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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Ryoo HD. The integrated stress response in metabolic adaptation. J Biol Chem 2024; 300:107151. [PMID: 38462161 PMCID: PMC10998230 DOI: 10.1016/j.jbc.2024.107151] [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: 11/15/2023] [Revised: 02/28/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024] Open
Abstract
The integrated stress response (ISR) refers to signaling pathways initiated by stress-activated eIF2α kinases. Distinct eIF2α kinases respond to different stress signals, including amino acid deprivation and mitochondrial stress. Such stress-induced eIF2α phosphorylation attenuates general mRNA translation and, at the same time, stimulates the preferential translation of specific downstream factors to orchestrate an adaptive gene expression program. In recent years, there have been significant new advances in our understanding of ISR during metabolic stress adaptation. Here, I discuss those advances, reviewing among others the ISR activation mechanisms in response to amino acid deprivation and mitochondrial stress. In addition, I review how ISR regulates the amino acid metabolic pathways and how changes in the ISR impact the physiology and pathology of various disease models.
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Affiliation(s)
- Hyung Don Ryoo
- Department of Cell Biology, New York University Grossman School of Medicine, New York, New York, USA.
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3
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Wang J, Liu J, Guo Z. Natural uORF variation in plants. TRENDS IN PLANT SCIENCE 2024; 29:290-302. [PMID: 37640640 DOI: 10.1016/j.tplants.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/04/2023] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Taking advantage of natural variation promotes our understanding of phenotypic diversity and trait evolution, ultimately accelerating plant breeding, in which the identification of causal variations is critical. To date, sequence variations in the coding region and transcription level polymorphisms caused by variations in the promoter have been prioritized. An upstream open reading frame (uORF) in the 5' untranslated region (5' UTR) regulates gene expression at the post-transcription or translation level. In recent years, studies have demonstrated that natural uORF variations shape phenotypic diversity. This opinion article highlights recent researches and speculates on future directions for natural uORF variation in plants.
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Affiliation(s)
- Jiangen Wang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Juhong Liu
- Fuzhou Institute for Data Technology Co., Ltd., Fuzhou 350207, China
| | - Zilong Guo
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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4
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Grove DJ, Russell PJ, Kearse MG. To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1833. [PMID: 38433101 DOI: 10.1002/wrna.1833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
Selection of the correct start codon is critical for high-fidelity protein synthesis. In eukaryotes, this is typically governed by a multitude of initiation factors (eIFs), including eIF2·GTP that directly delivers the initiator tRNA (Met-tRNAi Met ) to the P site of the ribosome. However, numerous reports, some dating back to the early 1970s, have described other initiation factors having high affinity for the initiator tRNA and the ability of delivering it to the ribosome, which has provided a foundation for further work demonstrating non-canonical initiation mechanisms using alternative initiation factors. Here we provide a critical analysis of current understanding of eIF2A, eIF2D, and the MCT-1·DENR dimer, the evidence surrounding their ability to initiate translation, their implications in human disease, and lay out important key questions for the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Mechanisms Translation > Regulation.
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Affiliation(s)
- Daisy J Grove
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Paul J Russell
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- The Cellular, Molecular, Biochemical Sciences Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Michael G Kearse
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- The Cellular, Molecular, Biochemical Sciences Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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5
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Vecchio E, Marino R, Mimmi S, Canale C, Caiazza C, Arcucci A, Ruocco MR, Schiavone M, Santamaria G, Palmieri C, Iaccino E, Mallardo M, Quinto I, Fiume G. Enhanced pro-apoptotic activity of rituximab through IBTK silencing in non-Hodgkin lymphoma B-cells. Front Oncol 2024; 14:1339584. [PMID: 38371626 PMCID: PMC10869532 DOI: 10.3389/fonc.2024.1339584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
Rituximab is a commonly used chemotherapeutic drug for patients with aggressive lymphomas, such as non-Hodgkin's lymphoma (NHL). Currently, the combination of Rituximab and chemotherapy (R-CHOP) stands as the most prevalent first-line therapy for NHL. Nevertheless, the development of new therapeutic approaches remains imperative. An increasing body of evidence highlights a novel role for IBTK in tumorigenesis and cancer growth. In this study, we aim to broaden our understanding of IBTK's function in B-lymphoma, with a particular focus on its impact on the expression of the oncogene MYC. Here, we assessed the effects of combining Rituximab with IBTK silencing on cell viability through cell cycle analysis and Annexin V assays in vitro. Furthermore, we leveraged the transplantability of Eμ-myc lymphomas to investigate whether the inhibition of IBTK could elicit anti-tumor effects in the treatment of lymphomas in vivo. Our data suggests that IBTK silencing may serve as an effective anti-tumor agent for aggressive B-Lymphomas, underscoring its role in promoting apoptosis when used in combination with Rituximab, both in in vitro and in vivo settings.
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Affiliation(s)
- Eleonora Vecchio
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Rossana Marino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Selena Mimmi
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Camilla Canale
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Carmen Caiazza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Alessandro Arcucci
- Department of Public Health, University of Naples “Federico II”, Naples, Italy
| | - Maria Rosaria Ruocco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Marco Schiavone
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Gianluca Santamaria
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Enrico Iaccino
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Massimo Mallardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Ileana Quinto
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, Italy
| | - Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, Italy
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6
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Hicks D, Giresh K, Wrischnik LA, Weiser DC. The PPP1R15 Family of eIF2-alpha Phosphatase Targeting Subunits (GADD34 and CReP). Int J Mol Sci 2023; 24:17321. [PMID: 38139150 PMCID: PMC10743859 DOI: 10.3390/ijms242417321] [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: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The vertebrate PPP1R15 family consists of the proteins GADD34 (growth arrest and DNA damage-inducible protein 34, the product of the PPP1R15A gene) and CReP (constitutive repressor of eIF2α phosphorylation, the product of the PPP1R15B gene), both of which function as targeting/regulatory subunits for protein phosphatase 1 (PP1) by regulating subcellular localization, modulating substrate specificity and assembling complexes with target proteins. The primary cellular function of these proteins is to facilitate the dephosphorylation of eukaryotic initiation factor 2-alpha (eIF2α) by PP1 during cell stress. In this review, we will provide a comprehensive overview of the cellular function, biochemistry and pharmacology of GADD34 and CReP, starting with a brief introduction of eIF2α phosphorylation via the integrated protein response (ISR). We discuss the roles GADD34 and CReP play as feedback inhibitors of the unfolded protein response (UPR) and highlight the critical function they serve as inhibitors of the PERK-dependent branch, which is particularly important since it can mediate cell survival or cell death, depending on how long the stressful stimuli lasts, and GADD34 and CReP play key roles in fine-tuning this cellular decision. We briefly discuss the roles of GADD34 and CReP homologs in model systems and then focus on what we have learned about their function from knockout mice and human patients, followed by a brief review of several diseases in which GADD34 and CReP have been implicated, including cancer, diabetes and especially neurodegenerative disease. Because of the potential importance of GADD34 and CReP in aspects of human health and disease, we will discuss several pharmacological inhibitors of GADD34 and/or CReP that show promise as treatments and the controversies as to their mechanism of action. This review will finish with a discussion of the biochemical properties of GADD34 and CReP, their regulation and the additional interacting partners that may provide insight into the roles these proteins may play in other cellular pathways. We will conclude with a brief outline of critical areas for future study.
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Affiliation(s)
- Danielle Hicks
- Department of Science, Mathematics and Engineering, Modesto Junior College, Modesto, CA 95350, USA
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Krithika Giresh
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Lisa A. Wrischnik
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Douglas C. Weiser
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
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7
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Grove DJ, Levine DJ, Kearse MG. Increased levels of eIF2A inhibit translation by sequestering 40S ribosomal subunits. Nucleic Acids Res 2023; 51:9983-10000. [PMID: 37602404 PMCID: PMC10570035 DOI: 10.1093/nar/gkad683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
eIF2A was the first eukaryotic initiator tRNA carrier discovered but its exact function has remained enigmatic. Uncharacteristic of translation initiation factors, eIF2A is reported to be non-cytosolic in multiple human cancer cell lines. Attempts to study eIF2A mechanistically have been limited by the inability to achieve high yield of soluble recombinant protein. Here, we developed a purification paradigm that yields ∼360-fold and ∼6000-fold more recombinant human eIF2A from Escherichia coli and insect cells, respectively, than previous reports. Using a mammalian in vitro translation system, we found that increased levels of recombinant human eIF2A inhibit translation of multiple reporter mRNAs, including those that are translated by cognate and near-cognate start codons, and does so prior to start codon recognition. eIF2A also inhibited translation directed by all four types of cap-independent viral IRESs, including the CrPV IGR IRES that does not require initiation factors or initiator tRNA, suggesting excess eIF2A sequesters 40S subunits. Supplementation with additional 40S subunits prevented eIF2A-mediated inhibition and pull-down assays demonstrated direct binding between recombinant eIF2A and purified 40S subunits. These data support a model that eIF2A must be kept away from the translation machinery to avoid sequestering 40S ribosomal subunits.
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Affiliation(s)
- Daisy J Grove
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel J Levine
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Kearse
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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8
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Zhang Y, Wan X, Yang X, Liu X, Huang Q, Zhou L, Zhang S, Liu S, Xiong Q, Wei M, Qiu L, Zhang B, Han J. eIF3i promotes colorectal cancer cell survival via augmenting PHGDH translation. J Biol Chem 2023; 299:105177. [PMID: 37611825 PMCID: PMC10511817 DOI: 10.1016/j.jbc.2023.105177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/03/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023] Open
Abstract
Translational regulation is one of the decisive steps in gene expression, and its dysregulation is closely related to tumorigenesis. Eukaryotic translation initiation factor 3 subunit i (eIF3i) promotes tumor growth by selectively regulating gene translation, but the underlying mechanisms are largely unknown. Here, we show that eIF3i is significantly increased in colorectal cancer (CRC) and reinforces the proliferation of CRC cells. Using ribosome profiling and proteomics analysis, several genes regulated by eIF3i at the translation level were identified, including D-3-phosphoglycerate dehydrogenase (PHGDH), a rate-limiting enzyme in the de novo serine synthesis pathway that participates in metabolic reprogramming of tumor cells. PHGDH knockdown significantly represses CRC cell proliferation and partially attenuates the excessive growth induced by eIF3i overexpression. Mechanistically, METTL3-mediated N6-methyladenosine modification on PHGDH mRNA promotes its binding with eIF3i, ultimately leading to a higher translational rate. In addition, knocking down eIF3i and PHGDH impedes tumor growth in vivo. Collectively, this study not only uncovered a novel regulatory mechanism for PHGDH translation but also demonstrated that eIF3i is a critical metabolic regulator in human cancer.
