1
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Jiao D, Sun H, Zhao X, Chen Y, Lv Z, Shi Q, Li Y, Wang C, Gao K. mTORC1/S6K1 signaling promotes sustained oncogenic translation through modulating CRL3 IBTK-mediated ubiquitination of eIF4A1 in cancer cells. eLife 2024; 12:RP92236. [PMID: 38738857 PMCID: PMC11090508 DOI: 10.7554/elife.92236] [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: 05/14/2024] Open
Abstract
Enhanced protein synthesis is a crucial molecular mechanism that allows cancer cells to survive, proliferate, metastasize, and develop resistance to anti-cancer treatments, and often arises as a consequence of increased signaling flux channeled to mRNA-bearing eukaryotic initiation factor 4F (eIF4F). However, the post-translational regulation of eIF4A1, an ATP-dependent RNA helicase and subunit of the eIF4F complex, is still poorly understood. Here, we demonstrate that IBTK, a substrate-binding adaptor of the Cullin 3-RING ubiquitin ligase (CRL3) complex, interacts with eIF4A1. The non-degradative ubiquitination of eIF4A1 catalyzed by the CRL3IBTK complex promotes cap-dependent translational initiation, nascent protein synthesis, oncogene expression, and cervical tumor cell growth both in vivo and in vitro. Moreover, we show that mTORC1 and S6K1, two key regulators of protein synthesis, directly phosphorylate IBTK to augment eIF4A1 ubiquitination and sustained oncogenic translation. This link between the CRL3IBTK complex and the mTORC1/S6K1 signaling pathway, which is frequently dysregulated in cancer, represents a promising target for anti-cancer therapies.
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Affiliation(s)
- Dongyue Jiao
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Huiru Sun
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Xiaying Zhao
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Yingji Chen
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Zeheng Lv
- Department of Clinical Laboratory, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghaiChina
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghaiChina
| | - Qing Shi
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Kun Gao
- Department of Clinical Laboratory, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghaiChina
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghaiChina
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2
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Eiler DR, Wimberly BT, Bilodeau DY, Taliaferro JM, Reigan P, Rissland OS, Kieft JS. The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function. Structure 2024; 32:400-410.e4. [PMID: 38242118 PMCID: PMC10997490 DOI: 10.1016/j.str.2023.12.015] [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: 06/19/2023] [Revised: 10/23/2023] [Accepted: 12/23/2023] [Indexed: 01/21/2024]
Abstract
Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure of the G. lamblia 80S ribosome bound to tRNA, mRNA, and the antibiotic emetine by cryo-electron microscopy, to an overall resolution of 2.49 Å. The structure reveals rapidly evolving protein and nucleotide regions, differences in the peptide exit tunnel, and likely altered ribosome quality control pathways. Examination of translation initiation factor binding sites suggests these interactions are conserved despite a divergent initiation mechanism. Highlighting the potential of G. lamblia to resolve conserved biological principles; our structure reveals the interactions of the translation inhibitor emetine with the ribosome and mRNA, thus providing insight into the mechanism of action for this widely used antibiotic. Our work defines key questions in G. lamblia and motivates future experiments to explore the diversity of eukaryotic gene regulation.
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Affiliation(s)
- Daniel R Eiler
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brian T Wimberly
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Danielle Y Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Philip Reigan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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3
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González-Sánchez AM, Castellanos-Silva EA, Díaz-Figueroa G, Cate JHD. JUN mRNA translation regulation is mediated by multiple 5' UTR and start codon features. PLoS One 2024; 19:e0299779. [PMID: 38483896 PMCID: PMC10939236 DOI: 10.1371/journal.pone.0299779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
Regulation of mRNA translation by eukaryotic initiation factors (eIFs) is crucial for cell survival. In humans, eIF3 stimulates translation of the JUN mRNA which encodes the transcription factor JUN, an oncogenic transcription factor involved in cell cycle progression, apoptosis, and cell proliferation. Previous studies revealed that eIF3 activates translation of the JUN mRNA by interacting with a stem loop in the 5' untranslated region (5' UTR) and with the 5' -7-methylguanosine cap structure. In addition to its interaction site with eIF3, the JUN 5' UTR is nearly one kilobase in length, and has a high degree of secondary structure, high GC content, and an upstream start codon (uAUG). This motivated us to explore the complexity of JUN mRNA translation regulation in human cells. Here we find that JUN translation is regulated in a sequence and structure-dependent manner in regions adjacent to the eIF3-interacting site in the JUN 5' UTR. Furthermore, we identify contributions of an additional initiation factor, eIF4A, in JUN regulation. We show that enhancing the interaction of eIF4A with JUN by using the compound Rocaglamide A (RocA) represses JUN translation. We also find that both the upstream AUG (uAUG) and the main AUG (mAUG) contribute to JUN translation and that they are conserved throughout vertebrates. Our results reveal additional layers of regulation for JUN translation and show the potential of JUN as a model transcript for understanding multiple interacting modes of translation regulation.
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Affiliation(s)
- Angélica M. González-Sánchez
- Comparative Biochemistry Graduate Program, University of California, Berkeley, Berkeley, CA, United States of America
| | - Eimy A. Castellanos-Silva
- Department of Biochemistry and Molecular Biology, University of California, Davis, Davis, CA, United States of America
| | - Gabriela Díaz-Figueroa
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
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4
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Essouma M. Autoimmune inflammatory myopathy biomarkers. Clin Chim Acta 2024; 553:117742. [PMID: 38176522 DOI: 10.1016/j.cca.2023.117742] [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: 07/18/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
The autoimmune inflammatory myopathy disease spectrum, commonly known as myositis, is a group of systemic diseases that mainly affect the muscles, skin and lungs. Biomarker assessment helps in understanding disease mechanisms, allowing for the implementation of precise strategies in the classification, diagnosis, and management of these diseases. This review examines the pathogenic mechanisms and highlights current data on blood and tissue biomarkers of autoimmune inflammatory myopathies.
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Affiliation(s)
- Mickael Essouma
- Network of Immunity in Infections, Malignancy and Autoimmunity, Universal Scientific Education and Research Network, Cameroon
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5
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Chang J, Shin MK, Park J, Hwang HJ, Locker N, Ahn J, Kim D, Baek D, Park Y, Lee Y, Boo SH, Kim HI, Kim YK. An interaction between eIF4A3 and eIF3g drives the internal initiation of translation. Nucleic Acids Res 2023; 51:10950-10969. [PMID: 37811880 PMCID: PMC10639049 DOI: 10.1093/nar/gkad763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
An RNA structure or modified RNA sequences can provide a platform for ribosome loading and internal translation initiation. The functional significance of internal translation has recently been highlighted by the discovery that a subset of circular RNAs (circRNAs) is internally translated. However, the molecular mechanisms underlying the internal initiation of translation in circRNAs remain unclear. Here, we identify eIF3g (a subunit of eIF3 complex) as a binding partner of eIF4A3, a core component of the exon-junction complex (EJC) that is deposited onto spliced mRNAs and plays multiple roles in the regulation of gene expression. The direct interaction between eIF4A3-eIF3g serves as a molecular linker between the eIF4A3 and eIF3 complex, thereby facilitating internal ribosomal entry. Protein synthesis from in vitro-synthesized circRNA demonstrates eIF4A3-driven internal translation, which relies on the eIF4A3-eIF3g interaction. Furthermore, our transcriptome-wide analysis shows that efficient polysomal association of endogenous circRNAs requires eIF4A3. Notably, a subset of endogenous circRNAs can express a full-length intact protein, such as β-catenin, in an eIF4A3-dependent manner. Collectively, our results expand the understanding of the protein-coding potential of the human transcriptome, including circRNAs.
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Affiliation(s)
- Jeeyoon Chang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Min-Kyung Shin
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Nicolas Locker
- Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7HX, UK
| | - Junhak Ahn
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Doyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonkyoung Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yujin Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sung Ho Boo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyeong-In Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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6
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Henne SK, Aldisi R, Sivalingam S, Hochfeld LM, Borisov O, Krawitz PM, Maj C, Nöthen MM, Heilmann-Heimbach S. Analysis of 72,469 UK Biobank exomes links rare variants to male-pattern hair loss. Nat Commun 2023; 14:5492. [PMID: 37737258 PMCID: PMC10517150 DOI: 10.1038/s41467-023-41186-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Male-pattern hair loss (MPHL) is common and highly heritable. While genome-wide association studies (GWAS) have generated insights into the contribution of common variants to MPHL etiology, the relevance of rare variants remains unclear. To determine the contribution of rare variants to MPHL etiology, we perform gene-based and single-variant analyses in exome-sequencing data from 72,469 male UK Biobank participants. While our population-level risk prediction suggests that rare variants make only a minor contribution to general MPHL risk, our rare variant collapsing tests identified a total of five significant gene associations. These findings provide additional evidence for previously implicated genes (EDA2R, WNT10A) and highlight novel risk genes at and beyond GWAS loci (HEPH, CEPT1, EIF3F). Furthermore, MPHL-associated genes are enriched for genes considered causal for monogenic trichoses. Together, our findings broaden the MPHL-associated allelic spectrum and provide insights into MPHL pathobiology and a shared basis with monogenic hair loss disorders.
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Affiliation(s)
- Sabrina Katrin Henne
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Rana Aldisi
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Sugirthan Sivalingam
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Department of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Lara Maleen Hochfeld
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter Michael Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Markus Maria Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
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7
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Dobrescu I, Hammam E, Dziekan JM, Claës A, Halby L, Preiser P, Bozdech Z, Arimondo PB, Scherf A, Nardella F. Plasmodium falciparum Eukaryotic Translation Initiation Factor 3 is Stabilized by Quinazoline-Quinoline Bisubstrate Inhibitors. ACS Infect Dis 2023; 9:1257-1266. [PMID: 37216290 PMCID: PMC10262199 DOI: 10.1021/acsinfecdis.3c00127] [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: 03/16/2023] [Indexed: 05/24/2023]
Abstract
Malaria drug resistance is hampering the fight against the deadliest parasitic disease affecting over 200 million people worldwide. We recently developed quinoline-quinazoline-based inhibitors (as compound 70) as promising new antimalarials. Here, we aimed to investigate their mode of action by using thermal proteome profiling (TPP). The eukaryotic translation initiation factor 3 (EIF3i) subunit I was identified as the main target protein stabilized by compound 70 in Plasmodium falciparum. This protein has never been characterized in malaria parasites. P. falciparum parasite lines were generated expressing either a HA tag or an inducible knockdown of the PfEIF3i gene to further characterize the target protein. PfEIF3i was stabilized in the presence of compound 70 in a cellular thermal shift Western blot assay, pointing that PfEIF3i indeed interacts with quinoline-quinazoline-based inhibitors. In addition, PfEIF3i-inducible knockdown blocks intra-erythrocytic development in the trophozoite stage, indicating that it has a vital function. We show that PfEIF3i is mostly expressed in late intra-erythrocytic stages and localizes in the cytoplasm. Previous mass spectrometry reports show that PfEIF3i is expressed in all parasite life cycle stages. Further studies will explore the potential of PfEIF3i as a target for the design of new antimalarial drugs active all along the life cycle of the parasite.
