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Ciudad MT, Quevedo R, Lamorte S, Jin R, Nzirorera N, Koritzinsky M, McGaha TL. Dabrafenib Alters MDSC Differentiation and Function by Activation of GCN2. CANCER RESEARCH COMMUNICATIONS 2024; 4:765-784. [PMID: 38421883 PMCID: PMC10936428 DOI: 10.1158/2767-9764.crc-23-0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/12/2023] [Accepted: 02/27/2024] [Indexed: 03/02/2024]
Abstract
The effect of targeted therapeutics on anticancer immune responses is poorly understood. The BRAF inhibitor dabrafenib has been reported to activate the integrated stress response (ISR) kinase GCN2, and the therapeutic effect has been partially attributed to GCN2 activation. Because ISR signaling is a key component of myeloid-derived suppressor cell (MDSC) development and function, we measured the effect of dabrafenib on MDSC differentiation and suppressive activity. Our data showed that dabrafenib attenuated MDSC ability to suppress T-cell activity, which was associated with a GCN2-dependent block of the transition from monocytic progenitor to polymorphonuclear (PMN)-MDSCs and proliferative arrest resulting in PMN-MDSC loss. Transcriptional profiling revealed that dabrafenib-driven GCN2 activation altered metabolic features in MDSCs enhancing oxidative respiration, and attenuated transcriptional programs required for PMN development. Moreover, we observed a broad downregulation of transcriptional networks associated with PMN developmental pathways, and increased activity of transcriptional regulons driven by Atf5, Mafg, and Zbtb7a. This transcriptional program alteration underlies the basis for PMN-MDSC developmental arrest, skewing immature MDSC development toward monocytic lineage cells. In vivo, we observed a pronounced reduction in PMN-MDSCs in dabrafenib-treated tumor-bearing mice suggesting that dabrafenib impacts MDSC populations systemically and locally, in the tumor immune infiltrate. Thus, our data reveal transcriptional networks that govern MDSC developmental programs, and the impact of GCN2 stress signaling on the innate immune landscape in tumors, providing novel insight into potentially beneficial off-target effects of dabrafenib. SIGNIFICANCE An important, but poorly understood, aspect of targeted therapeutics for cancer is the effect on antitumor immune responses. This article shows that off-target effects of dabrafenib activating the kinase GCN2 impact MDSC development and function reducing PMN-MDSCs in vitro and in vivo. This has important implications for our understanding of how this BRAF inhibitor impacts tumor growth and provides novel therapeutic target and combination possibilities.
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Affiliation(s)
- M. Teresa Ciudad
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Rene Quevedo
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Sara Lamorte
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Robbie Jin
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Nadine Nzirorera
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Marianne Koritzinsky
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Tracy L. McGaha
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
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Miller MJ, Akter D, Mahmud J, Chan GC. Human cytomegalovirus modulates mTORC1 to redirect mRNA translation within quiescently infected monocytes. J Virol 2024; 98:e0188823. [PMID: 38289104 PMCID: PMC10878035 DOI: 10.1128/jvi.01888-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/21/2024] Open
Abstract
Human cytomegalovirus (HCMV) utilizes peripheral blood monocytes as a means to systemically disseminate throughout the host. Following viral entry, HCMV stimulates non-canonical Akt signaling leading to the activation of mTORC1 and the subsequent translation of select antiapoptotic proteins within infected monocytes. However, the full extent to which the HCMV-initiated Akt/mTORC1 signaling axis reshapes the monocyte translatome is unclear. We found HCMV entry alone was able to stimulate widescale changes to mRNA translation levels and that inhibition of mTOR, a component of mTORC1, dramatically attenuated HCMV-induced protein synthesis. Although monocytes treated with normal myeloid growth factors also exhibited increased levels of translation, mTOR inhibition had no effect, suggesting HCMV activation of mTOR stimulates the acquisition of a unique translatome within infected monocytes. Indeed, polyribosomal profiling of HCMV-infected monocytes identified distinct prosurvival transcripts that were preferentially loaded with ribosomes when compared to growth factor-treated cells. Sirtuin 1 (SIRT1), a deacetylase that exerts prosurvival effects through regulation of the PI3K/Akt pathway, was found to be highly enriched following HCMV infection in an mTOR-dependent manner. Importantly, SIRT1 inhibition led to the death of HCMV-infected monocytes while having minimal effect on uninfected cells. SIRT1 also supported a positive feedback loop to sustain Akt/mTORC1 signaling following viral entry. Taken together, HCMV profoundly reshapes mRNA translation in an mTOR-dependent manner to enhance the synthesis of select factors necessary for the survival of infected monocytes.IMPORTANCEHuman cytomegalovirus (HCMV) infection is a significant cause of morbidity and mortality among the immunonaïve and immunocompromised. Peripheral blood monocytes are a major cell type responsible for disseminating the virus from the initial site of infection. In order for monocytes to mediate viral spread within the host, HCMV must subvert the naturally short lifespan of these cells. In this study, we performed polysomal profiling analysis, which demonstrated HCMV to globally redirect mRNA translation toward the synthesis of cellular prosurvival factors within infected monocytes. Specifically, HCMV entry into monocytes induced the translation of cellular SIRT1 to generate an antiapoptotic state. Defining the precise mechanisms through which HCMV stimulates survival will provide insight into novel anti-HCMV drugs able to target infected monocytes.