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Affiliation(s)
- Yaguang Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaowen Wan
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuyang Yang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xueqin Liu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Qing Huang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Lian Zhou
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Su Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Sicheng Liu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Qunli Xiong
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Mingtian Wei
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Qiu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Bo Zhang
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Junhong Han
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
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9
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Imai H, Utsumi D, Torihara H, Takahashi K, Kuroyanagi H, Yamashita A. Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification. Nucleic Acids Res 2023; 51:e76. [PMID: 37378452 PMCID: PMC10415123 DOI: 10.1093/nar/gkad545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Regulation of gene expression in response to various biological processes, including extracellular stimulation and environmental adaptation requires nascent RNA synthesis and translation. Analysis of the coordinated regulation of dynamic RNA synthesis and translation is required to determine functional protein production. However, reliable methods for the simultaneous measurement of nascent RNA synthesis and translation at the gene level are limited. Here, we developed a novel method for the simultaneous assessment of nascent RNA synthesis and translation by combining 4-thiouridine (4sU) metabolic RNA labeling and translating ribosome affinity purification (TRAP) using a monoclonal antibody against evolutionarily conserved ribosomal P-stalk proteins. The P-stalk-mediated TRAP (P-TRAP) technique recovered endogenous translating ribosomes, allowing easy translatome analysis of various eukaryotes. We validated this method in mammalian cells by demonstrating that acute unfolded protein response (UPR) in the endoplasmic reticulum (ER) induces dynamic reprogramming of nascent RNA synthesis and translation. Our nascent P-TRAP (nP-TRAP) method may serve as a simple and powerful tool for analyzing the coordinated regulation of transcription and translation of individual genes in various eukaryotes.
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Affiliation(s)
- Hirotatsu Imai
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Daisuke Utsumi
- Department of Dermatology, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Hidetsugu Torihara
- Department of Biochemistry, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Kenzo Takahashi
- Department of Dermatology, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Hidehito Kuroyanagi
- Department of Biochemistry, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Akio Yamashita
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
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10
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Wek RC, Anthony TG, Staschke KA. Surviving and Adapting to Stress: Translational Control and the Integrated Stress Response. Antioxid Redox Signal 2023; 39:351-373. [PMID: 36943285 PMCID: PMC10443206 DOI: 10.1089/ars.2022.0123] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/23/2023]
Abstract
Significance: Organisms adapt to changing environments by engaging cellular stress response pathways that serve to restore proteostasis and enhance survival. A primary adaptive mechanism is the integrated stress response (ISR), which features phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2). Four eIF2α kinases respond to different stresses, enabling cells to rapidly control translation to optimize management of resources and reprogram gene expression for stress adaptation. Phosphorylation of eIF2 blocks its guanine nucleotide exchange factor, eIF2B, thus lowering the levels of eIF2 bound to GTP that is required to deliver initiator transfer RNA (tRNA) to ribosomes. While bulk messenger RNA (mRNA) translation can be sharply lowered by heightened phosphorylation of eIF2α, there are other gene transcripts whose translation is unchanged or preferentially translated. Among the preferentially translated genes is ATF4, which directs transcription of adaptive genes in the ISR. Recent Advances and Critical Issues: This review focuses on how eIF2α kinases function as first responders of stress, the mechanisms by which eIF2α phosphorylation and other stress signals regulate the exchange activity of eIF2B, and the processes by which the ISR triggers differential mRNA translation. To illustrate the synergy between stress pathways, we describe the mechanisms and functional significance of communication between the ISR and another key regulator of translation, mammalian/mechanistic target of rapamycin complex 1 (mTORC1), during acute and chronic amino acid insufficiency. Finally, we discuss the pathological conditions that stem from aberrant regulation of the ISR, as well as therapeutic strategies targeting the ISR to alleviate disease. Future Directions: Important topics for future ISR research are strategies for modulating this stress pathway in disease conditions and drug development, molecular processes for differential translation and the coordinate regulation of GCN2 and other stress pathways during physiological and pathological conditions. Antioxid. Redox Signal. 39, 351-373.
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Affiliation(s)
- Ronald C. Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
| | - Tracy G. Anthony
- Department of Nutritional Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Kirk A. Staschke
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
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11
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Keramidas P, Papachristou E, Papi RM, Mantsou A, Choli-Papadopoulou T. Inhibition of PERK Kinase, an Orchestrator of the Unfolded Protein Response (UPR), Significantly Reduces Apoptosis and Inflammation of Lung Epithelial Cells Triggered by SARS-CoV-2 ORF3a Protein. Biomedicines 2023; 11:1585. [PMID: 37371681 DOI: 10.3390/biomedicines11061585] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 ORF3a accessory protein was found to be involved in virus release, immunomodulation and exhibited a pro-apoptotic character. In order to unravel a potential ORF3a-induced apoptotic and inflammatory death mechanism, lung epithelial cells (A549) were transfected with in vitro synthesized ORF3a mRNA. The protein's dynamic involvement as "stress factor" for the endoplasmic reticulum, causing the activation of PERK kinase and other UPR-involved proteins and therefore the upregulation of their signaling pathway executioners (ATF6, XBP-1s, PERK, phospho eIF2a, ATF4, CHOP, GADD34), has been clearly demonstrated. Furthermore, the overexpression of BAX and BH3-only pro-apoptotic protein PUMA, the upregulation of Bcl-2 family genes (BAX, BAK, BID, BAD), the reduced expression of Bcl-2 in mRNA and protein levels, and lastly, the cleavage of PARP-1 and caspase family members (caspase-3,-8 and -9) indicate that ORF3a displays its apoptotic character through the mitochondrial pathway of apoptosis. Moreover, the upregulation of NFκB, phosphorylation of p65 and IκΒα and the elevated expression of pro-inflammatory cytokines (IL-1b, IL-6, IL-8 and IL-18) in transfected cells with ORF3a mRNA indicate that this protein causes the inflammatory response through NFκB activation and therefore triggers lung injury. An intriguing finding of our study is that upon treatment of the ORF3a-transfected cells with GSK2606414, a selective PERK inhibitor, both complications (apoptosis and inflammatory response) were neutralized, and cell survival was favored, whereas treatment of transfected cells with z-VAD (a pan-caspase inhibitor) despite inhibiting cell death, could not ameliorate the inflammatory response of transfected A549 cells. Given the above, we point out that PERK kinase is a "master tactician" and its activation constitutes the main stimulus for the emergence of ORF3a apoptotic and inflammatory nature and therefore could serve as potential target for developing novel therapeutic approaches against COVID-19.
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Affiliation(s)
- Panagiotis Keramidas
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Eleni Papachristou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Rigini M Papi
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Aglaia Mantsou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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12
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Zhao N, Li N, Wang T. PERK prevents rhodopsin degradation during retinitis pigmentosa by inhibiting IRE1-induced autophagy. J Cell Biol 2023; 222:e202208147. [PMID: 37022709 PMCID: PMC10082367 DOI: 10.1083/jcb.202208147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/04/2023] [Accepted: 02/14/2023] [Indexed: 04/07/2023] Open
Abstract
Chronic endoplasmic reticulum (ER) stress is the underlying cause of many degenerative diseases, including autosomal dominant retinitis pigmentosa (adRP). In adRP, mutant rhodopsins accumulate and cause ER stress. This destabilizes wild-type rhodopsin and triggers photoreceptor cell degeneration. To reveal the mechanisms by which these mutant rhodopsins exert their dominant-negative effects, we established an in vivo fluorescence reporter system to monitor mutant and wild-type rhodopsin in Drosophila. By performing a genome-wide genetic screen, we found that PERK signaling plays a key role in maintaining rhodopsin homeostasis by attenuating IRE1 activities. Degradation of wild-type rhodopsin is mediated by selective autophagy of ER, which is induced by uncontrolled IRE1/XBP1 signaling and insufficient proteasome activities. Moreover, upregulation of PERK signaling prevents autophagy and suppresses retinal degeneration in the adRP model. These findings establish a pathological role for autophagy in this neurodegenerative condition and indicate that promoting PERK activity could be used to treat ER stress-related neuropathies, including adRP.
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Affiliation(s)
- Ning Zhao
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ning Li
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tao Wang
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
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13
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24032976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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14
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Amin PH, Carlson KR, Wek RC. An RNA stem-loop functions in conjunction with an upstream open reading frame to direct preferential translation in the integrated stress response. J Biol Chem 2023; 299:102864. [PMID: 36596357 PMCID: PMC9971878 DOI: 10.1016/j.jbc.2022.102864] [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: 06/07/2022] [Revised: 11/30/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023] Open
Abstract
In response to environmental stresses, cells invoke translational control to conserve resources and rapidly reprogram gene expression for optimal adaptation. A central mechanism for translational control involves phosphorylation of the α subunit of eIF2 (p-eIF2α), which reduces delivery of initiator tRNA to ribosomes. Because p-eIF2α is invoked by multiple protein kinases, each responding to distinct stresses, this pathway is named the integrated stress response (ISR). While p-eIF2α lowers bulk translation initiation, many stress-related mRNAs are preferentially translated. The process by which ribosomes delineate gene transcripts for preferential translation is known to involve upstream open reading frames (uORFs) embedded in the targeted mRNAs. In this study, we used polysome analyses and reporter assays to address the mechanisms directing preferential translation of human IBTKα in the ISR. The IBTKα mRNA encodes four uORFs, with only 5'-proximal uORF1 and uORF2 being translated. Of importance, the 5'-leader of IBTKα mRNA also contains a phylogenetically conserved stem-loop of moderate stability that is situated 11 nucleotides downstream of uORF2. The uORF2 is well translated and functions in combination with the stem-loop to effectively lower translation reinitiation at the IBTKα coding sequence. Upon stress-induced p-eIF2α, the uORF2/stem loop element can be bypassed to enhance IBTKα translation by a mechanism that may involve the modestly translated uORF1. Our study demonstrates that uORFs in conjunction with RNA secondary structures can be critical elements that serve as the "bar code" by which scanning ribosomes can delineate which mRNAs are preferentially translated in the ISR.
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Affiliation(s)
- Parth H Amin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kenneth R Carlson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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15
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Jürgens L, Wethmar K. The Emerging Role of uORF-Encoded uPeptides and HLA uLigands in Cellular and Tumor Biology. Cancers (Basel) 2022; 14:cancers14246031. [PMID: 36551517 PMCID: PMC9776223 DOI: 10.3390/cancers14246031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Recent technological advances have facilitated the detection of numerous non-canonical human peptides derived from regulatory regions of mRNAs, long non-coding RNAs, and other cryptic transcripts. In this review, we first give an overview of the classification of these novel peptides and summarize recent improvements in their annotation and detection by ribosome profiling, mass spectrometry, and individual experimental analysis. A large fraction of the novel peptides originates from translation at upstream open reading frames (uORFs) that are located within the transcript leader sequence of regular mRNA. In humans, uORF-encoded peptides (uPeptides) have been detected in both healthy and malignantly transformed cells and emerge as important regulators in cellular and immunological pathways. In the second part of the review, we focus on various functional implications of uPeptides. As uPeptides frequently act at the transition of translational regulation and individual peptide function, we describe the mechanistic modes of translational regulation through ribosome stalling, the involvement in cellular programs through protein interaction and complex formation, and their role within the human leukocyte antigen (HLA)-associated immunopeptidome as HLA uLigands. We delineate how malignant transformation may lead to the formation of novel uORFs, uPeptides, or HLA uLigands and explain their potential implication in tumor biology. Ultimately, we speculate on a potential use of uPeptides as peptide drugs and discuss how uPeptides and HLA uLigands may facilitate translational inhibition of oncogenic protein messages and immunotherapeutic approaches in cancer therapy.