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Affiliation(s)
- Irina Dobrescu
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Elie Hammam
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Jerzy M. Dziekan
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Aurélie Claës
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Ludovic Halby
- Epigenetic
Chemical Biology, Department of Structural Biology and Chemistry,
Institut Pasteur, Université de Paris-Cité,
UMR n3523 Chem4Life, CNRS, 28 Rue Du Dr Roux, Paris 75015, France
| | - Peter Preiser
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Zbynek Bozdech
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Paola B. Arimondo
- Epigenetic
Chemical Biology, Department of Structural Biology and Chemistry,
Institut Pasteur, Université de Paris-Cité,
UMR n3523 Chem4Life, CNRS, 28 Rue Du Dr Roux, Paris 75015, France
| | - Artur Scherf
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Flore Nardella
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
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8
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Bowazolo C, Morse D. Insights into daily metabolic changes of the dinoflagellate Lingulodinium from ribosome profiling. Cell Cycle 2023; 22:1343-1352. [PMID: 37125841 PMCID: PMC10228409 DOI: 10.1080/15384101.2023.2206771] [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: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 05/02/2023] Open
Abstract
The dinoflagellate Lingulodinium specializes its metabolism to perform different tasks better at specific times of day. For example, cells are specialized for photosynthesis during the day and bioluminescence and cell division at night. These rhythms are circadian as they are controlled by an endogenous circadian clock whose mechanism is currently unknown. Despite this, the metabolic rhythms follow coordinated changes in gene expression that occur at a translational level. These changes are revealed by ribosome profiling, a surrogate measure of protein synthesis rates in vivo. Lingulodinium regulates the synthesis rate of over three thousand transcripts. Peak synthesis rates for the different transcripts are clustered around three different times over a light/dark cycle. Furthermore, transcripts involved in the same metabolic process are coordinately regulated. We review the basic principles underlying the correlation of coordinated translation of cell metabolic pathway enzymes with known circadian rhythms, and offer examples where previously unsuspected rhythms are suggested by synchronized changes in gene expression.
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Affiliation(s)
- Carl Bowazolo
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - David Morse
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
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9
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Bose P, Baron N, Pullaiahgari D, Ben-Zvi A, Shapira M. LeishIF3d is a non-canonical cap-binding protein in Leishmania. Front Mol Biosci 2023; 10:1191934. [PMID: 37325473 PMCID: PMC10266417 DOI: 10.3389/fmolb.2023.1191934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Translation of most cellular mRNAs in eukaryotes proceeds through a cap-dependent pathway, whereby the cap-binding complex, eIF4F, anchors the pre-initiation complex at the 5' end of mRNAs driving translation initiation. The genome of Leishmania encodes a large repertoire of cap-binding complexes that fulfill a variety of functions possibly involved in survival along the life cycle. However, most of these complexes function in the promastigote life form that resides in the sand fly vector and decrease their activity in amastigotes, the mammalian life form. Here we examined the possibility that LeishIF3d drives translation in Leishmania using alternative pathways. We describe a non-canonical cap-binding activity of LeishIF3d and examine its potential role in driving translation. LeishIF3d is required for translation, as reducing its expression by a hemizygous deletion reduces the translation activity of the LeishIF3d(+/-) mutant cells. Proteomic analysis of the mutant cells highlights the reduced expression of flagellar and cytoskeletal proteins, as reflected in the morphological changes observed in the mutant cells. Targeted mutations in two predicted alpha helices diminish the cap-binding activity of LeishIF3d. Overall, LeishIF3d could serve as a driving force for alternative translation pathways, although it does not seem to offer an alternative pathway for translation in amastigotes.
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Affiliation(s)
- Priyanka Bose
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Anat Ben-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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10
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Yang HT, Wang G, Zhu PC, Xiao ZY. Silencing EIF3A ameliorates pulmonary arterial hypertension through HDAC1 and PTEN/PI3K/AKT pathway in vitro and in vivo. Exp Cell Res 2023; 426:113555. [PMID: 36921705 DOI: 10.1016/j.yexcr.2023.113555] [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: 12/29/2022] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Pulmonary vascular remodeling caused by the excessive proliferation of pulmonary arterial smooth muscle cells (PASMCs) is the hallmark feature of pulmonary arterial hypertension (PAH). Eukaryotic initiation factor 3 subunit A (EIF3A) exhibited proliferative activity in multiple cell types. The present study investigated the role of EIF3A in the progression of PAH. A monocrotaline (MCT)-induced PAH rat model was constructed, and adeno-associated virus type 1 (AAV1) carrying EIF3A shRNA was intratracheally delivered to PAH rats to block EIF3A expression. PASMCs were isolated from rats and treated with PDGF-BB to simulate PASMC proliferation, and shRNA for EIF3 was conducted to investigate the mechanism behind the role of EIF3A in PASMC function in vitro. EIF3A expression was upregulated in pulmonary arteries, and EIF3A inhibition effectively improved pulmonary hypertension and right ventricular hypertrophy and suppressed MCT-induced vascular remodeling in vivo. In addition, we found that genetic knockdown of EIF3A reduced PDGF-triggered proliferation and arrested cell cycle, accompanied by downregulated proliferation-related protein expression in PASMCs. Mechanistically, the histone deacetylase 1 (HDAC1)-mediated PTEN/PI3K/AKT pathway was recognized as a primary mechanism in PAH progression. Silencing EIF3A decreased HDAC1 expression, and further inhibited the excessive proliferation of PASMCs by increasing the phosphatase and tension homolog (PTEN) expression and suppressing the AKT phosphorylation. Notably, HDAC1 expression reversed the effect of silencing EIF3A on PAH and PTEN/PI3K/AKT pathway. Collectively, silencing EIF3A improved PAH by decreasing PASMC proliferation through the HDAC1-mediated PTEN/PI3K/AKT pathway. These findings suggest that targeting EIF3A may represent a potential approach for the treatment of PAH.
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Affiliation(s)
- Hai-Tao Yang
- Dalian Medical University, Dalian, Liaoning, China; Department of Anesthesiology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Guan Wang
- Department of Anesthesiology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Peng-Cheng Zhu
- Department of Anesthesiology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zhao-Yang Xiao
- Department of Anesthesiology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China.
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11
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Turner M. Regulation and function of poised mRNAs in lymphocytes. Bioessays 2023; 45:e2200236. [PMID: 37009769 DOI: 10.1002/bies.202200236] [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: 12/07/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 04/04/2023]
Abstract
Pre-existing but untranslated or 'poised' mRNA exists as a means to rapidly induce the production of specific proteins in response to stimuli and as a safeguard to limit the actions of these proteins. The translation of poised mRNA enables immune cells to express quickly genes that enhance immune responses. The molecular mechanisms that repress the translation of poised mRNA and, upon stimulation, enable translation have yet to be elucidated. They likely reflect intrinsic properties of the mRNAs and their interactions with trans-acting factors that direct poised mRNAs away from or into the ribosome. Here, I discuss mechanisms by which this might be regulated.
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Affiliation(s)
- Martin Turner
- Immunology Programme, The Babraham Institute, Cambridge, UK
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12
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Ahmadzada T, Vijayan A, Vafaee F, Azimi A, Reid G, Clarke S, Kao S, Grau GE, Hosseini-Beheshti E. Small and Large Extracellular Vesicles Derived from Pleural Mesothelioma Cell Lines Offer Biomarker Potential. Cancers (Basel) 2023; 15:cancers15082364. [PMID: 37190292 DOI: 10.3390/cancers15082364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 05/17/2023] Open
Abstract
Pleural mesothelioma, previously known as malignant pleural mesothelioma, is an aggressive and fatal cancer of the pleura, with one of the poorest survival rates. Pleural mesothelioma is in urgent clinical need for biomarkers to aid early diagnosis, improve prognostication, and stratify patients for treatment. Extracellular vesicles (EVs) have great potential as biomarkers; however, there are limited studies to date on their role in pleural mesothelioma. We conducted a comprehensive proteomic analysis on different EV populations derived from five pleural mesothelioma cell lines and an immortalized control cell line. We characterized three subtypes of EVs (10 K, 18 K, and 100 K), and identified a total of 4054 unique proteins. Major differences were found in the cargo between the three EV subtypes. We show that 10 K EVs were enriched in mitochondrial components and metabolic processes, while 18 K and 100 K EVs were enriched in endoplasmic reticulum stress. We found 46 new cancer-associated proteins for pleural mesothelioma, and the presence of mesothelin and PD-L1/PD-L2 enriched in 100 K and 10 K EV, respectively. We demonstrate that different EV populations derived from pleural mesothelioma cells have unique cancer-specific proteomes and carry oncogenic cargo, which could offer a novel means to extract biomarkers of interest for pleural mesothelioma from liquid biopsies.
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Affiliation(s)
- Tamkin Ahmadzada
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Abhishek Vijayan
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ali Azimi
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Dermatology, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Glen Reid
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Stephen Clarke
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Steven Kao
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
- Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW 2050, Australia
- Asbestos Diseases Research Institute, Sydney, NSW 2139, Australia
| | - Georges E Grau
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
- The Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Elham Hosseini-Beheshti
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
- The Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
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13
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Raus AM, Fuller TD, Nelson NE, Valientes DA, Bayat A, Ivy AS. Early-life exercise primes the murine neural epigenome to facilitate gene expression and hippocampal memory consolidation. Commun Biol 2023; 6:18. [PMID: 36611093 PMCID: PMC9825372 DOI: 10.1038/s42003-022-04393-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023] Open
Abstract
Aerobic exercise is well known to promote neuroplasticity and hippocampal memory. In the developing brain, early-life exercise (ELE) can lead to persistent improvements in hippocampal function, yet molecular mechanisms underlying this phenomenon have not been fully explored. In this study, transgenic mice harboring the "NuTRAP" (Nuclear tagging and Translating Ribosome Affinity Purification) cassette in Emx1 expressing neurons ("Emx1-NuTRAP" mice) undergo ELE during adolescence. We then simultaneously isolate and sequence translating mRNA and nuclear chromatin from single hippocampal homogenates containing Emx1-expressing neurons. This approach allowed us to couple translatomic with epigenomic sequencing data to evaluate the influence of histone modifications H4K8ac and H3K27me3 on translating mRNA after ELE. A subset of ELE mice underwent a hippocampal learning task to determine the gene expression and epigenetic underpinnings of ELE's contribution to improved hippocampal memory performance. From this experiment, we discover gene expression - histone modification relationships that may play a critical role in facilitated memory after ELE. Our data reveal candidate gene-histone modification interactions and implicate gene regulatory pathways involved in ELE's impact on hippocampal memory.