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Affiliation(s)
- Michael J. Miller
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Dilruba Akter
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jamil Mahmud
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Gary C. Chan
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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4
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Saba JA, Huang Z, Schole KL, Ye X, Bhatt SD, Li Y, Timp W, Cheng J, Green R. LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565189. [PMID: 37961604 PMCID: PMC10635049 DOI: 10.1101/2023.11.01.565189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand.
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Affiliation(s)
- James A. Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- These authors contributed equally
| | - Zixuan Huang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
- These authors contributed equally
| | - Kate L. Schole
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianwen Ye
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Shrey D. Bhatt
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yi Li
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Lu Y, Wang S, Jiao Y. The Effects of Deregulated Ribosomal Biogenesis in Cancer. Biomolecules 2023; 13:1593. [PMID: 38002277 PMCID: PMC10669593 DOI: 10.3390/biom13111593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/04/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Ribosomes are macromolecular ribonucleoprotein complexes assembled from RNA and proteins. Functional ribosomes arise from the nucleolus, require ribosomal RNA processing and the coordinated assembly of ribosomal proteins (RPs), and are frequently hyperactivated to support the requirement for protein synthesis during the self-biosynthetic and metabolic activities of cancer cells. Studies have provided relevant information on targeted anticancer molecules involved in ribosome biogenesis (RiBi), as increased RiBi is characteristic of many types of cancer. The association between unlimited cell proliferation and alterations in specific steps of RiBi has been highlighted as a possible critical driver of tumorigenesis and metastasis. Thus, alterations in numerous regulators and actors involved in RiBi, particularly in cancer, significantly affect the rate and quality of protein synthesis and, ultimately, the transcriptome to generate the associated proteome. Alterations in RiBi in cancer cells activate nucleolar stress response-related pathways that play important roles in cancer-targeted interventions and immunotherapies. In this review, we focus on the association between alterations in RiBi and cancer. Emphasis is placed on RiBi deregulation and its secondary consequences, including changes in protein synthesis, loss of RPs, adaptive transcription and translation, nucleolar stress regulation, metabolic changes, and the impaired ribosome biogenesis checkpoint.
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Affiliation(s)
| | - Shizhuo Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110055, China;
| | - Yisheng Jiao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110055, China;
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Ciudad MT, Quevedo R, Lamorte S, Jin R, Nzirorera N, Koritzinsky M, McGaha TL. Dabrafenib alters MDSC differentiation and function by activation of GCN2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.09.552588. [PMID: 37645997 PMCID: PMC10461929 DOI: 10.1101/2023.08.09.552588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The effect of targeted therapeutics on anti-cancer immune responses is poorly understood. The BRAF inhibitor dabrafenib has been reported to activate the integrated stress response (ISR) kinase GCN2, and the therapeutic effect has been partially attributed to GCN2 activation. Since ISR signaling is a key component of myeloid-derived suppressor cell (MDSC) development and function, we measured the effect of dabrafenib on MDSC differentiation and suppressive activity. Our data showed that dabrafenib attenuated MDSC ability to suppress T cell activity, which was associated with a GCN2-dependent block of the transition from monocytic progenitor to polymorphonuclear (PMN)-MDSCs and proliferative arrest resulting in PMN-MDSC loss. Transcriptional profiling revealed that dabrafenib-driven GCN2 activation altered metabolic features in MDSCs enhancing oxidative respiration, and attenuated transcriptional programs required for PMN development. Moreover, we observed a broad downregulation of transcriptional networks associated with PMN developmental pathways, and increased activity of transcriptional regulons driven by Atf5 , Mafg , and Zbtb7a . This transcriptional program alteration underlies the basis for PMN-MDSC developmental arrest, skewing immature MDSC development towards monocytic lineage cells. In vivo , we observed a pronounced reduction in PMN-MDSCs in dabrafenib-treated tumor-bearing mice suggesting that dabrafenib impacts MDSC populations systemically and locally, in the tumor immune infiltrate. Thus, our data reveals transcriptional networks that govern MDSC developmental programs, and the impact of GCN2 stress signaling on the innate immune landscape in tumors, providing novel insight into potentially beneficial off target effects of dabrafenib.