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16
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Bottorff TA, Park H, Geballe AP, Subramaniam AR. Translational buffering by ribosome stalling in upstream open reading frames. PLoS Genet 2022; 18:e1010460. [PMID: 36315596 PMCID: PMC9648851 DOI: 10.1371/journal.pgen.1010460] [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: 09/07/2022] [Revised: 11/10/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
Upstream open reading frames (uORFs) are present in over half of all human mRNAs. uORFs can potently regulate the translation of downstream open reading frames through several mechanisms: siphoning away scanning ribosomes, regulating re-initiation, and allowing interactions between scanning and elongating ribosomes. However, the consequences of these different mechanisms for the regulation of protein expression remain incompletely understood. Here, we performed systematic measurements on the uORF-containing 5' UTR of the cytomegaloviral UL4 mRNA to test alternative models of uORF-mediated regulation in human cells. We find that a terminal diproline-dependent elongating ribosome stall in the UL4 uORF prevents decreases in main ORF protein expression when ribosome loading onto the mRNA is reduced. This uORF-mediated buffering is insensitive to the location of the ribosome stall along the uORF. Computational kinetic modeling based on our measurements suggests that scanning ribosomes dissociate rather than queue when they collide with stalled elongating ribosomes within the UL4 uORF. We identify several human uORFs that repress main ORF protein expression via a similar terminal diproline motif. We propose that ribosome stalls in uORFs provide a general mechanism for buffering against reductions in main ORF translation during stress and developmental transitions.
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Affiliation(s)
- Ty A. Bottorff
- Basic Sciences Division and Computational Biology Program of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Program of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Adam P. Geballe
- Human Biology and Clinical Research Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Program of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, Washington, United States of America
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17
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Phan TP, Boatwright CA, Drown CG, Skinner MW, Strong MA, Jordan PW, Holland AJ. Upstream open reading frames control PLK4 translation and centriole duplication in primordial germ cells. Genes Dev 2022; 36:718-736. [PMID: 35772791 PMCID: PMC9296005 DOI: 10.1101/gad.349604.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022]
Abstract
Centrosomes are microtubule-organizing centers comprised of a pair of centrioles and the surrounding pericentriolar material. Abnormalities in centriole number are associated with cell division errors and can contribute to diseases such as cancer. Centriole duplication is limited to once per cell cycle and is controlled by the dosage-sensitive Polo-like kinase 4 (PLK4). Here, we show that PLK4 abundance is translationally controlled through conserved upstream open reading frames (uORFs) in the 5' UTR of the mRNA. Plk4 uORFs suppress Plk4 translation and prevent excess protein synthesis. Mice with homozygous knockout of Plk4 uORFs (Plk4 Δu/Δu ) are viable but display dramatically reduced fertility because of a significant depletion of primordial germ cells (PGCs). The remaining PGCs in Plk4 Δu/Δu mice contain extra centrioles and display evidence of increased mitotic errors. PGCs undergo hypertranscription and have substantially more Plk4 mRNA than somatic cells. Reducing Plk4 mRNA levels in mice lacking Plk4 uORFs restored PGC numbers and fully rescued fertility. Together, our data uncover a specific requirement for uORF-dependent control of PLK4 translation in counterbalancing the increased Plk4 transcription in PGCs. Thus, uORF-mediated translational suppression of PLK4 has a critical role in preventing centriole amplification and preserving the genomic integrity of future gametes.
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Affiliation(s)
- Thao P Phan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Christina A Boatwright
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Chelsea G Drown
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Marnie W Skinner
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Margaret A Strong
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Philip W Jordan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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18
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Wang R, Amoyel M. mRNA Translation Is Dynamically Regulated to Instruct Stem Cell Fate. Front Mol Biosci 2022; 9:863885. [PMID: 35433828 PMCID: PMC9008482 DOI: 10.3389/fmolb.2022.863885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Stem cells preserve tissue homeostasis by replacing the cells lost through damage or natural turnover. Thus, stem cells and their daughters can adopt two identities, characterized by different programs of gene expression and metabolic activity. The composition and regulation of these programs have been extensively studied, particularly by identifying transcription factor networks that define cellular identity and the epigenetic changes that underlie the progressive restriction in gene expression potential. However, there is increasing evidence that post-transcriptional mechanisms influence gene expression in stem cells and their progeny, in particular through the control of mRNA translation. Here, we review the described roles of translational regulation in controlling all aspects of stem cell biology, from the decision to enter or exit quiescence to maintaining self-renewal and promoting differentiation. We focus on mechanisms controlling global translation rates in cells, mTOR signaling, eIF2ɑ phosphorylation, and ribosome biogenesis and how they allow stem cells to rapidly change their gene expression in response to tissue needs or environmental changes. These studies emphasize that translation acts as an additional layer of control in regulating gene expression in stem cells and that understanding this regulation is critical to gaining a full understanding of the mechanisms that underlie fate decisions in stem cells.
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Affiliation(s)
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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19
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IBtkα Activates the β-Catenin-Dependent Transcription of MYC through Ubiquitylation and Proteasomal Degradation of GSK3β in Cancerous B Cells. Int J Mol Sci 2022; 23:ijms23042044. [PMID: 35216159 PMCID: PMC8875111 DOI: 10.3390/ijms23042044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 01/18/2023] Open
Abstract
The IBTK gene encodes the IBtkα protein that is a substrate receptor of E3 ubiquitin ligase, Cullin 3. We have previously reported the pro-tumorigenic activity of Ibtk in MYC-dependent B-lymphomagenesis observed in Eμ-myc transgenic mice. Here, we provide mechanistic evidence of the functional interplay between IBtkα and MYC. We show that IBtkα, albeit indirectly, activates the β-catenin-dependent transcription of the MYC gene. Of course, IBtkα associates with GSK3β and promotes its ubiquitylation, which is associated with proteasomal degradation. This event increases the protein level of β-catenin, a substrate of GSK3β, and results in the transcriptional activation of the MYC and CCND1 target genes of β-catenin, which are involved in the control of cell division and apoptosis. In particular, we found that in Burkitt’s lymphoma cells, IBtkα silencing triggered the downregulation of both MYC mRNA and protein expression, as well as a strong decrease of cell survival, mainly through the induction of apoptotic events, as assessed by using flow cytometry-based cell cycle and apoptosis analysis. Collectively, our results shed further light on the complex puzzle of IBtkα interactome and highlight IBtkα as a potential novel therapeutic target to be employed in the strategy for personalized therapy of B cell lymphoma.
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20
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Park CY, Lee SK, Kim J, Kim D, Choe H, Jeong JH, Choi KC, Park HS, Han SN, Jang YJ. Endoplasmic reticulum stress increases LECT2 expression via ATF4. Biochem Biophys Res Commun 2021; 585:169-176. [PMID: 34808500 DOI: 10.1016/j.bbrc.2021.11.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is frequently associated with obesity, insulin resistance, and endoplasmic reticulum (ER) stress. Elevated circulating levels of the hepatokine leukocyte cell-derived chemotaxin-2 (LECT2) have also been noted in NAFLD; however, the mechanism underlying this association is unclear. To investigate a possible link between ER stress/unfolded protein response (UPR) signaling and LECT2 secretion, HepG2 cells were incubated with ER stress inducers with or without an ER stress-reducing chemical chaperone. Additionally, UPR pathway genes were knocked down and overexpressed, and a ChIP assay was performed. In diet-induced obese mice, hepatic expression of LECT2 and activating transcription factor 4 (ATF4) was measured. In HepG2 cells, LECT2 expression was increased by ER stressors, an effect blocked by the chemical chaperone. Among UPR pathway proteins, only knockdown of ATF4 suppressed ER stress-induced LECT2 expression, while overexpression of ATF4 enhanced LECT2 expression. The ChIP assay revealed that ATF4 binds to three putative binding sites on the LECT2 promoter and binding is promoted by an ER stress inducer. In steatotic livers of obese mice, LECT2 and ATF4 expression was concomitantly elevated. Our data indicate that activation of ER stress/UPR signaling induces LECT2 expression in steatotic liver; specifically, ATF4 appears to mediate upregulation of LECT2 transcription.
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Affiliation(s)
- Chan Yoon Park
- Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea; Department of Food & Nutrition, College of Health Science, The University of Suwon, Hwaseong-si, Gyeonggi-do, South Korea
| | - Seul Ki Lee
- Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jimin Kim
- Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Donguk Kim
- Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Han Choe
- Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Ji-Hoon Jeong
- Department of Biomedical Sciences, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kyung-Chul Choi
- Department of Biomedical Sciences, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul, South Korea
| | - Hye Soon Park
- Department of Family Medicine, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sung Nim Han
- Department of Food and Nutrition & Research Institute of Human Ecology, College of Human Ecology, Seoul National University, Seoul, South Korea
| | - Yeon Jin Jang
- Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea.
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21
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Tian X, Zhang S, Zhou L, Seyhan AA, Hernandez Borrero L, Zhang Y, El-Deiry WS. Targeting the Integrated Stress Response in Cancer Therapy. Front Pharmacol 2021; 12:747837. [PMID: 34630117 PMCID: PMC8498116 DOI: 10.3389/fphar.2021.747837] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022] Open
Abstract
The integrated stress response (ISR) is an evolutionarily conserved intra-cellular signaling network which is activated in response to intrinsic and extrinsic stresses. Various stresses are sensed by four specialized kinases, PKR-like ER kinase (PERK), general control non-derepressible 2 (GCN2), double-stranded RNA-dependent protein kinase (PKR) and heme-regulated eIF2α kinase (HRI) that converge on phosphorylation of serine 51 of eIF2α. eIF2α phosphorylation causes a global reduction of protein synthesis and triggers the translation of specific mRNAs, including activating transcription factor 4 (ATF4). Although the ISR promotes cell survival and homeostasis, when stress is severe or prolonged the ISR signaling will shift to regulate cellular apoptosis. We review the ISR signaling pathway, regulation and importance in cancer therapy.