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Affiliation(s)
- Anthony M Raus
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Tyson D Fuller
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Nellie E Nelson
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - David A Valientes
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Anita Bayat
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Autumn S Ivy
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Neurobiology/Behavior, University of California- Irvine School of Biological Sciences, Irvine, CA, USA.
- Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Division of Neurology, Children's Hospital Orange County, Orange, CA, USA.
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14
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Mei Z, Mou Y, Zhang N, Liu X, He Z, Gu S. Emerging Mutual Regulatory Roles between m 6A Modification and microRNAs. Int J Mol Sci 2023; 24:ijms24010773. [PMID: 36614216 PMCID: PMC9821650 DOI: 10.3390/ijms24010773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 01/03/2023] Open
Abstract
N6-metyladenosine (m6A), one of the most common RNA methylation modifications in mammals, has attracted extensive attentions owing to its regulatory roles in a variety of physiological and pathological processes. As a reversible epigenetic modification on RNAs, m6A is dynamically mediated by the functional interplay among the regulatory proteins of methyltransferases, demethylases and methyl-binding proteins. In recent years, it has become increasingly clear that m6A modification is associated with the production and function of microRNAs (miRNAs). In this review, we summarize the specific kinds of m6A modification methyltransferases, demethylases and methyl-binding proteins. In particular, we focus on describing the roles of m6A modification and its regulatory proteins in the production and function of miRNAs in a variety of pathological and physiological processes. More importantly, we further discuss the mediating mechanisms of miRNAs in m6A modification and its regulatory proteins during the occurrence and development of various diseases.
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15
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Tingskov Pedersen CE, Eliasen AU, Ketzel M, Brandt J, Loft S, Frohn LM, Khan J, Brix S, Rasmussen MA, Stokholm J, Chawes B, Morin A, Ober C, Bisgaard H, Pedersen M, Bønnelykke K. Prenatal exposure to ambient air pollution is associated with early life immune perturbations. J Allergy Clin Immunol 2023; 151:212-221. [PMID: 36075322 DOI: 10.1016/j.jaci.2022.08.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Exposure to ambient air pollution has been linked to asthma, allergic rhinitis, and other inflammatory disorders, but little is known about the underlying mechanisms. OBJECTIVE We studied the potential mechanisms leading from prenatal ambient air pollution exposure to asthma and allergy in childhood. METHODS Long-term exposure to nitrogen dioxide (NO2) as well as to particulate matter with a diameter of ≤2.5 and ≤10 μm (PM2.5 and PM10) were modeled at the residence level from conception to 6 years of age in 700 Danish children followed clinically for development of asthma and allergy. Nasal mucosal immune mediators were assessed at age 4 weeks and 6 years, inflammatory markers in blood at 6 months, and nasal epithelial DNA methylation and gene expression at age 6 years. RESULTS Higher prenatal air pollution exposure with NO2, PM2.5, and PM10 was associated with an altered nasal mucosal immune profile at 4 weeks, conferring an increased odds ratio [95% confidence interval] of 2.68 [1.58, 4.62] for allergic sensitization and 2.63 [1.18, 5.81] for allergic rhinitis at age 6 years, and with an altered immune profile in blood at age 6 months conferring increased risk of asthma at age 6 years (1.80 [1.18, 2.76]). Prenatal exposure to ambient air pollution was not robustly associated with immune mediator, epithelial DNA methylation, or gene expression changes in nasal cells at age 6 years. CONCLUSION Prenatal exposure to ambient air pollution was associated with early life immune perturbations conferring risk of allergic rhinitis and asthma. These findings suggest potential mechanisms of prenatal exposure to ambient air pollution on the developing immune system.
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Affiliation(s)
- Casper-Emil Tingskov Pedersen
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Anders Ulrik Eliasen
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Matthias Ketzel
- Department of Environmental Science, Aarhus University of Copenhagen, Roskilde, Denmark
| | - Jørgen Brandt
- Department of Environmental Science, Aarhus University of Copenhagen, Roskilde, Denmark
| | - Steffen Loft
- Department of Public Health, Section of Environment and Health, University of Copenhagen, Copenhagen, Denmark; Department of Public Health, Section of Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University of Copenhagen, Roskilde, Denmark
| | - Lise Marie Frohn
- Department of Environmental Science, Aarhus University of Copenhagen, Roskilde, Denmark
| | - Jibran Khan
- Department of Environmental Science, Aarhus University of Copenhagen, Roskilde, Denmark; Department of Public Health, Section of Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University of Copenhagen, Roskilde, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Food Science, Roskilde, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Food Science, Roskilde, Denmark
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Andreanne Morin
- Department of Human Genetics, University of Copenhagen, Copenhagen, Denmark
| | - Carole Ober
- Department of Human Genetics, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Marie Pedersen
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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16
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Liang Z, Yang Y, Sun X, Du J, Wang Q, Zhang G, Zhang J, Yin X, Singh D, Su P, Zhang X. Integrated Analysis of MicroRNA and mRNA Expression Profiles in the Fat Bodies of MbMNPV-Infected Helicoverpa armigera. Viruses 2022; 15:19. [PMID: 36680059 PMCID: PMC9861407 DOI: 10.3390/v15010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs), are a novel class of gene expression regulators, that have been found to participate in regulating host-virus interactions. However, the function of insect-derived miRNAs in response to virus infection is poorly understood. We analyzed miRNA expression profiles in the fat bodies of Helicoverpa armigera (H. armigera) infected with Mamestra brassicae multiple nucleopolyhedroviruses (MbMNPV). A total of 52 differentially expressed miRNAs (DEmiRNAs) were filtered out through RNA-seq analysis. The targets of 52 DEmiRNAs were predicted and 100 miRNA-mRNA interaction pairs were obtained. The predicted targets of DEmiRNAs were mainly enriched in the Wnt signaling pathway, phagosome, and mTOR signaling pathway, which are related to the virus infection. Real-time PCR was used to verify the RNA sequencing results. ame-miR-317-3p, mse-miR-34, novel1-star, and sfr-miR-6094-5p were shown to be involved in the host response to MbMNPV infection. Results suggest that sfr-miR-6094-5p can negatively regulate the expression of four host genes eIF3-S7, CG7583, CG16901, and btf314, and inhibited MbMNPV infection significantly. Further studies showed that RNAi-mediated knockdown of eIF3-S7 inhibited the MbMNPV infection. These findings suggest that sfr-miR-6094-5p inhibits MbMNPV infection by negatively regulating the expression of eIF3-S7. This study provides new insights into MbMNPV and H. armigera interaction mechanisms.
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Affiliation(s)
- Zhenpu Liang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanqing Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoyan Sun
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Junyang Du
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Qiuyun Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Guozhi Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiran Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Deepali Singh
- School of Biotechnology, Gautam, Buddha University, Greater Noida 201312, India
| | - Ping Su
- Institute of Agricultural Sciences of the 14th Division of Xinjiang Production and Construction Corps, Kunyu 848116, China
| | - Xiaoxia Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
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17
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Ding L, Wang R, Zheng Q, Shen D, Wang H, Lu Z, Luo W, Xie H, Ren L, Jiang M, Yu C, Zhou Z, Lin Y, Lu H, Xue D, Su W, Xia L, Neuhaus J, Cheng S, Li G. circPDE5A regulates prostate cancer metastasis via controlling WTAP-dependent N6-methyladenisine methylation of EIF3C mRNA. J Exp Clin Cancer Res 2022; 41:187. [PMID: 35650605 PMCID: PMC9161465 DOI: 10.1186/s13046-022-02391-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/15/2022] [Indexed: 12/24/2022] Open
Abstract
Background Circular RNA (circRNA) is a novel class noncoding RNA (ncRNA) that plays a critical role in various cancers, including prostate cancer (PCa). However, the clinical significance, biological function, and molecular mechanisms of circRNAs in prostate cancer remain to be elucidated. Methods A circRNA array was performed to identified the differentially expressed circRNAs. circPDE5A was identified as a novel circRNA which downregulated in clinical samples. Functionally, the in vitro and in vivo assays were applied to explore the role of circPDE5A in PCa metastasis. Mechanistically, the interaction between circPDE5A and WTAP was verified using RNA pulldown followed by mass spectrometry, RNA Immunoprecipitation (RIP) assays. m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) was then used to identified the downstream target of circPDE5A. Chromatin immunoprecipitation assay (ChIP) and dual-luciferase reporter assay were used to identified transcriptional factor which regulated circPDE5A expression. Results circPDE5A was identified downregulated in PCa tissues compared to adjacent normal tissue and was negatively correlated with gleason score of PCa patients. circPDE5A inhibits PCa cells migration and invasion both in vitro and in vivo. circPDE5A blocks the WTAP-dependent N6-methyladenisine (m6A) methylation of eukaryotic translation initiation factor 3c (EIF3C) mRNA by forming the circPDE5A-WTAP complex, and finally disrupts the translation of EIF3C. Moreover, the circPDE5A-dependent decrease in EIF3C expression inactivates the MAPK pathway and then restrains PCa progression. Conclusions Our findings demonstrate that FOXO4-mediated upregulation of circPDE5A controls PCa metastasis via the circPDE5A-WTAP-EIF3C-MAPK signaling pathway and could serve as a potential therapeutic targer for PCa. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02391-5.
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18
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Song Z, Lin J, Su R, Ji Y, Jia R, Li S, Shan G, Huang C. eIF3j inhibits translation of a subset of circular RNAs in eukaryotic cells. Nucleic Acids Res 2022; 50:11529-11549. [PMID: 36330957 PMCID: PMC9723666 DOI: 10.1093/nar/gkac980] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Increasing studies have revealed that a subset of circular RNAs (circRNAs) harbor an open reading frame and can act as protein-coding templates to generate functional proteins that are closely associated with multiple physiological and disease-relevant processes, and thus proper regulation of synthesis of these circRNA-derived proteins is a fundamental cellular process required for homeostasis maintenance. However, how circRNA translation initiation is coordinated by different trans-acting factors remains poorly understood. In particular, the impact of different eukaryotic translation initiation factors (eIFs) on circRNA translation and the physiological relevance of this distinct regulation have not yet been characterized. In this study, we screened all 43 Drosophila eIFs and revealed the conflicting functions of eIF3 subunits in the translational control of the translatable circRNA circSfl: eIF3 is indispensable for circSfl translation, while the eIF3-associated factor eIF3j is the most potent inhibitor. Mechanistically, the binding of eIF3j to circSfl promotes the disassociation of eIF3. The C-terminus of eIF3j and an RNA regulon within the circSfl untranslated region (UTR) are essential for the inhibitory effect of eIF3j. Moreover, we revealed the physiological relevance of eIF3j-mediated circSfl translation repression in response to heat shock. Finally, additional translatable circRNAs were identified to be similarly regulated in an eIF3j-dependent manner. Altogether, our study provides a significant insight into the field of cap-independent translational regulation and undiscovered functions of eIF3.
