associate with the protein arginine methyltransferase PRMT1 through a motif, boxC, conserved only in this subset of proteins. We recently demonstrated that BTG1 and BTG2 also contact the first RRM domain of the cytoplasmic poly(A) binding protein PABPC1. To decipher the mode of interaction of BTG1 and BTG2 with partners, we performed nuclear magnetic resonance experiments as well as mutational and biochemical analyses. Our data demonstrate that, in the context of an APRO domain, the boxC motif is necessary and sufficient to allow interaction with PABPC1 but, unexpectedly, that it is not required for BTG2 association with PRMT1. We show further that the presence of a boxC motif in an APRO domain endows it with the ability to stimulate deadenylation in cellulo and in vitro. Overall, our results identify the molecular interface allowing BTG1 and BTG2 to activate deadenylation, a process recently shown to be necessary for maintaining T-cell quiescence.
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Affiliation(s)
- Hamza Amine
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nina Ripin
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland
| | - Sahil Sharma
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Cancer Research Center (DKFZ)-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Georg Stoecklin
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Cancer Research Center (DKFZ)-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Frédéric H Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zürich, Switzerland
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Fabienne Mauxion
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
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15
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Meijer HA, Schmidt T, Gillen SL, Langlais C, Jukes-Jones R, de Moor CH, Cain K, Wilczynska A, Bushell M. DEAD-box helicase eIF4A2 inhibits CNOT7 deadenylation activity. Nucleic Acids Res 2019; 47:8224-8238. [PMID: 31180491 PMCID: PMC6736043 DOI: 10.1093/nar/gkz509] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 05/26/2019] [Accepted: 06/05/2019] [Indexed: 01/16/2023] Open
Abstract
The CCR4-NOT complex plays an important role in the translational repression and deadenylation of mRNAs. However, little is known about the specific roles of interacting factors. We demonstrate that the DEAD-box helicases eIF4A2 and DDX6 interact directly with the MA3 and MIF domains of CNOT1 and compete for binding. Furthermore, we now show that incorporation of eIF4A2 into the CCR4-NOT complex inhibits CNOT7 deadenylation activity in contrast to DDX6 which enhances CNOT7 activity. Polyadenylation tests (PAT) on endogenous mRNAs determined that eIF4A2 bound mRNAs have longer poly(A) tails than DDX6 bound mRNAs. Immunoprecipitation experiments show that eIF4A2 does not inhibit CNOT7 association with the CCR4-NOT complex but instead inhibits CNOT7 activity. We identified a CCR4-NOT interacting factor, TAB182, that modulates helicase recruitment into the CCR4-NOT complex, potentially affecting the outcome for the targeted mRNA. Together, these data show that the fate of an mRNA is dependent on the specific recruitment of either eIF4A2 or DDX6 to the CCR4-NOT complex which results in different pathways for translational repression and mRNA deadenylation.
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Affiliation(s)
- Hedda A Meijer
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Tobias Schmidt
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Sarah L Gillen
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Claudia Langlais
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Rebekah Jukes-Jones
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Cornelia H de Moor
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kelvin Cain
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Ania Wilczynska
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Martin Bushell
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
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16
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Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation. Nat Commun 2019; 10:3173. [PMID: 31320642 PMCID: PMC6639331 DOI: 10.1038/s41467-019-11094-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
CCR4-NOT is a conserved multiprotein complex which regulates eukaryotic gene expression principally via shortening of poly(A) tails of messenger RNA or deadenylation. Here, we reconstitute a complete, recombinant human CCR4-NOT complex. Our reconstitution strategy permits strict compositional control to test mechanistic hypotheses with purified component variants. CCR4-NOT is more active and selective for poly(A) than the isolated exonucleases, CCR4a and CAF1, which have distinct deadenylation profiles in vitro. The exonucleases require at least two out of three conserved non-enzymatic modules (CAF40, NOT10:NOT11 or NOT) for full activity in CCR4-NOT. CAF40 and the NOT10:NOT11 module both bind RNA directly and stimulate deadenylation in a partially redundant manner. Linear motifs from different RNA-binding factors that recruit CCR4-NOT to specific mRNAs via protein-protein interactions with CAF40 can inhibit bulk deadenylation. We reveal an additional layer of regulatory complexity to the human deadenylation machinery, which may prime it either for general or target-specific degradation. The CCR4-NOT complex shortens poly(A) tails of messenger RNAs. By biochemical reconstitution of the entire human CCR4-NOT complex, the authors show the stimulatory roles of non-enzymatic subunits and the importance of the interaction between CAF40 and RNA binding proteins in targeted deadenylation.
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17
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Airhihen B, Pavanello L, Jadhav GP, Fischer PM, Winkler GS. 1-Hydroxy-xanthine derivatives inhibit the human Caf1 nuclease and Caf1-containing nuclease complexes via Mg 2+-dependent binding. FEBS Open Bio 2019; 9:717-727. [PMID: 30984545 PMCID: PMC6443996 DOI: 10.1002/2211-5463.12605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/18/2019] [Accepted: 02/07/2019] [Indexed: 01/11/2023] Open
Abstract
In eukaryotic cells, cytoplasmic mRNA is characterised by a 3′ poly(A) tail. The shortening and removal of poly(A) tails (deadenylation) by the Ccr4‐Not nuclease complex leads to reduced translational efficiency and RNA degradation. Using recombinant human Caf1 (CNOT7) enzyme as a screening tool, we recently described the discovery and synthesis of a series of substituted 1‐hydroxy‐3,7‐dihydro‐1H‐purine‐2,6‐diones (1‐hydroxy‐xanthines) as inhibitors of the Caf1 catalytic subunit of the Ccr4‐Not complex. Here, we used a chemiluminescence‐based AMP detection assay to show that active 1‐hydroxy‐xanthines inhibit both isolated Caf1 enzyme and human Caf1‐containing complexes that also contain the second nuclease subunit Ccr4 (CNOT6L) to a similar extent, indicating that the active site of the Caf1 nuclease subunit does not undergo substantial conformational change when bound to other Ccr4‐Not subunits. Using differential scanning fluorimetry, we also show that binding of active 1‐hydroxy‐xanthines requires the presence of Mg2+ ions, which are present in the active site of Caf1.
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Affiliation(s)
- Blessing Airhihen
- School of Pharmacy University of Nottingham UK.,Present address: Department of Pharmacology School of Pharmacy Niger Delta University Wilberforce Island Nigeria
| | - Lorenzo Pavanello
- School of Pharmacy University of Nottingham UK.,Present address: Domainex Ltd Chesterford Research Park Little Chesterford, Saffron Walden, Essex UK
| | - Gopal P Jadhav
- School of Pharmacy Centre for Biomolecular Sciences University of Nottingham UK.,Present address: School of Medicine Department of Clinical & Translational Sciences Creighton University Omaha NE USA
| | - Peter M Fischer
- School of Pharmacy Centre for Biomolecular Sciences University of Nottingham UK
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