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Affiliation(s)
- Xiaobing Tian
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI, United States.,Cancer Center at Brown University, Providence, RI, United States
| | - Shengliang Zhang
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI, United States.,Cancer Center at Brown University, Providence, RI, United States
| | - Lanlan Zhou
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI, United States.,Cancer Center at Brown University, Providence, RI, United States
| | - Attila A Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI, United States.,Cancer Center at Brown University, Providence, RI, United States
| | - Liz Hernandez Borrero
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Yiqun Zhang
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Wafik S El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI, United States.,Cancer Center at Brown University, Providence, RI, United States.,Hematology/Oncology Division, Department of Medicine, Lifespan Health System and Brown University, Providence, RI, United States
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22
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Brown B, Mitra S, Roach FD, Vasudevan D, Ryoo HD. The transcription factor Xrp1 is required for PERK-mediated antioxidant gene induction in Drosophila. eLife 2021; 10:74047. [PMID: 34605405 PMCID: PMC8514241 DOI: 10.7554/elife.74047] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
PERK is an endoplasmic reticulum (ER) transmembrane sensor that phosphorylates eIF2α to initiate the Unfolded Protein Response (UPR). eIF2α phosphorylation promotes stress-responsive gene expression most notably through the transcription factor ATF4 that contains a regulatory 5’ leader. Possible PERK effectors other than ATF4 remain poorly understood. Here, we report that the bZIP transcription factor Xrp1 is required for ATF4-independent PERK signaling. Cell-type-specific gene expression profiling in Drosophila indicated that delta-family glutathione-S-transferases (gstD) are prominently induced by the UPR-activating transgene Rh1G69D. Perk was necessary and sufficient for such gstD induction, but ATF4 was not required. Instead, Perk and other regulators of eIF2α phosphorylation regulated Xrp1 protein levels to induce gstDs. The Xrp1 5’ leader has a conserved upstream Open Reading Frame (uORF) analogous to those that regulate ATF4 translation. The gstD-GFP reporter induction required putative Xrp1 binding sites. These results indicate that antioxidant genes are highly induced by a previously unrecognized UPR signaling axis consisting of PERK and Xrp1.
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Affiliation(s)
- Brian Brown
- NYU Grossman School of Medicine, New York, United States
| | - Sahana Mitra
- NYU Grossman School of Medicine, New York, United States
| | | | | | - Hyung Don Ryoo
- NYU Grossman School of Medicine, New York, United States
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23
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Jin D, Wek SA, Kudlapur NT, Cantara WA, Bakhtina M, Wek RC, Musier-Forsyth K. Disease-associated mutations in a bifunctional aminoacyl-tRNA synthetase gene elicit the integrated stress response. J Biol Chem 2021; 297:101203. [PMID: 34537243 PMCID: PMC8511952 DOI: 10.1016/j.jbc.2021.101203] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) catalyze the charging of specific amino acids onto cognate tRNAs, an essential process for protein synthesis. Mutations in ARSs are frequently associated with a variety of human diseases. The human EPRS1 gene encodes a bifunctional glutamyl-prolyl-tRNA synthetase (EPRS) with two catalytic cores and appended domains that contribute to nontranslational functions. In this study, we report compound heterozygous mutations in EPRS1, which lead to amino acid substitutions P14R and E205G in two patients with diabetes and bone diseases. While neither mutation affects tRNA binding or association of EPRS with the multisynthetase complex, E205G in the glutamyl-tRNA synthetase (ERS) region of EPRS is defective in amino acid activation and tRNAGlu charging. The P14R mutation induces a conformational change and altered tRNA charging kinetics in vitro. We propose that the altered catalytic activity and conformational changes in the EPRS variants sensitize patient cells to stress, triggering an increased integrated stress response (ISR) that diminishes cell viability. Indeed, patient-derived cells expressing the compound heterozygous EPRS show heightened induction of the ISR, suggestive of disruptions in protein homeostasis. These results have important implications for understanding ARS-associated human disease mechanisms and development of new therapeutics.
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Affiliation(s)
- Danni Jin
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA
| | - Sheree A Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis Indiana, USA
| | - Nathan T Kudlapur
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA
| | - William A Cantara
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis Indiana, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA.
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24
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Kusnadi EP, Timpone C, Topisirovic I, Larsson O, Furic L. Regulation of gene expression via translational buffering. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119140. [PMID: 34599983 DOI: 10.1016/j.bbamcr.2021.119140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022]
Abstract
Translation of an mRNA represents a critical step during the expression of protein-coding genes. As mechanisms governing post-transcriptional regulation of gene expression are progressively unveiled, it is becoming apparent that transcriptional programs are not fully reflected in the proteome. Herein, we highlight a previously underappreciated post-transcriptional mode of regulation of gene expression termed translational buffering. In principle, translational buffering opposes the impact of alterations in mRNA levels on the proteome. We further describe three types of translational buffering: compensation, which maintains protein levels e.g. across species or individuals; equilibration, which retains pathway stoichiometry; and offsetting, which acts as a reversible mechanism that maintains the levels of selected subsets of proteins constant despite genetic alteration and/or stress-induced changes in corresponding mRNA levels. While mechanisms underlying compensation and equilibration have been reviewed elsewhere, the principal focus of this review is on the less-well understood mechanism of translational offsetting. Finally, we discuss potential roles of translational buffering in homeostasis and disease.
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Affiliation(s)
- Eric P Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Clelia Timpone
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivan Topisirovic
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada.
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
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25
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Inhibition of cardiac PERK signaling promotes peripartum cardiac dysfunction. Sci Rep 2021; 11:18687. [PMID: 34548576 PMCID: PMC8455649 DOI: 10.1038/s41598-021-98344-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/31/2021] [Indexed: 11/08/2022] Open
Abstract
Peripartum cardiomyopathy (PPCM) is a life-threatening heart failure occurring in the peripartum period. Although mal-angiogenesis, induced by the 16-kDa N-terminal prolactin fragment (16 K PRL), is involved in the pathogenesis, the effect of full-length prolactin (23 K PRL) is poorly understood. We transfected neonate rat cardiomyocytes with plasmids containing 23 K PRL or 16 K PRL in vitro and found that 23 K PRL, but not 16 K PRL, upregulated protein kinase RNA-like endoplasmic reticulum kinase (PERK) signaling, and hypoxia promoted this effect. During the perinatal period, cardiomyocyte-specific PERK homogenous knockout (CM-KO) mice showed PPCM phenotypes after consecutive deliveries. Downregulation of PERK or JAK/STAT signaling and upregulation of apoptosis were observed in CM-KO mouse hearts. Moreover, in bromocriptine-treated CM-KO mice, cardiac function did not improve and cardiomyocyte apoptosis was not suppressed during the peripartum period. These results demonstrate that interaction between 23 K PRL and PERK signaling is cardioprotective during the peripartum term.
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26
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Ghaddar N, Wang S, Woodvine B, Krishnamoorthy J, van Hoef V, Darini C, Kazimierczak U, Ah-Son N, Popper H, Johnson M, Officer L, Teodósio A, Broggini M, Mann KK, Hatzoglou M, Topisirovic I, Larsson O, Le Quesne J, Koromilas AE. The integrated stress response is tumorigenic and constitutes a therapeutic liability in KRAS-driven lung cancer. Nat Commun 2021; 12:4651. [PMID: 34330898 PMCID: PMC8324901 DOI: 10.1038/s41467-021-24661-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
The integrated stress response (ISR) is an essential stress-support pathway increasingly recognized as a determinant of tumorigenesis. Here we demonstrate that ISR is pivotal in lung adenocarcinoma (LUAD) development, the most common histological type of lung cancer and a leading cause of cancer death worldwide. Increased phosphorylation of the translation initiation factor eIF2 (p-eIF2α), the focal point of ISR, is related to invasiveness, increased growth, and poor outcome in 928 LUAD patients. Dissection of ISR mechanisms in KRAS-driven lung tumorigenesis in mice demonstrated that p-eIF2α causes the translational repression of dual specificity phosphatase 6 (DUSP6), resulting in increased phosphorylation of the extracellular signal-regulated kinase (p-ERK). Treatments with ISR inhibitors, including a memory-enhancing drug with limited toxicity, provides a suitable therapeutic option for KRAS-driven lung cancer insofar as they substantially reduce tumor growth and prolong mouse survival. Our data provide a rationale for the implementation of ISR-based regimens in LUAD treatment.
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Affiliation(s)
- Nour Ghaddar
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
- Division of Experimental Medicine, Department of Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Shuo Wang
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
| | - Bethany Woodvine
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | - Jothilatha Krishnamoorthy
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
| | - Vincent van Hoef
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Cedric Darini
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
| | - Urszula Kazimierczak
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Nicolas Ah-Son
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
| | - Helmuth Popper
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Myriam Johnson
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
- Division of Experimental Medicine, Department of Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Leah Officer
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | - Ana Teodósio
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | - Massimo Broggini
- Laboratory of Molecular Pharmacology IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milan, Italy
| | - Koren K Mann
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Maria Hatzoglou
- Department of Genetics, Case Western Reserve University, Cleveland, OH, USA
| | - Ivan Topisirovic
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - John Le Quesne
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK.
- MRC Toxicology Unit, University of Cambridge, Leicester, UK.
- Beatson Cancer Research Institute, Glasgow, UK.
| | - Antonis E Koromilas
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada.
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27
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Silva J, Nina P, Romão L. Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells. Biomedicines 2021; 9:biomedicines9080911. [PMID: 34440115 PMCID: PMC8389594 DOI: 10.3390/biomedicines9080911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5′-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5′-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments.
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Affiliation(s)
- Joana Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Pedro Nina
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-21-750-8155
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28
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Witte F, Ruiz-Orera J, Mattioli CC, Blachut S, Adami E, Schulz JF, Schneider-Lunitz V, Hummel O, Patone G, Mücke MB, Šilhavý J, Heinig M, Bottolo L, Sanchis D, Vingron M, Chekulaeva M, Pravenec M, Hubner N, van Heesch S. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biol 2021; 22:191. [PMID: 34183069 PMCID: PMC8240307 DOI: 10.1186/s13059-021-02397-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.
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Affiliation(s)
- Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: NUVISAN ICB GmbH, Lead Discovery-Structrual Biology, 13353, Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
- Present Address: Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Michael Benedikt Mücke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
| | - Jan Šilhavý
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Munich, Germany
- Department of Informatics, Technische Universitaet Muenchen (TUM), Boltzmannstr. 3, 85748 Garching, Munich, Germany
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Daniel Sanchis
- Institut de Recerca Biomedica de Lleida (IRBLLEIDA), Universitat de Lleida, Edifici Biomedicina-I. Av. Rovira Roure, 80, 25198, Lleida, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany.
- Charité-Universitätsmedizin, 10117, Berlin, Germany.