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Affiliation(s)
| | | | - Rui Su
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yu Ji
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- To whom correspondence should be addressed. Tel: +86 19956025374;
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19
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Luo Y, Yao Q. Circ_0085315 promotes cell proliferation, invasion, and migration in colon cancer through miR-1200/MAP3K1 signaling pathway. Cell Cycle 2022; 21:1194-1211. [PMID: 35230926 PMCID: PMC9103513 DOI: 10.1080/15384101.2022.2044137] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/02/2022] [Accepted: 02/06/2022] [Indexed: 12/30/2022] Open
Abstract
Colon cancer (CC) is a common malignant tumor of the digestive tract. Circular RNAs (circRNAs) play important roles in the progression of CC. This study aimed to explore the role and mechanism of circRNA_0085315 in CC. In this study, we used qRT-PCR and Western blot assays to analyze the expressions of circRNA, miRNA, and mRNA as well as the expression of the related proteins. Luciferase reporter, RNA pull-down, and qRT-PCR assays were used to prove the relationship among circRNA, miRNA, and mRNA. CCK-8, colony formation, and transwell assays were used to perform the analysis of cell proliferation, migration, and invasion. Our results showed that the higher circRNA_0085315 expression led to the poorer prognosis of CC patients. The function of circRNA_0085315 as a ceRNA in competing with MAP3K1 mRNA to sponge miR-1200. CircRNA_0085315 sponged miR-1200 to promote cell proliferation, migration, and invasion and affected the expression of Ki67, MMP2, E-cadherin, and N-cadherin, but not circRNA_0085315-mut without the binding site of miR-1200. MAP3K1-overexpression or miR-1200 mimics prevented the suppression on the enhanced cell proliferation, migration, and invasion caused by circRNA_0085315-overexpression. circRNA_0085315 increased the phosphorylation levels of JNK, p38, and ERK1/2 by stimulating MAP3K1 up-regulation caused by miR-1200 inhibition. In conclusion, circRNA_0085315 serves as a ceRNA and promotes CC progression through the activation of the MAPK signaling pathway mediated via the miR-1200/MAP3K1 axis, suggesting that circRNA_0085315 may be a promising diagnostic and therapeutic target for CC.
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Affiliation(s)
- Yuan Luo
- Department of Geriatrics, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Qi Yao
- Department of Geriatrics, Ningbo First Hospital, Ningbo, Zhejiang Province, China
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20
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Kim JG, Shan L. Beyond Inhibition: A Novel Strategy of Targeting HIV-1 Protease to Eliminate Viral Reservoirs. Viruses 2022; 14:1179. [PMID: 35746649 PMCID: PMC9231271 DOI: 10.3390/v14061179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 02/06/2023] Open
Abstract
HIV-1 protease (PR) is a viral enzyme that cleaves the Gag and Gag-Pol polyprotein precursors to convert them into their functional forms, a process which is essential to generate infectious viral particles. Due to its broad substrate specificity, HIV-1 PR can also cleave certain host cell proteins. Several studies have identified host cell substrates of HIV-1 PR and described the potential impact of their cleavage on HIV-1-infected cells. Of particular interest is the interaction between PR and the caspase recruitment domain-containing protein 8 (CARD8) inflammasome. A recent study demonstrated that CARD8 can sense HIV-1 PR activity and induce cell death. While PR typically has low levels of intracellular activity prior to viral budding, premature PR activation can be achieved using certain non-nucleoside reverse transcriptase inhibitors (NNRTIs), resulting in CARD8 cleavage and downstream pyroptosis. Used together with latency reversal agents, the induction of premature PR activation to trigger CARD8-mediated cell killing may help eliminate latent reservoirs in people living with HIV. This represents a novel strategy of utilizing PR as an antiviral target through premature activation rather than inhibition. In this review, we discuss the viral and host substrates of HIV-1 protease and highlight potential applications and advantages of targeting CARD8 sensing of HIV-1 PR.
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Affiliation(s)
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA;
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21
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Yi SH, Petrychenko V, Schliep JE, Goyal A, Linden A, Chari A, Urlaub H, Stark H, Rodnina MV, Adio S, Fischer N. Conformational rearrangements upon start codon recognition in human 48S translation initiation complex. Nucleic Acids Res 2022; 50:5282-5298. [PMID: 35489072 PMCID: PMC9122606 DOI: 10.1093/nar/gkac283] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 01/10/2023] Open
Abstract
Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct ribosome populations formed on an mRNA with a cognate AUG codon in the presence of eIF1, eIF1A, eIF2–GTP–Met-tRNAiMet and eIF3. The ‘open’ 40S subunit conformation differs from the human 48S scanning complex and represents an intermediate preceding the codon recognition step. The ‘closed’ form is similar to reported structures of complexes from yeast and mammals formed upon codon recognition, except for the orientation of eIF1A, which is unique in our structure. Kinetic experiments show how various initiation factors mediate the population distribution of open and closed conformations until 60S subunit docking. Our results provide insights into the timing and structure of human translation initiation intermediates and suggest the differences in the mechanisms of start codon selection between mammals and yeast.
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Affiliation(s)
- Sung-Hui Yi
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Valentyn Petrychenko
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Jan Erik Schliep
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Akanksha Goyal
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectroscopy Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Ashwin Chari
- Research Group Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectroscopy Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Sarah Adio
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Georg-August University of Göttingen, Göttingen 37077, Germany
| | - Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
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22
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Chen S, Tian Y, Ju A, Li B, Fu Y, Luo Y. Suppression of CCT3 Inhibits Tumor Progression by Impairing ATP Production and Cytoplasmic Translation in Lung Adenocarcinoma. Int J Mol Sci 2022; 23:ijms23073983. [PMID: 35409343 PMCID: PMC9000022 DOI: 10.3390/ijms23073983] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/26/2022] Open
Abstract
Heat shock proteins are highly expressed in various cancers and exert critical functions in tumor progression. However, their expression patterns and functions in lung adenocarcinoma (LUAD) remain largely unknown. We identified that chaperonin-containing T-complex protein-1 subunit 3 (CCT3) was highly expressed in LUAD cells and was positively correlated with LUAD malignancy in the clinical samples. Animal studies showed that silencing CCT3 dramatically inhibited tumor growth and metastasis of LUAD. Proliferation and migration were markedly suppressed in CCT3-deficient LUAD cells. Moreover, the knockdown of CCT3 promoted apoptosis and cell cycle arrest. Mechanistically, the function of glycolysis was significantly inhibited and the total intracellular ATP levels were reduced by at least 25% in CCT3-deficient cells. In addition, the knockdown of CCT3 decreased the protein translation and led to a significant reduction in eukaryotic translation initiation factor 3 (EIF3G) protein, which was identified as a protein that interacts with CCT3. Impaired protein synthesis and cell growth in EIF3G-deficient cells were consistent with those caused by CCT3 knockdown in LUAD cells. Taken together, our study demonstrated in multiple ways that CCT3 is a critical factor for supporting growth and metastasis of LUAD, and for the first time, its roles in maintaining intracellular ATP levels and cytoplasmic translation are reported. Our novel findings provide a potential therapeutic target for lung adenocarcinoma.
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Affiliation(s)
- Shuohua Chen
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; (S.C.); (Y.T.); (A.J.); (B.L.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, Beijing 100084, China
| | - Yang Tian
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; (S.C.); (Y.T.); (A.J.); (B.L.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, Beijing 100084, China
| | - Anji Ju
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; (S.C.); (Y.T.); (A.J.); (B.L.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, Beijing 100084, China
| | - Boya Li
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; (S.C.); (Y.T.); (A.J.); (B.L.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, Beijing 100084, China
| | - Yan Fu
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; (S.C.); (Y.T.); (A.J.); (B.L.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, Beijing 100084, China
| | - Yongzhang Luo
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; (S.C.); (Y.T.); (A.J.); (B.L.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- The National Engineering Research Center for Protein Technology, Tsinghua University, Beijing 100084, China
- Correspondence:
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23
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Detection of Target Genes for Drug Repurposing to Treat Skeletal Muscle Atrophy in Mice Flown in Spaceflight. Genes (Basel) 2022; 13:genes13030473. [PMID: 35328027 PMCID: PMC8953707 DOI: 10.3390/genes13030473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle atrophy is a common condition in aging, diabetes, and in long duration spaceflights due to microgravity. This article investigates multi-modal gene disease and disease drug networks via link prediction algorithms to select drugs for repurposing to treat skeletal muscle atrophy. Key target genes that cause muscle atrophy in the left and right extensor digitorum longus muscle tissue, gastrocnemius, quadriceps, and the left and right soleus muscles are detected using graph theoretic network analysis, by mining the transcriptomic datasets collected from mice flown in spaceflight made available by GeneLab. We identified the top muscle atrophy gene regulators by the Pearson correlation and Bayesian Markov blanket method. The gene disease knowledge graph was constructed using the scalable precision medicine knowledge engine. We computed node embeddings, random walk measures from the networks. Graph convolutional networks, graph neural networks, random forest, and gradient boosting methods were trained using the embeddings, network features for predicting links and ranking top gene-disease associations for skeletal muscle atrophy. Drugs were selected and a disease drug knowledge graph was constructed. Link prediction methods were applied to the disease drug networks to identify top ranked drugs for therapeutic treatment of skeletal muscle atrophy. The graph convolution network performs best in link prediction based on receiver operating characteristic curves and prediction accuracies. The key genes involved in skeletal muscle atrophy are associated with metabolic and neurodegenerative diseases. The drugs selected for repurposing using the graph convolution network method were nutrients, corticosteroids, anti-inflammatory medications, and others related to insulin.
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24
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The role of RNA binding proteins in hepatocellular carcinoma. Adv Drug Deliv Rev 2022; 182:114114. [PMID: 35063534 DOI: 10.1016/j.addr.2022.114114] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/02/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of overall cancer deaths worldwide with limited therapeutic options. Due to the heterogeneity of HCC pathogenesis, the molecular mechanisms underlying HCC development are not fully understood. Emerging evidence indicates that RNA-binding proteins (RBPs) play a vital role throughout hepatocarcinogenesis. Thus, a deeper understanding of how RBPs contribute to HCC progression will provide new tools for early diagnosis and prognosis of this devastating disease. In this review, we summarize the tumor suppressive and oncogenic roles of RBPs and their roles in hepatocarcinogenesis. The diagnostic and therapeutic potential of RBPs in HCC, including their limitations, are also discussed.