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7
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Jonsson WO, Borowik AK, Pranay A, Kinter MT, Mirek ET, Levy JL, Snyder EM, Miller BF, Anthony TG. Kinetic proteomics identifies targeted changes in liver metabolism and the ribo-interactome by dietary sulfur amino acid restriction. GeroScience 2023; 45:2425-2441. [PMID: 36976488 PMCID: PMC10651627 DOI: 10.1007/s11357-023-00758-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/19/2023] [Indexed: 03/29/2023] Open
Abstract
Dietary sulfur amino acid restriction (SAAR) protects against diet-induced obesity, extends healthspan, and coincides with an overall reduction in hepatic protein synthesis. To explore the underpinnings of SAAR-induced slowed growth and its impact on liver metabolism and proteostasis, we resolved changes in hepatic mRNA and protein abundances and compared synthesis rates of individual liver proteins. To achieve this, adult male mice were provided deuterium-labeled drinking water while freely consuming either a regular-fat or high-fat diet that was SAA restricted. Livers from these mice and their respective dietary controls were used to conduct transcriptomic, proteomic, and kinetic proteomic analyses. We found that remodeling of the transcriptome by SAAR was largely agnostic to dietary fat content. Shared signatures included activation of the integrated stress response alongside alterations in metabolic processes impacting lipids, fatty acids, and amino acids. Changes to the proteome correlated poorly with the transcriptome, and yet, functional clustering of kinetic proteomic changes in the liver during SAAR revealed that the management of fatty acids and amino acids were altered to support central metabolism and redox balance. Dietary SAAR also strongly influenced the synthesis rates of ribosomal proteins and ribosome-interacting proteins regardless of dietary fat. Taken together, dietary SAAR alters the transcriptome and proteome in the liver to safely manage increased fatty acid flux and energy use and couples this with targeted changes in the ribo-interactome to support proteostasis and slowed growth.
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Affiliation(s)
- William O Jonsson
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, 59 Dudley Road - Foran Hall, Room 166, New Brunswick, NJ, 08901, USA
| | - Agnieszka K Borowik
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Atul Pranay
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael T Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Emily T Mirek
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, 59 Dudley Road - Foran Hall, Room 166, New Brunswick, NJ, 08901, USA
| | - Jordan L Levy
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, 59 Dudley Road - Foran Hall, Room 166, New Brunswick, NJ, 08901, USA
| | - Elizabeth M Snyder
- Department of Animal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Oklahoma City VA, Oklahoma City, OK, USA
| | - Tracy G Anthony
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, 59 Dudley Road - Foran Hall, Room 166, New Brunswick, NJ, 08901, USA.