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- Present Address: The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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29
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The role of upstream open reading frames in translation regulation in the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii. Parasitology 2021; 148:1277-1287. [PMID: 34099078 PMCID: PMC8383288 DOI: 10.1017/s0031182021000937] [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] [Indexed: 12/11/2022]
Abstract
During their complex life cycles, the Apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii employ several layers of regulation of their gene expression. One such layer is mediated at the level of translation through upstream open reading frames (uORFs). As uORFs are found in the upstream regions of a majority of transcripts in both the parasites, it is essential that their roles in translational regulation be appreciated to a greater extent. This review provides a comprehensive summary of studies that show uORF-mediated gene regulation in these parasites and highlights examples of clinically and physiologically relevant genes, including var2csa in P. falciparum, and ApiAT1 in T. gondii, that exhibit uORF-mediated regulation. In addition to these examples, several studies that use bioinformatics, transcriptomics, proteomics and ribosome profiling also indicate the possibility of widespread translational regulation by uORFs. Further analysis of these genome-wide datasets, taking into account uORFs associated with each gene, will reveal novel genes involved in key biological pathways such as cell-cycle progression, stress-response and pathogenicity. The cumulative evidence from studies presented in this review suggests that uORFs will play crucial roles in regulating gene expression during clinical disease caused by these important human pathogens.
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30
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Barragan-Iglesias P, Kunder N, Wanghzou A, Black B, Ray PR, Lou TF, de la Peña JB, Atmaramani R, Shukla T, Pancrazio JJ, Price TJ, Campbell ZT. A peptide encoded within a 5' untranslated region promotes pain sensitization in mice. Pain 2021; 162:1864-1875. [PMID: 33449506 PMCID: PMC8119312 DOI: 10.1097/j.pain.0000000000002191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022]
Abstract
ABSTRACT Translational regulation permeates neuronal function. Nociceptors are sensory neurons responsible for the detection of harmful stimuli. Changes in their activity, termed plasticity, are intimately linked to the persistence of pain. Although inhibitors of protein synthesis robustly attenuate pain-associated behavior, the underlying targets that support plasticity are largely unknown. Here, we examine the contribution of protein synthesis in regions of RNA annotated as noncoding. Based on analyses of previously reported ribosome profiling data, we provide evidence for widespread translation in noncoding transcripts and regulatory regions of mRNAs. We identify an increase in ribosome occupancy in the 5' untranslated regions of the calcitonin gene-related peptide (CGRP/Calca). We validate the existence of an upstream open reading frame (uORF) using a series of reporter assays. Fusion of the uORF to a luciferase reporter revealed active translation in dorsal root ganglion neurons after nucleofection. Injection of the peptide corresponding to the calcitonin gene-related peptide-encoded uORF resulted in pain-associated behavioral responses in vivo and nociceptor sensitization in vitro. An inhibitor of heterotrimeric G protein signaling blocks both effects. Collectively, the data suggest pervasive translation in regions of the transcriptome annotated as noncoding in dorsal root ganglion neurons and identify a specific uORF-encoded peptide that promotes pain sensitization through GPCR signaling.
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Affiliation(s)
- Paulino Barragan-Iglesias
- University of Texas at Dallas, School of Behavioral and
Brain Sciences, Richardson, TX, 75080, USA
- Department of Physiology and Pharmacology, Center for Basic
Sciences, Autonomous University of Aguascalientes, Aguascalientes, 20130,
Mexico
| | - Nikesh Kunder
- University of Texas at Dallas, Department of Biological
Sciences, Richardson, TX, 75080, USA
| | - Andi Wanghzou
- University of Texas at Dallas, School of Behavioral and
Brain Sciences, Richardson, TX, 75080, USA
| | - Bryan Black
- University of Texas at Dallas, Department of
Bioengineering, Richardson, TX, 75080, USA
| | - Pradipta R. Ray
- University of Texas at Dallas, School of Behavioral and
Brain Sciences, Richardson, TX, 75080, USA
| | - Tzu-Fang Lou
- University of Texas at Dallas, Department of Biological
Sciences, Richardson, TX, 75080, USA
| | - June Bryan de la Peña
- University of Texas at Dallas, Department of Biological
Sciences, Richardson, TX, 75080, USA
| | - Rahul Atmaramani
- University of Texas at Dallas, Department of
Bioengineering, Richardson, TX, 75080, USA
| | - Tarjani Shukla
- University of Texas at Dallas, Department of Biological
Sciences, Richardson, TX, 75080, USA
| | - Joseph J. Pancrazio
- University of Texas at Dallas, Department of
Bioengineering, Richardson, TX, 75080, USA
- Center for Advanced Pain Studies, University of Texas at
Dallas, Richardson, TX, 75080, USA
| | - Theodore J. Price
- University of Texas at Dallas, School of Behavioral and
Brain Sciences, Richardson, TX, 75080, USA
- Center for Advanced Pain Studies, University of Texas at
Dallas, Richardson, TX, 75080, USA
| | - Zachary T. Campbell
- University of Texas at Dallas, Department of Biological
Sciences, Richardson, TX, 75080, USA
- Center for Advanced Pain Studies, University of Texas at
Dallas, Richardson, TX, 75080, USA
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31
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Jürgens L, Manske F, Hubert E, Kischka T, Flötotto L, Klaas O, Shabardina V, Schliemann C, Makalowski W, Wethmar K. Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer. Biomedicines 2021; 9:biomedicines9060618. [PMID: 34072580 PMCID: PMC8227997 DOI: 10.3390/biomedicines9060618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Upstream open reading frame (uORF)-mediated translational control has emerged as an important regulatory mechanism in human health and disease. However, a systematic search for cancer-associated somatic uORF mutations has not been performed. Here, we analyzed the genetic variability at canonical (uAUG) and alternative translational initiation sites (aTISs), as well as the associated upstream termination codons (uStops) in 3394 whole-exome-sequencing datasets from patient samples of breast, colon, lung, prostate, and skin cancer and of acute myeloid leukemia, provided by The Cancer Genome Atlas research network. We found that 66.5% of patient samples were affected by at least one of 5277 recurrent uORF-associated somatic single nucleotide variants altering 446 uAUG, 347 uStop, and 4733 aTIS codons. While twelve uORF variants were detected in all entities, 17 variants occurred in all five types of solid cancer analyzed here. Highest frequencies of individual somatic variants in the TLSs of NBPF20 and CHCHD2 reached 10.1% among LAML and 8.1% among skin cancer patients, respectively. Functional evaluation by dual luciferase reporter assays identified 19 uORF variants causing significant translational deregulation of the associated main coding sequence, ranging from 1.73-fold induction for an AUG.1 > UUG variant in SETD4 to 0.006-fold repression for a CUG.6 > GUG variant in HLA-DRB1. These data suggest that somatic uORF mutations are highly prevalent in human malignancies and that defective translational regulation of protein expression may contribute to the onset or progression of cancer.
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Affiliation(s)
- Lara Jürgens
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Felix Manske
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Elvira Hubert
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Tabea Kischka
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Lea Flötotto
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Oliver Klaas
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Victoria Shabardina
- Institute of Evolutionary Biology, CSIC-Unversitat Pompeu Frabra, 08002 Barcelona, Spain;
| | - Christoph Schliemann
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Klaus Wethmar
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
- Correspondence: ; Tel.: +49-251-8347587; Fax: +49-251-8347588
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Ribosome-Profiling Reveals Restricted Post Transcriptional Expression of Antiviral Cytokines and Transcription Factors during SARS-CoV-2 Infection. Int J Mol Sci 2021; 22:ijms22073392. [PMID: 33806254 PMCID: PMC8036502 DOI: 10.3390/ijms22073392] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
The global COVID-19 pandemic caused by SARS-CoV-2 has resulted in over 2.2 million deaths. Disease outcomes range from asymptomatic to severe with, so far, minimal genotypic change to the virus so understanding the host response is paramount. Transcriptomics has become incredibly important in understanding host-pathogen interactions; however, post-transcriptional regulation plays an important role in infection and immunity through translation and mRNA stability, allowing tight control over potent host responses by both the host and the invading virus. Here, we apply ribosome profiling to assess post-transcriptional regulation of host genes during SARS-CoV-2 infection of a human lung epithelial cell line (Calu-3). We have identified numerous transcription factors (JUN, ZBTB20, ATF3, HIVEP2 and EGR1) as well as select antiviral cytokine genes, namely IFNB1, IFNL1,2 and 3, IL-6 and CCL5, that are restricted at the post-transcriptional level by SARS-CoV-2 infection and discuss the impact this would have on the host response to infection. This early phase restriction of antiviral transcripts in the lungs may allow high viral load and consequent immune dysregulation typically seen in SARS-CoV-2 infection.
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Reprogramming translation for gene therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:439-476. [PMID: 34175050 DOI: 10.1016/bs.pmbts.2021.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Translational control plays a fundamental role in the regulation of gene expression in eukaryotes. Modulating translational efficiency allows the cell to fine-tune the expression of genes, spatially control protein localization, and trigger fast responses to environmental stresses. Translational regulation involves mechanisms acting on multiple steps of the protein synthesis pathway: initiation, elongation, and termination. Many cis-acting elements present in the 5' UTR of transcripts can influence translation at the initiation step. Among them, the Kozak sequence impacts translational efficiency by regulating the recognition of the start codon; upstream open reading frames (uORFs) are associated with inhibition of translation of the downstream protein; internal ribosomal entry sites (IRESs) can promote cap-independent translation. CRISPR-Cas technology is a revolutionary gene-editing tool that has also been applied to the regulation of gene expression. In this chapter, we focus on the genome editing approaches developed to modulate the translational efficiency with the aim to find novel therapeutic approaches, in particular acting on the cis-elements, that regulate the initiation of protein synthesis.
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Jonsson WO, Margolies NS, Mirek ET, Zhang Q, Linden MA, Hill CM, Link C, Bithi N, Zalma B, Levy JL, Pettit AP, Miller JW, Hine C, Morrison CD, Gettys TW, Miller BF, Hamilton KL, Wek RC, Anthony TG. Physiologic Responses to Dietary Sulfur Amino Acid Restriction in Mice Are Influenced by Atf4 Status and Biological Sex. J Nutr 2021; 151:785-799. [PMID: 33512502 PMCID: PMC8030708 DOI: 10.1093/jn/nxaa396] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/19/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Dietary sulfur amino acid restriction (SAAR) improves body composition and metabolic health across several model organisms in part through induction of the integrated stress response (ISR). OBJECTIVE We investigate the hypothesis that activating transcription factor 4 (ATF4) acts as a converging point in the ISR during SAAR. METHODS Using liver-specific or global gene ablation strategies, in both female and male mice, we address the role of ATF4 during dietary SAAR. RESULTS We show that ATF4 is dispensable in the chronic induction of the hepatokine fibroblast growth factor 21 while being essential for the sustained production of endogenous hydrogen sulfide. We also affirm that biological sex, independent of ATF4 status, is a determinant of the response to dietary SAAR. CONCLUSIONS Our results suggest that auxiliary components of the ISR, which are independent of ATF4, are critical for SAAR-mediated improvements in metabolic health in mice.