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25
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Barut J, Rafa-Zabłocka K, Jurga AM, Bagińska M, Nalepa I, Parlato R, Kreiner G. Genetic lesions of the noradrenergic system trigger induction of oxidative stress and inflammation in the ventral midbrain. Neurochem Int 2022; 155:105302. [PMID: 35150790 DOI: 10.1016/j.neuint.2022.105302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by motor deficits caused by the loss of dopaminergic neurons in the substantia nigra (SN) and ventral tegmental area (VTA). However, clinical data revealed that not only the dopaminergic system is affected in PD. Postmortem studies showed degeneration of noradrenergic cells in the locus coeruleus (LC) to an even greater extent than that observed in the SN/VTA. Pharmacological models support the concept that modification of noradrenergic transmission can influence the PD-like phenotype induced by neurotoxins. Nevertheless, there are no existing data on animal models regarding the distant impact of noradrenergic degeneration on intact SN/VTA neurons. The aim of this study was to create a transgenic mouse model with endogenously evoked progressive degeneration restricted to noradrenergic neurons and investigate its long-term impact on the dopaminergic system. To this end, we selectively ablated the transcription initiation factor-IA (TIF-IA) in neurons expressing dopamine β-hydroxylase (DBH) by the Cre-loxP system. This mutation mimics a condition of nucleolar stress affecting neuronal survival. TIF-IADbhCre mice were characterized by selective, progressive degeneration of noradrenergic neurons, followed by phenotypic alterations associated with sympathetic system impairment. Our studies did not show any loss of tyrosine hydroxylase (TH)-positive cells in the SN/VTA of mutant mice; however, we observed increased indices of oxidative stress, enhanced markers of glial cell activation, inflammatory processes and isolated degenerating cells positive for FluoroJade C. These results were supported by gene expression profiling of VTA and SN from TIF-IADbhCre mice, revealing that 34 out of 246 significantly regulated genes in the SN/VTA were related to PD. Overall, our results shed new light on the possible negative influence of noradrenergic degeneration on dopaminergic neurons, reinforcing the neuroprotective role of noradrenaline.
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Affiliation(s)
- Justyna Barut
- Dept. Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343, Kraków, Smętna 12, Poland
| | - Katarzyna Rafa-Zabłocka
- Dept. Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343, Kraków, Smętna 12, Poland
| | - Agnieszka M Jurga
- Dept. Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343, Kraków, Smętna 12, Poland
| | - Monika Bagińska
- Dept. Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343, Kraków, Smętna 12, Poland
| | - Irena Nalepa
- Dept. Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343, Kraków, Smętna 12, Poland
| | - Rosanna Parlato
- Division of Neurodegenerative Disorders, Department of Neurology, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim Heidelberg University, Mannheim, Germany; Institute of Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany.
| | - Grzegorz Kreiner
- Dept. Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343, Kraków, Smętna 12, Poland.
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26
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Su R, Dong L, Li Y, Gao M, He PC, Liu W, Wei J, Zhao Z, Gao L, Han L, Deng X, Li C, Prince E, Tan B, Qing Y, Qin X, Shen C, Xue M, Zhou K, Chen Z, Xue J, Li W, Qin H, Wu X, Sun M, Nam Y, Chen CW, Huang W, Horne D, Rosen ST, He C, Chen J. METTL16 exerts an m 6A-independent function to facilitate translation and tumorigenesis. Nat Cell Biol 2022; 24:205-216. [PMID: 35145225 PMCID: PMC9070413 DOI: 10.1038/s41556-021-00835-2] [Citation(s) in RCA: 146] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 12/21/2021] [Indexed: 12/23/2022]
Abstract
METTL16 has recently been identified as an RNA methyltransferase responsible for the deposition of N6-methyladenosine (m6A) in a few transcripts. Whether METTL16 methylates a large set of transcripts, similar to METTL3 and METTL14, remains unclear. Here we show that METTL16 exerts both methyltransferase activity-dependent and -independent functions in gene regulation. In the cell nucleus, METTL16 functions as an m6A writer to deposit m6A into hundreds of its specific messenger RNA targets. In the cytosol, METTL16 promotes translation in an m6A-independent manner. More specifically, METTL16 directly interacts with the eukaryotic initiation factors 3a and -b as well as ribosomal RNA through its Mtase domain, thereby facilitating the assembly of the translation-initiation complex and promoting the translation of over 4,000 mRNA transcripts. Moreover, we demonstrate that METTL16 is critical for the tumorigenesis of hepatocellular carcinoma. Collectively, our studies reveal previously unappreciated dual functions of METTL16 as an m6A writer and a translation-initiation facilitator, which together contribute to its essential function in tumorigenesis.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Cytosol/enzymology
- Eukaryotic Initiation Factor-3/genetics
- Eukaryotic Initiation Factor-3/metabolism
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Hep G2 Cells
- Humans
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mice, Inbred NOD
- Mice, SCID
- Protein Biosynthesis
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Signal Transduction
- Tumor Burden
- Mice
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Affiliation(s)
- Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Min Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Pharmaceutics, School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - P Cody He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Wei Liu
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhicong Zhao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- School of Pharmacy, China Medical University, Shenyang, China
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Chenying Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Key Laboratory of Hematopoietic Malignancies, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Emily Prince
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Brandon Tan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Xi Qin
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Meilin Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Jianhuang Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Hanjun Qin
- The Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- The Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Miao Sun
- Keck School of Medicine, University of Southern California, and Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Yunsun Nam
- Laboratory of RNA Biology, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Graduate School of Biological Science, City of Hope, Duarte, CA, USA
| | - David Horne
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, CA, USA
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA.
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27
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Identification of long non-coding RNAs in Verticillium dahliae following inoculation of cotton. Microbiol Res 2022; 257:126962. [PMID: 35042052 DOI: 10.1016/j.micres.2022.126962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 11/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, these functions have not been assessed in Verticillium dahliae, a soil-borne fungal pathogen that causes devastating wilt diseases in many crops. The discovery and identity of novel lncRNAs and their association with virulence may contribute to an increased understanding of the regulation of virulence in V. dahliae. Here, we identified a total of 352 lncRNAs in V. dahliae. The lncRNAs were transcribed from all V. dahliae chromosomes, typically with shorter open reading frames, lower GC content, and fewer exons than protein-coding genes. In addition, 308 protein-coding genes located within 10 kb upstream and 10 kb downstream of lncRNAs were identified as neighboring genes, and which were considered as potential targets of lncRNA. These neighboring genes encode products involved in development, stress responses, and pathogenicity of V. dahliae, such as transcription factors (TF), kinase, and members of the secretome. Furthermore, 47 lncRNAs were significantly differentially expressed in V. dahliae following inoculation of susceptible cotton (Gossyoiumhisutum) cultivar Junmian No.1, suggesting that lncRNAs may be involved in the regulation of virulence in V. dahliae. Moreover, correlations in expression patterns between lncRNA and their neighboring genes were detected. Expression of lncRNA012077 and its neighboring gene was up-regulated 6 h following inoculation of cotton, while the expression of lncRNA007722 was down-regulated at 6 h but up-regulated at 24 h, in a pattern opposite to that of its neighboring gene. Overexpression of lncRNA012077 in wild-type strain (Vd991) enhanced its virulence on cotton while overexpression of lncRNA009491 reduced virulence. Identification of novel lncRNAs and their association with virulence may provide new targets for disease control.
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28
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Blazie SM, Takayanagi-Kiya S, McCulloch KA, Jin Y. Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity. eLife 2021; 10:68336. [PMID: 34323215 PMCID: PMC8354637 DOI: 10.7554/elife.68336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
The translation initiation complex eIF3 imparts specialized functions to regulate protein expression. However, understanding of eIF3 activities in neurons remains limited despite widespread dysregulation of eIF3 subunits in neurological disorders. Here, we report a selective role of the C. elegans RNA-binding subunit EIF-3.G in shaping the neuronal protein landscape. We identify a missense mutation in the conserved Zinc-Finger (ZF) of EIF-3.G that acts in a gain-of-function manner to dampen neuronal hyperexcitation. Using neuron-type-specific seCLIP, we systematically mapped EIF-3.G-mRNA interactions and identified EIF-3.G occupancy on GC-rich 5′UTRs of a select set of mRNAs enriched in activity-dependent functions. We demonstrate that the ZF mutation in EIF-3.G alters translation in a 5′UTR-dependent manner. Our study reveals an in vivo mechanism for eIF3 in governing neuronal protein levels to control neuronal activity states and offers insights into how eIF3 dysregulation contributes to neurological disorders.
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Affiliation(s)
- Stephen M Blazie
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Seika Takayanagi-Kiya
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Katherine A McCulloch
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, United States
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29
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Chang Z, Yang M, Ji H. Molecular characterization and functional analysis of apoptosis-inducing factor (AIF) in palmitic acid-induced apoptosis in Ctenopharyngodon idellus kidney (CIK) cells. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:213-224. [PMID: 33528736 DOI: 10.1007/s10695-020-00907-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Palmitic acid (PA), the most common saturated free fatty acid, may cause apoptosis when overloaded in non-fat cells. Apoptosis-inducing factor (AIF) is known to translocate from the mitochondria into the nucleus to induce apoptosis. However, it remains to be investigated whether AIF involved in palmitic acid-induced lipoapoptosis in fish. In the present study, we cloned a coding sequence of grass carp (Ctenopharyngodon idella) AIF (CiAIF) gene, and determined its function in Ctenopharyngodon idellus kidney (CIK) cells. The open reading frame (ORF) of CiAIF gene is 1863 bp, encoding a precursor protein of 620 amino acids (aa). Sequence analysis indicated that CiAIF contains a mitochondrial localization sequence, a conserved Pyr_redox and a C-terminal domain. Phylogenetic analyses showed that the CiAIF gene tended to cluster with sequences from Danio rerio. CiAIF gene was ubiquitously expressed in all tested tissues, including heart, liver, spleen, muscle, brain, eye, kidney, intestine, and fat. Moreover, we demonstrated that PA treatment induced the expression level of CiAIF and increases in markers of endoplasmic reticulum (ER) stress and apoptosis. Meanwhile, ER stress-inducing agent thapsigargin (TG) induced CiAIF translocated into the nucleus in CIK cells, whereas the suppression of ER stress inhibited PA-induced CiAIF expression and apoptosis. In addition, overexpression of CiAIF caused apoptosis by upregulating capase9, capase8, and capase3b, and affects protein translation via directly interacting with CieIF3g. Taken together, our data indicate that in Ctenopharyngodon idellus, PA is key elements that affect not only ER stress and mitochondrial apoptosis but also different physiological functions, such as protein translation, and CiAIF might play a key role in this progress.
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Affiliation(s)
- Zhiguang Chang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Minghui Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Hong Ji
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
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30
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Vo DK, Engler A, Stoimenovski D, Hartig R, Kaehne T, Kalinski T, Naumann M, Haybaeck J, Nass N. Interactome Mapping of eIF3A in a Colon Cancer and an Immortalized Embryonic Cell Line Using Proximity-Dependent Biotin Identification. Cancers (Basel) 2021; 13:cancers13061293. [PMID: 33799492 PMCID: PMC7999522 DOI: 10.3390/cancers13061293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
Translation initiation comprises complex interactions of eukaryotic initiation factor (eIF) subunits and the structural elements of the mRNAs. Translation initiation is a key process for building the cell's proteome. It not only determines the total amount of protein synthesized but also controls the translation efficiency for individual transcripts, which is important for cancer or ageing. Thus, understanding protein interactions during translation initiation is one key that contributes to understanding how the eIF subunit composition influences translation or other pathways not yet attributed to eIFs. We applied the BioID technique to two rapidly dividing cell lines (the immortalized embryonic cell line HEK-293T and the colon carcinoma cell line HCT-166) in order to identify interacting proteins of eIF3A, a core subunit of the eukaryotic initiation factor 3 complex. We identified a total of 84 interacting proteins, with very few proteins being specific to one cell line. When protein biosynthesis was blocked by thapsigargin-induced endoplasmic reticulum (ER) stress, the interacting proteins were considerably smaller in number. In terms of gene ontology, although eIF3A interactors are mainly part of the translation machinery, protein folding and RNA binding were also found. Cells suffering from ER-stress show a few remaining interactors which are mainly ribosomal proteins or involved in RNA-binding.