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Affiliation(s)
- William O Jonsson
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | | | - Emily T Mirek
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Qian Zhang
- Department of Health and Exercise Science, Colorado State University, Ft. Collins, CO, USA
| | - Melissa A Linden
- Department of Health and Exercise Science, Colorado State University, Ft. Collins, CO, USA,Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA
| | - Cristal M Hill
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA
| | - Christopher Link
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Nazmin Bithi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Brian Zalma
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Jordan L Levy
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Ashley P Pettit
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Joshua W Miller
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Christopher Hine
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | | | - Thomas W Gettys
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA
| | - Benjamin F Miller
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Karyn L Hamilton
- Department of Health and Exercise Science, Colorado State University, Ft. Collins, CO, USA
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
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Rozpędek W, Pytel D, Popławski T, Walczak A, Gradzik K, Wawrzynkiewicz A, Wojtczak R, Mucha B, Diehl JA, Majsterek I. Inhibition of the PERK-Dependent Unfolded Protein Response Signaling Pathway Involved in the Pathogenesis of Alzheimer's Disease. Curr Alzheimer Res 2020; 16:209-218. [PMID: 30819079 DOI: 10.2174/1567205016666190228121157] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/07/2019] [Accepted: 01/31/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVES There is a body of evidence that neurodegenerative disease entities are directly correlated with the perturbations on the molecular level. Hence, the ER stress-mediated Unfolded Protein Response (UPR) is activated resulting in PERK-dependent phosphorylation of the Eukaryotic initiation factor 2 (eIF2α). Thus, the levels of ATF4 and CHOP proteins are significantly increased, which subsequently switches the pro-adaptive branch of the UPR into the pro-apoptotic directly leading to neuronal loss and initiation of the neurodegenerative process. The aim of the presented study was the evaluation of the biological activity of highly specific, small-molecule inhibitors of the PERKdependent UPR signaling pathway. METHODS The study was conducted on rat astrocytic DI TNC1 cell line. The level of p-eIF2α was measured by Western blot technique, the cytotoxicity of the investigated compound was assessed by the MTT assay and using the FITC-conjugated Annexin V (Annexin V-FITC) to indicate apoptosis and propidium iodide (PI) to indicate necrosis. The effect of tested compound on cell cycle progression was measured by flow cytometry, where the PI-labelled nuclei were analysed for DNA content. RESULTS As a result one of the investigated compound LDN-0060609 triggers a significant inhibition of the eIF2α phosphorylation in DI TNC1 cell line. Moreover, we showed that compound LDN-0060609 is non-cytotoxic and has no effect on cell cycle progression. CONCLUSION In conclusion, LDN-0060609 may constitute a novel, targeted treatment approach against neurodegenerative diseases, including Alzheimer's disease (AD), where pathogenesis and progression are closely associated with the overactivation of the PERK-dependent UPR signaling pathway.
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Affiliation(s)
- Wioletta Rozpędek
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Dariusz Pytel
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, United States
| | - Tomasz Popławski
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Anna Walczak
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Kinga Gradzik
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Adam Wawrzynkiewicz
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Radosław Wojtczak
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Bartosz Mucha
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland.,Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, United States
| | - John Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, United States
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
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36
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Back SH. Roles of the Translation Initiation Factor eIF2α Phosphorylation in Cell Structure and Function. Cell Struct Funct 2020; 45:65-76. [PMID: 32350191 PMCID: PMC10511048 DOI: 10.1247/csf.20013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/24/2020] [Indexed: 12/17/2023] Open
Abstract
It is often assumed that α-subunit phosphorylation of the eukaryotic translation initiation factor 2 (eIF2) complex is just a mechanism to control protein synthesis. However, eIF2α phosphorylation induced by multiple kinases can recognize various intracellular and extracellular stress conditions, and it is involved in various other cellular processes beyond protein synthesis. This review introduces the roles of eIF2α phosphorylation in translational regulation, the generation of reactive oxygen species, changes in mitochondria structure and shape, and mitochondrial retrograde signaling pathways in response to diverse stress conditions.Key words: eIF2α phosphorylation, Translation, Unfolded Protein Response, Reactive Oxygen Species, Mitochondria.
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Affiliation(s)
- Sung Hoon Back
- School of Biological Sciences, University of Ulsan, Ulsan 44610, Korea
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37
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Scholz A, Rappl P, Böffinger N, Mota AC, Brüne B, Schmid T. Translation of TNFAIP2 is tightly controlled by upstream open reading frames. Cell Mol Life Sci 2020; 77:2017-2027. [PMID: 31392347 PMCID: PMC11104949 DOI: 10.1007/s00018-019-03265-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
Translation is a highly regulated process, both at the global as well as on a transcript-specific level. Regulatory upstream open reading frames (uORFs) represent a mode to alter cap-dependent translation efficiency in a transcript-specific manner and are found in numerous mRNAs. In the majority of cases, uORFs inhibit the translation of their associated main ORFs. Consequently, their inactivation results in enhanced translation of the main ORF, a phenomenon best characterized in the context of the integrated stress response. In the present study, we identified potent translation-inhibitory uORFs in the transcript leader sequence (TLS) of tumor necrosis factor alpha induced protein 2 (TNFAIP2). The initial description of the uORFs was based on the observation that despite a massive induction of TNFAIP2 mRNA expression in response to interleukin 1β (IL1β), TNFAIP2 protein levels remained low in MCF7 cells. While we were able to characterize the uORFs with respect to their exact size and sequential requirements in this cellular context, only TPA stimulation partially overcame the translation-inhibitory activity of the TNFAIP2 uORFs. Characterization of TNFAIP2 translation in the context of monocyte-to-macrophage differentiation suggested that, while the uORFs efficiently block TNFAIP2 protein synthesis in monocytes, they are inactivated in mature macrophages, thus allowing for a massive increase in TNFAIP2 protein expression. In summary, we establish TNFAIP2 as a novel target of uORF-mediated translational regulation. Furthermore, our findings suggest that during macrophage differentiation a major uORF-dependent translational switch occurs.
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Affiliation(s)
- Anica Scholz
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Peter Rappl
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Nicola Böffinger
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Ana Carolina Mota
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Bernhard Brüne
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
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38
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Guimaraes JC, Mittal N, Gnann A, Jedlinski D, Riba A, Buczak K, Schmidt A, Zavolan M. A rare codon-based translational program of cell proliferation. Genome Biol 2020; 21:44. [PMID: 32102681 PMCID: PMC7045563 DOI: 10.1186/s13059-020-1943-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The speed of translation elongation is primarily determined by the abundance of tRNAs. Thus, the codon usage influences the rate with which individual mRNAs are translated. As the nature of tRNA pools and modifications can vary across biological conditions, codon elongation rates may also vary, leading to fluctuations in the protein production from individual mRNAs. Although it has been observed that functionally related mRNAs exhibit similar codon usage, presumably to provide an effective way to coordinate expression of multiple proteins, experimental evidence for codon-mediated translation efficiency modulation of functionally related mRNAs in specific conditions is scarce and the associated mechanisms are still debated. RESULTS Here, we reveal that mRNAs whose expression increases during cell proliferation are enriched in rare codons, poorly adapted to tRNA pools. Ribosome occupancy profiling and proteomics measurements show that upon increased cell proliferation, transcripts enriched in rare codons undergo a higher translation boost than transcripts with common codons. Re-coding of a fluorescent reporter with rare codons increased protein output by ~ 30% relative to a reporter re-coded with common codons. Although the translation capacity of proliferating cells was higher compared to resting cells, we did not find evidence for the regulation of individual tRNAs. Among the models that were proposed so far to account for codon-mediated translational regulation upon changing conditions, the one that seems most consistent with our data involves a global upregulation of ready-to-translate tRNAs, which we show can lead to a higher increase in the elongation velocity at rare codons compared to common codons. CONCLUSIONS We propose that the alleviation of translation bottlenecks in rapidly dividing cells enables preferential upregulation of pro-proliferation proteins, encoded by mRNAs that are enriched in rare codons.
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Affiliation(s)
- Joao C Guimaraes
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland.
| | - Nitish Mittal
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Alexandra Gnann
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
- Department of Biomedicine, University of Basel/University Hospital Basel, Hebelstrasse 20, 4031, Basel, Switzerland
| | - Dominik Jedlinski
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Andrea Riba
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch CEDEX, France
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland.
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Jaud M, Philippe C, Di Bella D, Tang W, Pyronnet S, Laurell H, Mazzolini L, Rouault-Pierre K, Touriol C. Translational Regulations in Response to Endoplasmic Reticulum Stress in Cancers. Cells 2020; 9:cells9030540. [PMID: 32111004 PMCID: PMC7140484 DOI: 10.3390/cells9030540] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022] Open
Abstract
During carcinogenesis, almost all the biological processes are modified in one way or another. Among these biological processes affected, anomalies in protein synthesis are common in cancers. Indeed, cancer cells are subjected to a wide range of stresses, which include physical injuries, hypoxia, nutrient starvation, as well as mitotic, oxidative or genotoxic stresses. All of these stresses will cause the accumulation of unfolded proteins in the Endoplasmic Reticulum (ER), which is a major organelle that is involved in protein synthesis, preservation of cellular homeostasis, and adaptation to unfavourable environment. The accumulation of unfolded proteins in the endoplasmic reticulum causes stress triggering an unfolded protein response in order to promote cell survival or to induce apoptosis in case of chronic stress. Transcription and also translational reprogramming are tightly controlled during the unfolded protein response to ensure selective gene expression. The majority of stresses, including ER stress, induce firstly a decrease in global protein synthesis accompanied by the induction of alternative mechanisms for initiating the translation of mRNA, later followed by a translational recovery. After a presentation of ER stress and the UPR response, we will briefly present the different modes of translation initiation, then address the specific translational regulatory mechanisms acting during reticulum stress in cancers and highlight the importance of translational control by ER stress in tumours.