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Affiliation(s)
- Diep-Khanh Vo
- Department of Pathology, Medical Faculty, Otto-von-Guericke University Magdeburg, D-39120 Magdeburg, Germany; (D.-K.V.); (D.S.); (T.K.); (J.H.)
| | - Alexander Engler
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, D-39120 Magdeburg, Germany; (A.E.); (T.K.); (M.N.)
| | - Darko Stoimenovski
- Department of Pathology, Medical Faculty, Otto-von-Guericke University Magdeburg, D-39120 Magdeburg, Germany; (D.-K.V.); (D.S.); (T.K.); (J.H.)
| | - Roland Hartig
- Institute of Molecular and Clinical Immunology, Otto von Guericke University Magdeburg, Leipziger Str. 44, D-39120 Magdeburg, Germany;
| | - Thilo Kaehne
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, D-39120 Magdeburg, Germany; (A.E.); (T.K.); (M.N.)
| | - Thomas Kalinski
- Department of Pathology, Medical Faculty, Otto-von-Guericke University Magdeburg, D-39120 Magdeburg, Germany; (D.-K.V.); (D.S.); (T.K.); (J.H.)
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, D-39120 Magdeburg, Germany; (A.E.); (T.K.); (M.N.)
| | - Johannes Haybaeck
- Department of Pathology, Medical Faculty, Otto-von-Guericke University Magdeburg, D-39120 Magdeburg, Germany; (D.-K.V.); (D.S.); (T.K.); (J.H.)
- Department of Pathology, Neuropathology, and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria
- Department of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, A-8010 Graz, Austria
- Center for Biomarker Research in Medicine, A-8010 Graz, Austria
| | - Norbert Nass
- Department of Pathology, Medical Faculty, Otto-von-Guericke University Magdeburg, D-39120 Magdeburg, Germany; (D.-K.V.); (D.S.); (T.K.); (J.H.)
- Correspondence:
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Long non-coding RNA LINC02446 suppresses the proliferation and metastasis of bladder cancer cells by binding with EIF3G and regulating the mTOR signalling pathway. Cancer Gene Ther 2021; 28:1376-1389. [PMID: 33526846 DOI: 10.1038/s41417-020-00285-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022]
Abstract
Accumulating evidence has been obtained to understand the mechanisms of long non-coding RNAs (lncRNAs) in bladder cancer (BC). However, due to the recurrence and metastasis of BC, searching for lncRNAs that are related to prognosis and metastasis and exploring the pathogenesis of BC might provide new insights for the treatment of BC. In the present study, we used the TCGA and GEO databases and identified LINC02446 as associated with prognosis and differentially expressed in bladder cancer tissues and para-cancer tissues. Then, we found that LINC02446 could affect the proliferation, migration and invasion of BC cells. Additionally, we found that LINC02446 could bind to the EIF3G protein and regulate the protein stability of EIF3G and then inhibit the mTOR signalling pathway. In summary, all these findings show that LINC02446 might serve as a promising therapeutic target for BC intervention.
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Zheng W, Li Y, Su Z, Zhang J, Shi F, Liang W. EIF3H knockdown inhibits malignant melanoma through regulating cell proliferation, apoptosis and cell cycle. Exp Cell Res 2021; 402:112488. [PMID: 33508274 DOI: 10.1016/j.yexcr.2021.112488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 12/24/2022]
Abstract
Malignant melanoma (MM) causes 80% of skin cancer-related deaths and becomes the most lethal type of skin cancer. The molecular mechanism of MM is still not clear. This study aimed to reveal the relationship between MM and EIF3H. Clinical specimens were collected to preliminarily explore the role of EIF3H in MM. MM cell lines with EIF3H knockdown were constructed for investigating the effects of EIF3H on cell proliferation, apoptosis, cell cycle and cell motility. Mice xenograft model was constructed for verification in vivo. We found that EIF3H was obviously upregulated in MM tissues compared with normal skin tissues, which was correlated with tumor stage and risk of lymphatic metastasis. The in vitro results indicated that silencing EIF3H in MM cells could significantly suppress cell proliferation, promote cell apoptosis and induce cell cycle arrest. Moreover, EIF3H knockdown significantly restrained cell motility through regulating EMT-related proteins. The effects of EIF3H knockdown were also verified in mice xenograft model, which were represented by slower growth rate, smaller volume and lighter weight of tumors. Therefore, EIF3H was identified as a critical factor in the development and progression of MM which may be used as a novel therapeutic target in the treatment of MM.
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Affiliation(s)
- Wenjun Zheng
- Department of Dermatology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yong Li
- Department of Dermatology, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zheng Su
- Department of Plastic and Reconstructive Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jian Zhang
- Department of Plastic and Reconstructive Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Fen Shi
- Department of Plastic and Reconstructive Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Weiqiang Liang
- Department of Plastic and Reconstructive Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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Molecular Mechanisms of DUBs Regulation in Signaling and Disease. Int J Mol Sci 2021; 22:ijms22030986. [PMID: 33498168 PMCID: PMC7863924 DOI: 10.3390/ijms22030986] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
The large family of deubiquitinating enzymes (DUBs) are involved in the regulation of a plethora of processes carried out inside the cell by protein ubiquitination. Ubiquitination is a basic pathway responsible for the correct protein homeostasis in the cell, which could regulate the fate of proteins through the ubiquitin–proteasome system (UPS). In this review we will focus on recent advances on the molecular mechanisms and specificities found for some types of DUBs enzymes, highlighting illustrative examples in which the regulatory mechanism for DUBs has been understood in depth at the molecular level by structural biology. DUB proteases are responsible for cleavage and regulation of the multiple types of ubiquitin linkages that can be synthesized inside the cell, known as the ubiquitin-code, which are tightly connected to specific substrate functions. We will display some strategies carried out by members of different DUB families to provide specificity on the cleavage of particular ubiquitin linkages. Finally, we will also discuss recent progress made for the development of drug compounds targeting DUB proteases, which are usually correlated to the progress of many pathologies such as cancer and neurodegenerative diseases.
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Smith RCL, Kanellos G, Vlahov N, Alexandrou C, Willis AE, Knight JRP, Sansom OJ. Translation initiation in cancer at a glance. J Cell Sci 2021; 134:jcs248476. [PMID: 33441326 DOI: 10.1242/jcs.248476] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cell division, differentiation and function are largely dependent on accurate proteome composition and regulated gene expression. To control this, protein synthesis is an intricate process governed by upstream signalling pathways. Eukaryotic translation is a multistep process and can be separated into four distinct phases: initiation, elongation, termination and recycling of ribosomal subunits. Translation initiation, the focus of this article, is highly regulated to control the activity and/or function of eukaryotic initiation factors (eIFs) and permit recruitment of mRNAs to the ribosomes. In this Cell Science at a Glance and accompanying poster, we outline the mechanisms by which tumour cells alter the process of translation initiation and discuss how this benefits tumour formation, proliferation and metastasis.
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Affiliation(s)
- Rachael C L Smith
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, G61 1QH, UK
| | - Georgios Kanellos
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Nikola Vlahov
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | | | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QW, UK
| | - John R P Knight
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Owen J Sansom
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, G61 1QH, UK
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35
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Liu H, Qin Y, Zhou N, Ma D, Wang Y. ZNF280A promotes lung adenocarcinoma development by regulating the expression of EIF3C. Cell Death Dis 2021; 12:39. [PMID: 33414445 PMCID: PMC7791122 DOI: 10.1038/s41419-020-03309-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022]
Abstract
Lung adenocarcinoma (LUAD) is the most common histological subtype in non-small cell lung cancer, which is the malignant tumor with the highest mortality and morbidity in the world. Herein, ZNF280A, a member of the zinc finger protein family carrying two consecutive Cys2His2 zinc finger domains, was shown by us to act as a tumor driver in LUAD. The immunohistochemical analysis of ZNF280A in LUAD indicated its positive correlation with tumor grade, pathological stage and lymphatic metastasis, and negative relationship with patients’ survival. A loss-of-function study revealed the inhibition of LUAD development by ZNF280A in vitro and in vivo, whereas ZNF280A overexpression induced opposite effects. Statistical analysis of gene expression profiling in LUAD cells with or without ZNF280A knockdown identified EIF3C as a potential downstream of ZNF280A, which possesses similar regulatory effects on phenotypes of LUAD cells with ZNF280A. Moreover, downregulation of EIF3C in ZNF280A-overexpressed cells could attenuate neutralize the ZNF280A-induced promotion of LUAD. In summary, our study demonstrated that ZNF280A may promote the development of LUAD by regulating cell proliferation, apoptosis, cell cycle, and cell migration and probably via interacting EIF3C.
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Affiliation(s)
- Hongsheng Liu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Yingzhi Qin
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Na Zhou
- Department of Medical Oncology, Peking Union Medical College Hospital, Beijing, China
| | - Dongjie Ma
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Yingyi Wang
- Department of Medical Oncology, Peking Union Medical College Hospital, Beijing, China.
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36
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Translational regulation of Chk1 expression by eIF3a via interaction with the RNA-binding protein HuR. Biochem J 2020; 477:1939-1950. [PMID: 32391557 DOI: 10.1042/bcj20200025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 01/10/2023]
Abstract
eIF3a is a putative subunit of the eukaryotic translation initiation factor 3 complex. Accumulating evidence suggests that eIF3a may have a translational regulatory function by suppressing translation of a subset of mRNAs while accelerating that of other mRNAs. Albeit the suppression of mRNA translation may derive from eIF3a binding to the 5'-UTRs of target mRNAs, how eIF3a may accelerate mRNA translation remains unknown. In this study, we show that eIF3a up-regulates translation of Chk1 but not Chk2 mRNA by interacting with HuR, which binds directly to the 3'-UTR of Chk1 mRNA. The interaction between eIF3a and HuR occurs at the 10-amino-acid repeat domain of eIF3a and the RNA recognition motif domain of HuR. This interaction may effectively circularize Chk1 mRNA to form an end-to-end complex that has recently been suggested to accelerate mRNA translation. Together with previous findings, we conclude that eIF3a may regulate mRNA translation by directly binding to the 5'-UTR to suppress or by interacting with RNA-binding proteins at 3'-UTRs to accelerate mRNA translation.
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37
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Translational control in the naked mole-rat as a model highly resistant to cancer. Biochim Biophys Acta Rev Cancer 2020; 1875:188455. [PMID: 33148499 DOI: 10.1016/j.bbcan.2020.188455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/23/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Dysregulation of mRNA translation is involved in the onset and progression of different types of cancer. To gain insight into novel genetic strategies to avoid this malady, we reviewed the available genomic, transcriptomic, and proteomic data about the translational machinery from the naked-mole rat (NMR) Heterocephalus glaber, a new model of study that exhibits high resistance to cancer. The principal features that might confer cancer resistance are 28S rRNA fragmentation, RPL26 and eIF4G overexpression, global downregulation of mTOR pathway, specific amino acid residues in RAPTOR (P908) and RICTOR (V1695), and the absence of 4E-BP3. These features are not only associated with cancer but also might couple longevity and adaptation to hypoxia. We propose that the regulation of translation is among the strategies endowing NMR cancer resistance.
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38
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Jiao H, Zeng L, Yang S, Zhang J, Lou W. Knockdown EIF3C Suppresses Cell Proliferation and Increases Apoptosis in Pancreatic Cancer Cell. Dose Response 2020; 18:1559325820950061. [PMID: 32973416 PMCID: PMC7493259 DOI: 10.1177/1559325820950061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/02/2020] [Accepted: 05/29/2020] [Indexed: 11/16/2022] Open
Abstract
Increasing evidence shows that eukaryotic initiation factor subunit (EIF3C) plays a crucial role in development of tumors. However, the underlying roles of EIF3Cin the development of pancreatic cancer (PC) remain unknown. In this study, we examined the expression of EIF3C in PC tissues, their adjacent normal tissues and 3 cell lines (SW1990, PANC-1 and AsPC-1). Moreover, the EIF3C-shRNA lentivirus was constructed to suppress EIF3C expression. Following this, the cell colony formation assay was employed to evaluate proliferation ability of PC cells. Meanwhile, the cell cycle and apoptotic assays were also performed by flow cytometry. We found that level of EIF3C in PC tissues was significantly increased compared with that in adjacent normal tissues. Furthermore, the knockdown of EIF3C can significantly reduce cell proliferation, block cell cycle in G2/M and induce apoptosis in both SW1990 and PANC-1 cells. Our findings suggest that EIF3C plays a crucial role in the progression of PC and may be a potential target in the treatment of PC.
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Affiliation(s)
- Heng Jiao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingxiao Zeng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shengsheng Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
| | - Jianpeng Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
| | - Wenhui Lou
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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39
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Skariah G, Todd PK. Translational control in aging and neurodegeneration. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1628. [PMID: 32954679 DOI: 10.1002/wrna.1628] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Protein metabolism plays central roles in age-related decline and neurodegeneration. While a large body of research has explored age-related changes in protein degradation, alterations in the efficiency and fidelity of protein synthesis with aging are less well understood. Age-associated changes occur in both the protein synthetic machinery (ribosomal proteins and rRNA) and within regulatory factors controlling translation. At the same time, many of the interventions that prolong lifespan do so in part by pre-emptively decreasing protein synthesis rates to allow better harmonization to age-related declines in protein catabolism. Here we review the roles of translation regulation in aging, with a specific focus on factors implicated in age-related neurodegeneration. We discuss how emerging technologies such as ribosome profiling and superior mass spectrometric approaches are illuminating age-dependent mRNA-specific changes in translation rates across tissues to reveal a critical interplay between catabolic and anabolic pathways that likely contribute to functional decline. These new findings point to nodes in posttranscriptional gene regulation that both contribute to aging and offer targets for therapy. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Biogenesis Translation > Translation Mechanisms.
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Affiliation(s)
- Geena Skariah
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
- Ann Arbor VA Healthcare System, Department of Veterans Affairs, Ann Arbor, Michigan, USA
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40
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Burgenson D, Linton J, Ge X, Kostov Y, Tolosa L, Szeto GL, Rao G. A Cell-Free Protein Expression System Derived from Human Primary Peripheral Blood Mononuclear Cells. ACS Synth Biol 2020; 9:2188-2196. [PMID: 32698572 DOI: 10.1021/acssynbio.0c00256] [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] [Indexed: 12/16/2022]
Abstract
Historically, some of the first cell-free protein expression systems studied in vitro translation in various human blood cells. However, because of limited knowledge of eukaryotic translation and the advancement of cell line development, interest in these systems decreased. Eukaryotic translation is a complex system of factors that contribute to the overall translation of mRNA to produce proteins. The intracellular translateome of a cell can be modified by various factors and disease states, but it is impossible to individually measure all factors involved when there is no comprehensive understanding of eukaryotic translation. The present work outlines the use of a coupled transcription and translation cell-free protein expression system to produce recombinant proteins derived from human donor peripheral blood mononuclear cells (PBMCs) activated with phytohemagglutinin-M (PHA-M). The methods outlined here could result in tools to aid immunology, gene therapy, cell therapy, and synthetic biology research and provide a convenient and holistic method to study and assess the intracellular translation environment of primary immune cells.
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Affiliation(s)
- David Burgenson
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Jonathan Linton
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Xudong Ge
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Yordan Kostov
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Leah Tolosa
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Gregory L. Szeto
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland 21201, United States
| | - Govind Rao
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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41
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Wagner S, Herrmannová A, Hronová V, Gunišová S, Sen ND, Hannan RD, Hinnebusch AG, Shirokikh NE, Preiss T, Valášek LS. Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes. Mol Cell 2020; 79:546-560.e7. [PMID: 32589964 PMCID: PMC7447980 DOI: 10.1016/j.molcel.2020.06.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/10/2020] [Accepted: 05/18/2020] [Indexed: 11/25/2022]
Abstract
Translational control targeting the initiation phase is central to the regulation of gene expression. Understanding all of its aspects requires substantial technological advancements. Here we modified yeast translation complex profile sequencing (TCP-seq), related to ribosome profiling, and adapted it for mammalian cells. Human TCP-seq, capable of capturing footprints of 40S subunits (40Ss) in addition to 80S ribosomes (80Ss), revealed that mammalian and yeast 40Ss distribute similarly across 5'TRs, indicating considerable evolutionary conservation. We further developed yeast and human selective TCP-seq (Sel-TCP-seq), enabling selection of 40Ss and 80Ss associated with immuno-targeted factors. Sel-TCP-seq demonstrated that eIF2 and eIF3 travel along 5' UTRs with scanning 40Ss to successively dissociate upon AUG recognition; notably, a proportion of eIF3 lingers on during the initial elongation cycles. Highlighting Sel-TCP-seq versatility, we also identified four initiating 48S conformational intermediates, provided novel insights into ATF4 and GCN4 mRNA translational control, and demonstrated co-translational assembly of initiation factor complexes.
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Affiliation(s)
- Susan Wagner
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Neelam D Sen
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ross D Hannan
- Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
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Wolf DA, Lin Y, Duan H, Cheng Y. eIF-Three to Tango: emerging functions of translation initiation factor eIF3 in protein synthesis and disease. J Mol Cell Biol 2020; 12:403-409. [PMID: 32279082 PMCID: PMC7333474 DOI: 10.1093/jmcb/mjaa018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/20/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Studies over the past three years have substantially expanded the involvements of eukaryotic initiation factor 3 (eIF3) in messenger RNA (mRNA) translation. It now appears that this multi-subunit complex is involved in every possible form of mRNA translation, controlling every step of protein synthesis from initiation to elongation, termination, and quality control in positive as well as negative fashion. Through the study of eIF3, we are beginning to appreciate protein synthesis as a highly integrated process coordinating protein production with protein folding, subcellular targeting, and degradation. At the same time, eIF3 subunits appear to have specific functions that probably vary between different tissues and individual cells. Considering the broad functions of eIF3 in protein homeostasis, it comes as little surprise that eIF3 is increasingly implicated in major human diseases and first attempts at therapeutically targeting eIF3 have been undertaken. Much remains to be learned, however, about subunit- and tissue-specific functions of eIF3 in protein synthesis and disease and their regulation by environmental conditions and post-translational modifications.
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Affiliation(s)
- Dieter A Wolf
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Yingying Lin
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Haoran Duan
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Yabin Cheng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
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43
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Du J, Lin Z, Volovych O, Lu Z, Zou Z. A RhoGAP venom protein from Microplitis mediator suppresses the cellular response of its host Helicoverpa armigera. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 108:103675. [PMID: 32173445 DOI: 10.1016/j.dci.2020.103675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Female parasitoid wasps normally inject virulence factors together with eggs into their host to counter host immunity defenses. A newly identified RhoGAP protein in the venom of Microplitis mediator compromises the cellular immunity of its host, Helicoverpa armigera. RhoGAP1 proteins entered H. armigera hemocytes, and the host cellular cytoskeleton was disrupted. Depletion of MmGAP1 by injection of dsRNA or antibody increased the wasp egg encapsulation rate. An immunoprecipitation assay of overexpressed MmGAP1 protein in a Helicoverpa cell line showed that MmGAP1 interacts with many cellular cytoskeleton associated proteins as well as Rho GTPases. A yeast two-hybrid and a pull-down assay demonstrated that MmGAP1 interacts with H. armigera RhoA and Cdc42. These results show that the RhoGAP protein in M. mediator can destroy the H. armigera hemocyte cellular cytoskeleton, restrain host cellular immune defense, and increase the probability of successful parasitism.
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Affiliation(s)
- Jie Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhe Lin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Olga Volovych
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiqiang Lu
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, 311300, China.
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44
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Zhang S, Chen ZW, Meng SM, Ding QL, Zhong ZB, Wei YH, Ye QF, Hu KH. Eukaryotic initiation factor 3e subunit is positively associated with tumorigenesis and development of hepatocellular carcinoma. Shijie Huaren Xiaohua Zazhi 2020; 28:475-485. [DOI: 10.11569/wcjd.v28.i12.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Eukaryotic initiation factor 3 (eIF3) is one of the most complex translation initiation factors in mammalian cells. Eukaryotic initiation factor 3e subunit (eIF3e) is a member of the 13 subunits of eIF3, and its dysregulated expression is closely related to the occurrence and development of cancer. However, the role of eIF3e in different types of malignant tumor is contradictory. So far, the role of eIF3e in primary hepatocellular carcinoma (HCC) has been unknown.
AIM To study the role of eIF3e during tumorigenesis and development of HCC.
METHODS Freshly isolated liver cancer tissues and adjacent tissues from five randomly selected patients with HCC were collected during operation of liver transplantation. The levels of mRNA and protein expression of eIF3e in liver cancer tissues and adjacent tissues were detected by qRT-PCR and Western blot, respectively. An eIF3e-containing plasmid, pcDNA3.1-eIF3e, or an eIF3e-silencing short hairpin RNA plasmid, pSuper-sheIF3e, was transiently transfected into HepG2 cells, and the levels of mRNA and protein expression of eIF3e were analyzed by qRT-PCR and Western Blot, respectively, to confirm that eIF3e expression was up-regulated by pcDNA3.1-eIF3e or down-regulated by pSuper-sheIF3e. To study the effect of altered eIF3e expression on cellular behavior, Cell Counting Kit-8 approach was used to evaluate cell proliferation, scratch test was used to observe cell migration, and flow cytometric analysis was performed to assess cell apoptosis. Finally, the effect of eIF3e on tumor growth was evaluated by tumor-forming experiment in nude mice.