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Affiliation(s)
- Manon Jaud
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Céline Philippe
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Doriana Di Bella
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Weiwei Tang
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Stéphane Pyronnet
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Henrik Laurell
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Inserm UMR1048, I2MC (Institut des Maladies Métaboliques et Cardiovasculaires), BP 84225, CEDEX 04, 31 432 Toulouse, France
| | - Laurent Mazzolini
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- CNRS ERL5294, CRCT, F-31037 Toulouse, France
| | - Kevin Rouault-Pierre
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Christian Touriol
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Correspondence:
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40
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IBTK Haploinsufficiency Affects the Tumor Microenvironment of Myc-Driven Lymphoma in E-myc Mice. Int J Mol Sci 2020; 21:ijms21030885. [PMID: 32019112 PMCID: PMC7038122 DOI: 10.3390/ijms21030885] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
The tumor microenvironment is a dynamic and interactive supporting network of various components, including blood vessels, cytokines, chemokines, and immune cells, which sustain the tumor cell’s survival and growth. Murine models of lymphoma are useful to study tumor biology, the microenvironment, and mechanisms of response to therapy. Lymphomas are heterogeneous hematologic malignancies, and the complex microenvironment from which they arise and their multifaceted genetic basis represents a challenge for the generation and use of an appropriate murine model. So, it is important to choose the correct methodology. Recently, we supported the first evidence on the pro-oncogenic action of IBTK in Myc-driven B cell lymphomagenesis in mice, inhibiting apoptosis in the pre-cancerous stage. We used the transgenic Eμ-myc mouse model of non-Hodgkin’s lymphoma and Ibtk hemizygous mice to evaluate the tumor development of Myc-driven lymphoma. Here, we report that the allelic loss of Ibtk alters the immunophenotype of Myc-driven B cell lymphomas, increasing the rate of pre-B cells and affecting the tumor microenvironment in Eμ-myc mice. In particular, we observed enhanced tumor angiogenesis, increasing pro-angiogenic and lymphangiogenic factors, such as VEGF, MMP-9, CCL2, and VEGFD, and a significant recruitment of tumor-associated macrophages in lymphomas of Ibtk+/-Eμ-myc compared to Ibtk+/+Eμ-myc mice. In summary, these results indicate that IBTK haploinsufficiency promotes Myc tumor development by modifying the tumor microenvironment.
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41
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Lorent J, Kusnadi EP, van Hoef V, Rebello RJ, Leibovitch M, Ristau J, Chen S, Lawrence MG, Szkop KJ, Samreen B, Balanathan P, Rapino F, Close P, Bukczynska P, Scharmann K, Takizawa I, Risbridger GP, Selth LA, Leidel SA, Lin Q, Topisirovic I, Larsson O, Furic L. Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression. EMBO J 2019; 38:e101323. [PMID: 31556460 DOI: 10.15252/embj.2018101323] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
Estrogen receptor alpha (ERα) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ERα on cancer-associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ERα coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ERα largely manifest as "translational offsetting" of the transcriptome, whereby amounts of translated mRNAs and corresponding protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome association, are reduced following ERα depletion lack features which limit translation efficiency including structured 5'UTRs and miRNA target sites. In contrast, mRNAs induced upon ERα depletion whose polysome association remains unaltered are enriched in codons requiring U34-modified tRNAs for efficient decoding. Consistently, ERα regulates levels of U34-modifying enzymes and thereby controls levels of U34-modified tRNAs. These findings unravel a hitherto unprecedented mechanism of ERα-dependent orchestration of transcriptional and translational programs that may be a pervasive mechanism of proteome maintenance in hormone-dependent cancers.
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Affiliation(s)
- Julie Lorent
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Eric P Kusnadi
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Vincent van Hoef
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Richard J Rebello
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia
| | - Matthew Leibovitch
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, Lady Davis Institute, McGill University, Montreal, QC, Canada
| | - Johannes Ristau
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Shan Chen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Mitchell G Lawrence
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Krzysztof J Szkop
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Baila Samreen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Preetika Balanathan
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia
| | - Francesca Rapino
- Laboratory of Cancer Signaling, GIGA-Institute, University of Liège, Liège, Belgium
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA-Institute, University of Liège, Liège, Belgium
| | - Patricia Bukczynska
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia
| | - Karin Scharmann
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, Münster, Germany
| | - Itsuhiro Takizawa
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia
| | - Gail P Risbridger
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, Münster, Germany.,Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Qishan Lin
- RNA Epitranscriptomics & Proteomics Resource, Department of Chemistry, University at Albany, Albany, NY, USA
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, Lady Davis Institute, McGill University, Montreal, QC, Canada
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Luc Furic
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic., Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
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42
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Zhao L, Wang L, Zhang C, Liu Z, Piao Y, Yan J, Xiang R, Yao Y, Shi Y. E6-induced selective translation of WNT4 and JIP2 promotes the progression of cervical cancer via a noncanonical WNT signaling pathway. Signal Transduct Target Ther 2019; 4:32. [PMID: 31637011 PMCID: PMC6799841 DOI: 10.1038/s41392-019-0060-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/24/2022] Open
Abstract
mRNA translation reprogramming occurs frequently in many pathologies, including cancer and viral infection. It remains largely unknown whether viral-induced alterations in mRNA translation contribute to carcinogenesis. Most cervical cancer is caused by high-risk human papillomavirus infection, resulting in the malignant transformation of normal epithelial cells mainly via viral E6 and E7 oncoproteins. Here, we utilized polysome profiling and deep RNA sequencing to systematically evaluate E6-regulated mRNA translation in HPV18-infected cervical cancer cells. We found that silencing E6 can cause over a two-fold change in the translation efficiency of ~653 mRNAs, most likely in an eIF4E- and eIF2α-independent manner. In addition, we identified that E6 can selectively upregulate the translation of WNT4, JIP1, and JIP2, resulting in the activation of the noncanonical WNT/PCP/JNK pathway to promote cell proliferation in vitro and tumor growth in vivo. Ectopic expression of WNT4/JIP2 can effectively rescue the decreased cell proliferation caused by E6 silencing, strongly suggesting that the WNT4/JIP2 pathway mediates the role of E6 in promoting cell proliferation. Thus, our results revealed a novel oncogenic mechanism of E6 via regulating the translation of mRNAs.
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Affiliation(s)
- Lin Zhao
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, 28 Fuxing Road, 100853 Beijing, China
| | - Longlong Wang
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Chenglan Zhang
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Ze Liu
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Yongjun Piao
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Jie Yan
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Rong Xiang
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Yuanqing Yao
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, 28 Fuxing Road, 100853 Beijing, China
| | - Yi Shi
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
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43
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Shao Y, Wichern E, Childress PJ, Adaway M, Misra J, Klunk A, Burr DB, Wek RC, Mosley AL, Liu Y, Robling AG, Brustovetsky N, Hamilton J, Jacobs K, Vashishth D, Stayrook KR, Allen MR, Wallace JM, Bidwell JP. Loss of Nmp4 optimizes osteogenic metabolism and secretion to enhance bone quality. Am J Physiol Endocrinol Metab 2019; 316:E749-E772. [PMID: 30645175 PMCID: PMC6580174 DOI: 10.1152/ajpendo.00343.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 12/11/2022]
Abstract
A goal of osteoporosis therapy is to restore lost bone with structurally sound tissue. Mice lacking the transcription factor nuclear matrix protein 4 (Nmp4, Zfp384, Ciz, ZNF384) respond to several classes of osteoporosis drugs with enhanced bone formation compared with wild-type (WT) animals. Nmp4-/- mesenchymal stem/progenitor cells (MSPCs) exhibit an accelerated and enhanced mineralization during osteoblast differentiation. To address the mechanisms underlying this hyperanabolic phenotype, we carried out RNA-sequencing and molecular and cellular analyses of WT and Nmp4-/- MSPCs during osteogenesis to define pathways and mechanisms associated with elevated matrix production. We determined that Nmp4 has a broad impact on the transcriptome during osteogenic differentiation, contributing to the expression of over 5,000 genes. Phenotypic anchoring of transcriptional data was performed for the hypothesis-testing arm through analysis of cell metabolism, protein synthesis and secretion, and bone material properties. Mechanistic studies confirmed that Nmp4-/- MSPCs exhibited an enhanced capacity for glycolytic conversion: a key step in bone anabolism. Nmp4-/- cells showed elevated collagen translation and secretion. The expression of matrix genes that contribute to bone material-level mechanical properties was elevated in Nmp4-/- cells, an observation that was supported by biomechanical testing of bone samples from Nmp4-/- and WT mice. We conclude that loss of Nmp4 increases the magnitude of glycolysis upon the metabolic switch, which fuels the conversion of the osteoblast into a super-secretor of matrix resulting in more bone with improvements in intrinsic quality.
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Affiliation(s)
- Yu Shao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis, Indiana
| | - Emily Wichern
- Department of Anatomy and Cell Biology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Paul J Childress
- Department of Orthopaedic Surgery, Indiana University School of Medicine , Indianapolis, Indiana
- Indiana Center for Musculoskeletal Health Indiana University School of Medicine , Indianapolis, Indiana
| | - Michele Adaway
- Department of Anatomy and Cell Biology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Jagannath Misra
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Angela Klunk
- Department of Anatomy and Cell Biology, Indiana University School of Medicine , Indianapolis, Indiana
| | - David B Burr
- Department of Anatomy and Cell Biology, Indiana University School of Medicine , Indianapolis, Indiana
- Indiana Center for Musculoskeletal Health Indiana University School of Medicine , Indianapolis, Indiana
- Department of Biomedical Engineering, Indiana University-Purdue University , Indianapolis, Indiana
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis, Indiana
| | - Alexander G Robling
- Department of Anatomy and Cell Biology, Indiana University School of Medicine , Indianapolis, Indiana
- Indiana Center for Musculoskeletal Health Indiana University School of Medicine , Indianapolis, Indiana
| | - Nickolay Brustovetsky
- Department of Pharmacology and Toxicology, Indiana University School of Medicine , Indianapolis, Indiana
| | - James Hamilton
- Department of Pharmacology and Toxicology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Kylie Jacobs
- Department of Microbiology and Immunology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Deepak Vashishth
- Center for Biotechnology and Interdisciplinary Studies and Department of Biomedical Engineering, Rensselaer Polytechnic Institute , Troy, New York
| | - Keith R Stayrook
- Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana
| | - Matthew R Allen
- Department of Anatomy and Cell Biology, Indiana University School of Medicine , Indianapolis, Indiana
- Indiana Center for Musculoskeletal Health Indiana University School of Medicine , Indianapolis, Indiana
- Roudebush Veterans Administration Medical Center , Indianapolis, Indiana
| | - Joseph M Wallace
- Department of Orthopaedic Surgery, Indiana University School of Medicine , Indianapolis, Indiana
- Indiana Center for Musculoskeletal Health Indiana University School of Medicine , Indianapolis, Indiana
- Department of Biomedical Engineering, Indiana University-Purdue University , Indianapolis, Indiana
| | - Joseph P Bidwell
- Department of Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis, Indiana
- Department of Anatomy and Cell Biology, Indiana University School of Medicine , Indianapolis, Indiana
- Indiana Center for Musculoskeletal Health Indiana University School of Medicine , Indianapolis, Indiana
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44
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Vecchio E, Golino G, Pisano A, Albano F, Falcone C, Ceglia S, Iaccino E, Mimmi S, Fiume G, Giurato G, Britti D, Scala G, Quinto I. IBTK contributes to B-cell lymphomagenesis in Eμ-myc transgenic mice conferring resistance to apoptosis. Cell Death Dis 2019; 10:320. [PMID: 30975981 PMCID: PMC6459904 DOI: 10.1038/s41419-019-1557-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/17/2022]
Abstract
Increasing evidence supports the involvement of IBTK in cell survival and tumor growth. Previously, we have shown that IBTK RNA interference affects the wide genome expression and RNA splicing in cell-type specific manner. Further, the expression of IBTK gene progressively increases from indolent to aggressive stage of chronic lymphocytic leukemia and decreases in disease remission after therapy. However, the role of IBTK in tumorigenesis has not been elucidated. Here, we report that loss of the murine Ibtk gene raises survival and delays tumor onset in Eμ-myc transgenic mice, a preclinical model of Myc-driven lymphoma. In particular, we found that the number of pre-cancerous B cells of bone marrow and spleen is reduced in Ibtk-/-Eμ-myc mice owing to impaired viability and increased apoptosis, as measured by Annexin V binding, Caspase 3/7 cleavage assays and cell cycle profile analysis. Instead, the proliferation rate of pre-cancerous B cells is unaffected by the loss of Ibtk. We observed a direct correlation between Ibtk and myc expression and demonstrated a Myc-dependent regulation of Ibtk expression in murine B cells, human hematopoietic and nonhematopoietic cell lines by analysis of ChIP-seq data. By tet-repressible Myc system, we confirmed a Myc-dependent expression of IBTK in human B cells. Further, we showed that Ibtk loss affected the main apoptotic pathways dependent on Myc overexpression in pre-cancerous Eμ-myc mice, in particular, MCL-1 and p53. Of note, we found that loss of IBTK impaired cell cycle and increased apoptosis also in a human epithelial cell line, HeLa cells, in Myc-independent manner. Taken together, these results suggest that Ibtk sustains the oncogenic activity of Myc by inhibiting apoptosis of murine pre-cancerous B cells, as a cell-specific mechanism. Our findings could be relevant for the development of IBTK inhibitors sensitizing tumor cells to apoptosis.
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Affiliation(s)
- Eleonora Vecchio
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy.
| | - Gaetanina Golino
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Antonio Pisano
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Francesco Albano
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Cristina Falcone
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Simona Ceglia
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Enrico Iaccino
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Selena Mimmi
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy.,Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Domenico Britti
- Department of Health Science, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy.,Interdepartmental Services Centre of Veterinary for Human and Animal Health, University "Magna Græcia" of Catanzaro, Catanzaro, 88100, Italy
| | - Giuseppe Scala
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy
| | - Ileana Quinto
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Catanzaro, 88100, Italy.
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45
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Activation of PERK-eIF2α-ATF4 pathway contributes to diabetic hepatotoxicity: Attenuation of ER stress by Morin. Cell Signal 2019; 59:41-52. [PMID: 30877037 DOI: 10.1016/j.cellsig.2019.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/22/2019] [Accepted: 03/06/2019] [Indexed: 01/12/2023]
Abstract
Hyperglycemia associated ER stress has been found as a critical contributor in the pathogenesis of type 2 diabetes mellitus. However, reports regarding molecular mechanisms involved are limited. This study was aimed to identify the role of ER stress in regulating hepatic glucose metabolism and its link with oxidative stress. Further, this study explores the novel role of Morin, a flavonol, in modulating ER stress in STZ/nicotinamide induced type 2 diabetic male Wistar rats. Results demonstrate that hyperglycemia induced ER stress in rats and significantly lowered the expression of glucose transporter proteins resulting in impaired glucose metabolism during diabetes. Morin was found to downregulate PERK-eIF2α-ATF4 pathway by interacting with PERK protein as confirmed through pull-down assay. Additionally, Morin maintained the reducing environment in ER and enhanced PDI activity compared to diabetic rats. Morin prevented cell death by suppressing the expression of PERK dependent pro-apoptotic proteins including ATF4 and CHOP. Findings from this study affirm the role of ER stress in hyperglycemia induced gluco-metabolic aberrations and liver injury as confirmed by ISRIB, a standard chemical ER stress inhibitor. Notably, Morin promoted deactivation of UPR sensors and upregulated PDI activity endorsing its anti-ER stress potential which may allow the development of new therapeutic avenues to target hyperglycemic hepatotoxicity.
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46
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Epithelial to Mesenchymal transition, eIF2α phosphorylation and Hsp70 expression enable greater tolerance in A549 cells to TiO 2 over ZnO nanoparticles. Sci Rep 2019; 9:436. [PMID: 30679528 PMCID: PMC6346025 DOI: 10.1038/s41598-018-36716-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/03/2018] [Indexed: 12/15/2022] Open
Abstract
Type II alveolar cells are highly robust in nature, yet susceptible to aerosolized nanoparticles (NPs). Dysfunction in these specialized cells, can often lead to emphysema, edema, and pulmonary inflammation. Long-time exposure can also lead to dangerous epigenetic modifications and cancer. Among the manufactured nanomaterials, metal oxide nanoparticles are widely encountered owing to their wide range of applications. Scores of published literatures affirm ZnO NPs are more toxic to human alveolar cells than TiO2. However, signalling cascades deducing differences in human alveolar responses to their exposure is not well documented. With A549 cells, we have demonstrated that epithelial to mesenchymal transition and an increased duration of phosphorylation of eIF2α are crucial mechanisms routing better tolerance to TiO2 NP treatment over exposure to ZnO. The increased migratory capacity may help cells escape away from the zone of stress. Further, expression of chaperone such as Hsp70 is also enhanced during the same dose-time investigations. This is the first report of its kind. These novel findings could be successfully developed in the future to design relief strategies to alleviate metal oxide nanoparticle mediated stress.
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47
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Naz S, Battu S, Khan RA, Afroz S, Giddaluru J, Vishwakarma SK, Satti V, Habeeb MA, Khan AA, Khan N. Activation of integrated stress response pathway regulates IL-1β production through posttranscriptional and translational reprogramming in macrophages. Eur J Immunol 2019; 49:277-289. [PMID: 30578631 DOI: 10.1002/eji.201847513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 10/27/2018] [Accepted: 12/10/2018] [Indexed: 01/06/2023]
Abstract
Immune cells sense and programme its cellular machinery appropriately to the environmental changes through the activation of cytoprotective adaptive pathway so-called the "integrated stress response (ISR)". However, the mechanisms implicated in ISR-induced protective responses are poorly understood. Here, we show that ISR activation by arsenite (Ar) results in suppression of IL-1β production in macrophages and inhibition of DSS-induced colitis in a murine model through a novel posttranscriptional and translation regulatory (PTR) mechanism. Ar triggers PTR events through eIF2α-phosphorylation, which results in the attenuation of active polysome formation leading to the accumulation of translationally stalled IL-1β mRNAs. Translationally stalled IL-1β mRNAs recruit RNA-binding proteins (TIA-1/TIAR), resulting in the formation of RBP-RNA complexes known as stress granules (SGs). The SGs bound IL-1β mRNAs might undergo degradation through induction of autophagy. Also, we show that Ar posttranslationally impairs processing and secretion of IL-1β by diminishing inflammasome activation. Altogether, this study unveils a novel mechanism of IL-1β regulation and further suggests that pharmacological activation of cytoprotective ISR pathway might provide an effective therapeutic intervention against inflammatory diseases.
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Affiliation(s)
- Saima Naz
- Central Laboratory for Stem Cell Research and Translational Medicine, Center for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad, India
| | - Srikanth Battu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Rafiq Ahmad Khan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sumbul Afroz
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Jeevan Giddaluru
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sandeep Kumar Vishwakarma
- Central Laboratory for Stem Cell Research and Translational Medicine, Center for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad, India
| | | | - Md Aejaz Habeeb
- Central Laboratory for Stem Cell Research and Translational Medicine, Center for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad, India
| | - Aleem Ahmed Khan
- Central Laboratory for Stem Cell Research and Translational Medicine, Center for Liver Research and Diagnostics, Deccan College of Medical Sciences, Hyderabad, India
| | - Nooruddin Khan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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48
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Silva J, Fernandes R, Romão L. Translational Regulation by Upstream Open Reading Frames and Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:99-116. [DOI: 10.1007/978-3-030-19966-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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49
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Rendleman J, Cheng Z, Maity S, Kastelic N, Munschauer M, Allgoewer K, Teo G, Zhang YBM, Lei A, Parker B, Landthaler M, Freeberg L, Kuersten S, Choi H, Vogel C. New insights into the cellular temporal response to proteostatic stress. eLife 2018; 7:39054. [PMID: 30272558 PMCID: PMC6185107 DOI: 10.7554/elife.39054] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
Maintaining a healthy proteome involves all layers of gene expression regulation. By quantifying temporal changes of the transcriptome, translatome, proteome, and RNA-protein interactome in cervical cancer cells, we systematically characterize the molecular landscape in response to proteostatic challenges. We identify shared and specific responses to misfolded proteins and to oxidative stress, two conditions that are tightly linked. We reveal new aspects of the unfolded protein response, including many genes that escape global translation shutdown. A subset of these genes supports rerouting of energy production in the mitochondria. We also find that many genes change at multiple levels, in either the same or opposing directions, and at different time points. We highlight a variety of putative regulatory pathways, including the stress-dependent alternative splicing of aminoacyl-tRNA synthetases, and protein-RNA binding within the 3’ untranslated region of molecular chaperones. These results illustrate the potential of this information-rich resource.
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Affiliation(s)
- Justin Rendleman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Zhe Cheng
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Shuvadeep Maity
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Nicolai Kastelic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mathias Munschauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Kristina Allgoewer
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Guoshou Teo
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Yun Bin Matteo Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Amy Lei
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Brian Parker
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Integrative Research Institute for the Life Sciences, Institute of Biology, Humboldt University, Berlin, Germany
| | | | | | - Hyungwon Choi
- National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
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50
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Akazawa Y, Nakao K. To die or not to die: death signaling in nonalcoholic fatty liver disease. J Gastroenterol 2018; 53:893-906. [PMID: 29574534 PMCID: PMC6061666 DOI: 10.1007/s00535-018-1451-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/09/2018] [Indexed: 02/07/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is an emerging liver disease worldwide. In subset of patients, NAFLD progresses to its advanced form, nonalcoholic steatohepatitis (NASH), which is accompanied with inflammation and fibrosis. Saturated free fatty acid-induced hepatocyte apoptosis is a feature of NASH. Death signaling in NASH does not always result in apoptosis, but can alternatively lead to the survival of cells presenting signs of pro-inflammatory and pro-fibrotic signals. With the current lack of established treatments for NASH, it is important to understand the molecular mechanisms responsible for disease development and progression. This review focuses on the latest findings in hepatocyte death signaling and discusses possible targets for intervention, including caspases, death receptor and c-Jun N-terminal kinase 1 signaling, oxidative stress, and endoplasmic reticulum stress, as well as epigenomic factors.
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Affiliation(s)
- Yuko Akazawa
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki City, 852-8501, Nagasaki, Japan.
- Department of Gastroenterology and Hepatology, Nagasaki University Hospital, Nagasaki City, 852-8501, Nagasaki, Japan.
| | - Kazuhiko Nakao
- Department of Gastroenterology and Hepatology, Nagasaki University Hospital, Nagasaki City, 852-8501, Nagasaki, Japan
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