RESULTS Compared with the adjacent tissues, eIF3e was up-regulated in HCC tissues. Cellular experiments showed that the transcription levels of eIF3e mRNA in HepG2 and Huh7 cells were higher than those in HL7702 cells. After HepG2 cells were transiently transfected by pcDNA3.1-eIF3e or pSuper-sheIF3e, it was found that up-regulated eIF3e increased proliferation and migration of HepG2 cells, but had no effect on cellular apoptosis, while down-regulated eIF3e decreased proliferation and migration, and accelerated apoptosis. The results in nude mice showed that eIF3e promoted tumor growth in vivo.
CONCLUSION Overexpression of eIF3e is positively associated with tumorigenesis and development of HCC. Therefore, eIF3e has the potential to become a novel target for clinical treatment of HCC.
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Affiliation(s)
- Shan Zhang
- School of Bioengineering and Food Science, Hubei Provincial Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, Hubei Province, China
| | - Zhong-Wei Chen
- School of Bioengineering and Food Science, Hubei Provincial Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, Hubei Province, China
| | - Shi-Min Meng
- School of Bioengineering and Food Science, Hubei Provincial Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, Hubei Province, China
| | - Qing-Lin Ding
- School of Bioengineering and Food Science, Hubei Provincial Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, Hubei Province, China
| | - Zhi-Biao Zhong
- Institute of Hepatobiliary Diseases of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Yan-Hong Wei
- School of Bioengineering and Food Science, Hubei Provincial Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, Hubei Province, China
| | - Qi-Fa Ye
- Institute of Hepatobiliary Diseases of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Kang-Hong Hu
- School of Bioengineering and Food Science, Hubei Provincial Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, Hubei Province, China
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Genetic Profiles Playing Opposite Roles of Pathogenesis in Schizophrenia and Glioma. JOURNAL OF ONCOLOGY 2020; 2020:3656841. [PMID: 32565801 PMCID: PMC7275202 DOI: 10.1155/2020/3656841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/27/2020] [Indexed: 11/17/2022]
Abstract
Background Patients diagnosed with schizophrenia were found having lower risks to develop cancers, including glioma. Based on this epidemiology, we hypothesized that there were gene profiles playing opposite roles in pathogenesis of schizophrenia and glioma. Methods Based on GEO datasets and TCGA, key genes of schizophrenia genes on the opposite development of glioma were screened by different expressed genes (DEGs) screening, weighted gene coexpression network analysis (WGCNA), disease-specific survival (DSS), and glioma grading and verified by gene set enrichment analysis (GSEA). Results First, 612 DEGs were screened from schizophrenia and control brain samples. Second, 134 key genes more specific to schizophrenia were left by WGCNA, with 93 key genes having annotations in TCGA. Third, DSS of glioma helped to find 42 key gene expressions of schizophrenia oppositely associated with survival of glioma. Finally, 24 key genes showed opposite expression trends in schizophrenia and different glioma grading, i.e., the upregulated key genes in schizophrenia expressed increasingly in higher grade glioma, and vice versa. CAMK2D and MPC2 were taken as the examples and evaluated by GSEA, which indeed showed opposite trends in the same pathways of schizophrenia and glioma. Conclusion This workflow of selecting novel targeted genes which may have opposite roles in pathogenesis of two diseases was firstly and innovatively generated by our team. Some filtered key genes were indeed found by their potential effects in several mechanism studies, indicating our process could be effective to generate novel targeted genes. These 24 key genes may provide potential directions for future biochemical and pharmacotherapeutic research studies.
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Herrmannová A, Prilepskaja T, Wagner S, Šikrová D, Zeman J, Poncová K, Valášek LS. Adapted formaldehyde gradient cross-linking protocol implicates human eIF3d and eIF3c, k and l subunits in the 43S and 48S pre-initiation complex assembly, respectively. Nucleic Acids Res 2020; 48:1969-1984. [PMID: 31863585 PMCID: PMC7039009 DOI: 10.1093/nar/gkz1185] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/18/2022] Open
Abstract
One of the key roles of the 12-subunit eukaryotic translation initiation factor 3 (eIF3) is to promote the formation of the 43S and 48S pre-initiation complexes (PICs). However, particular contributions of its individual subunits to these two critical initiation reactions remained obscure. Here, we adapted formaldehyde gradient cross-linking protocol to translation studies and investigated the efficiency of the 43S and 48S PIC assembly in knockdowns of individual subunits of human eIF3 known to produce various partial subcomplexes. We revealed that eIF3d constitutes an important intermolecular bridge between eIF3 and the 40S subunit as its elimination from the eIF3 holocomplex severely compromised the 43S PIC assembly. Similarly, subunits eIF3a, c and e were found to represent an important binding force driving eIF3 binding to the 40S subunit. In addition, we demonstrated that eIF3c, and eIF3k and l subunits alter the efficiency of mRNA recruitment to 43S PICs in an opposite manner. Whereas the eIF3c knockdown reduces it, downregulation of eIF3k or eIF3l increases mRNA recruitment, suggesting that the latter subunits possess a regulatory potential. Altogether this study provides new insights into the role of human eIF3 in the initial assembly steps of the translational machinery.
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Affiliation(s)
- Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Terezie Prilepskaja
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Darina Šikrová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Kristýna Poncová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
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Zeman J, Itoh Y, Kukačka Z, Rosůlek M, Kavan D, Kouba T, Jansen ME, Mohammad MP, Novák P, Valášek LS. Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes. Nucleic Acids Res 2019; 47:8282-8300. [PMID: 31291455 PMCID: PMC6735954 DOI: 10.1093/nar/gkz570] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/12/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
eIF3 is a large multiprotein complex serving as an essential scaffold promoting binding of other eIFs to the 40S subunit, where it coordinates their actions during translation initiation. Perhaps due to a high degree of flexibility of multiple eIF3 subunits, a high-resolution structure of free eIF3 from any organism has never been solved. Employing genetics and biochemistry, we previously built a 2D interaction map of all five yeast eIF3 subunits. Here we further improved the previously reported in vitro reconstitution protocol of yeast eIF3, which we cross-linked and trypsin-digested to determine its overall shape in 3D by advanced mass-spectrometry. The obtained cross-links support our 2D subunit interaction map and reveal that eIF3 is tightly packed with its WD40 and RRM domains exposed. This contrasts with reported cryo-EM structures depicting eIF3 as a molecular embracer of the 40S subunit. Since the binding of eIF1 and eIF5 further fortified the compact architecture of eIF3, we suggest that its initial contact with the 40S solvent-exposed side makes eIF3 to open up and wrap around the 40S head with its extended arms. In addition, we mapped the position of eIF5 to the region below the P- and E-sites of the 40S subunit.
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Affiliation(s)
- Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Yuzuru Itoh
- Institute of Genetics and Molecular and Cellular Biology, CNRS UMR7104, INSERM UMR964, Illkirch, France
| | - Zdeněk Kukačka
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Michal Rosůlek
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Daniel Kavan
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Tomáš Kouba
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Myrte E Jansen
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Mahabub P Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Leoš S Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
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Overexpression of eIF3D in Lung Adenocarcinoma Is a New Independent Prognostic Marker of Poor Survival. DISEASE MARKERS 2019; 2019:6019637. [PMID: 31885740 PMCID: PMC6925810 DOI: 10.1155/2019/6019637] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/02/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022]
Abstract
The eukaryotic initiation factor 3 (eIF3) is the largest and most complex translation initiation factor in mammalian cells. It consists of 13 subunits and among which several were implicated to have significant prognostic effects on multiple human cancer entities. To examine the expression profiles of eIF3 subunits and determine their prognostic value in patients with lung adenocarcinoma (LUAD), the genomic data, survival data, and related clinical information were obtained from The Cancer Genome Atlas (TCGA) project for a secondary analysis. The results showed that among ten aberrantly expressed eIF3 subunits in tumours compared with adjacent normal counterparts (p < 0.05), only upregulated eIF3D could predict poor overall survival (OS) outcome independent of multiple clinicopathological parameters (HR = 2.043, 95% CI: 1.132-3.689, p = 0.018). Chi-square analysis revealed that the highly expressed eIF3D group had larger ratios of patients with advanced pathological stage (68/40 vs. 184/206, p = 0.0046), residual tumour (13/4 vs. 163/176, p = 0.0257), and targeted molecular therapy (85/65 vs. 138/164, p = 0.0357). In silico analysis demonstrated that the altered expression of eIF3D was at least regulated by both copy number alterations (CNAs) and the hypomethylation of cg14297023 site. In conclusion, high eIF3D expression might serve as a valuable independent prognostic indicator of shorter OS in patients with LUAD.
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Zou RC, Shi ZT, Xiao SF, Ke Y, Tang HR, Wu TG, Guo ZT, Ni F, An S, Wang L. Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma. PeerJ 2019; 7:e8101. [PMID: 31824761 PMCID: PMC6894432 DOI: 10.7717/peerj.8101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma. METHODS Transcriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data. RESULTS The integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs. CONCLUSIONS By identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer.
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Affiliation(s)
- Ren-chao Zou
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
| | - Zhi-tian Shi
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
| | - Shu-feng Xiao
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
- Department of General Surgery, Puer People’s Hospital, Puer, China
| | - Yang Ke
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
| | - Hao-ran Tang
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
| | - Tian-gen Wu
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
| | - Zhi-tang Guo
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
| | - Fan Ni
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
| | - Sanqi An
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory of Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Lin Wang
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China
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Raabe K, Honys D, Michailidis C. The role of eukaryotic initiation factor 3 in plant translation regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:75-83. [PMID: 31665669 DOI: 10.1016/j.plaphy.2019.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Regulation of translation represents a critical step in the regulation of gene expression. In plants, the translation regulation plays an important role at all stages of development and, during stress responses, functions as a fast and flexible tool which not only modulates the global translation rate but also controls the production of specific proteins. Regulation of translation is mostly focused on the initiation phase. There, one of essential initiation factors is the large multisubunit protein complex of eukaryotic translation initiation factor 3 (eIF3). In all eukaryotes, the general eIF3 function is to scaffold the formation of the translation initiation complex and to enhance the accuracy of scanning mechanism for start codon selection. Over the past decades, additional eIF3 functions were described as necessary for development in various eukaryotic organisms, including plants. The importance of the eIF3 complex lies not only at the global level of initiation event, but also in the precise translation regulation of specific transcripts. This review gathers the available information on functions of the plant eIF3 complex.
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Affiliation(s)
- Karel Raabe
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic
| | - David Honys
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic.
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