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8
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Mijit M, Boner M, Cordova RA, Gampala S, Kpenu E, Klunk AJ, Zhang C, Kelley MR, Staschke KA, Fishel ML. Activation of the integrated stress response (ISR) pathways in response to Ref-1 inhibition in human pancreatic cancer and its tumor microenvironment. Front Med (Lausanne) 2023; 10:1146115. [PMID: 37181357 PMCID: PMC10174294 DOI: 10.3389/fmed.2023.1146115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
Pancreatic cancer or pancreatic ductal adenocarcinoma (PDAC) is characterized by a profound inflammatory tumor microenvironment (TME) with high heterogeneity, metastatic propensity, and extreme hypoxia. The integrated stress response (ISR) pathway features a family of protein kinases that phosphorylate eukaryotic initiation factor 2 (eIF2) and regulate translation in response to diverse stress conditions, including hypoxia. We previously demonstrated that eIF2 signaling pathways were profoundly affected in response to Redox factor-1 (Ref-1) knockdown in human PDAC cells. Ref-1 is a dual function enzyme with activities of DNA repair and redox signaling, responds to cellular stress, and regulates survival pathways. The redox function of Ref-1 directly regulates multiple transcription factors including HIF-1α, STAT3, and NF-κB, which are highly active in the PDAC TME. However, the mechanistic details of the crosstalk between Ref-1 redox signaling and activation of ISR pathways are unclear. Following Ref-1 knockdown, induction of ISR was observed under normoxic conditions, while hypoxic conditions were sufficient to activate ISR irrespective of Ref-1 levels. Inhibition of Ref-1 redox activity increased expression of p-eIF2 and ATF4 transcriptional activity in a concentration-dependent manner in multiple human PDAC cell lines, and the effect on eIF2 phosphorylation was PERK-dependent. Treatment with PERK inhibitor, AMG-44 at high concentrations resulted in activation of the alternative ISR kinase, GCN2 and induced levels of p-eIF2 and ATF4 in both tumor cells and cancer-associated fibroblasts (CAFs). Combination treatment with inhibitors of Ref-1 and PERK enhanced cell killing effects in both human pancreatic cancer lines and CAFs in 3D co-culture, but only at high doses of PERK inhibitors. This effect was completely abrogated when Ref-1 inhibitors were used in combination with GCN2 inhibitor, GCN2iB. We demonstrate that targeting of Ref-1 redox signaling activates the ISR in multiple PDAC lines and that this activation of ISR is critical for inhibition of the growth of co-culture spheroids. Combination effects were only observed in physiologically relevant 3D co-cultures, suggesting that the model system utilized can greatly affect the outcome of these targeted agents. Inhibition of Ref-1 signaling induces cell death through ISR signaling pathways, and combination of Ref-1 redox signaling blockade with ISR activation could be a novel therapeutic strategy for PDAC treatment.
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Affiliation(s)
- Mahmut Mijit
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Megan Boner
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Ricardo A Cordova
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Silpa Gampala
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Eyram Kpenu
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Angela J Klunk
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Chi Zhang
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of BioHealth Informatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - MarK R Kelley
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kirk A Staschke
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Melissa L Fishel
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
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9
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Fang Q, Tian GG, Wang Q, Liu M, He L, Li S, Wu J. YTHDF1 phase separation triggers the fate transition of spermatogonial stem cells by activating the IκB-NF-κB-CCND1 axis. Cell Rep 2023; 42:112403. [PMID: 37060562 DOI: 10.1016/j.celrep.2023.112403] [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: 09/23/2022] [Revised: 12/29/2022] [Accepted: 04/03/2023] [Indexed: 04/16/2023] Open
Abstract
N6-methyladenosine (m6A) modification controls cell fate determination. Here, we show that liquid-liquid phase separation (LLPS) of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), a pivotal m6A "reader" protein, promotes the transdifferentiation of spermatogonial stem cells (SSCs) into neural stem cell-like cells by activating the IκB-nuclear factor κB (NF-κB)-CCND1 axis. The inhibition of IκBα/β mRNA translation mediated by YTHDF1 LLPS is the key to the activation of the IκB-NF-κB-CCND1 axis. Disrupting either YTHDF1 LLPS or NF-κB activation inhibits transdifferentiation efficiency. Moreover, overexpression of the YTH domain of YTHDF1 inhibits the activation of the IκB-NF-κB-CCND1 axis by promoting IκBα/β mRNA translation. Overexpression of the tau-YTH fusion protein reactivates IκB-NF-κB-CCND1 axis by inhibiting the translation of IκBα/β mRNAs, and tau LLPS is observed, which can restore transdifferentiation efficiency. Our findings demonstrate that the protein-RNA LLPS plays essential roles in cell fate transition and provide insights into translational medicine and the therapy of neurological diseases.
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Affiliation(s)
- Qian Fang
- Key Laboratory for the Genetics of Development & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Geng G Tian
- Key Laboratory for the Genetics of Development & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Wang
- Key Laboratory for the Genetics of Development & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengyao Liu
- Key Laboratory for the Genetics of Development & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin He
- Key Laboratory for the Genetics of Development & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Shengtian Li
- Key Laboratory for the Genetics of Development & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ji Wu
- Key Laboratory for the Genetics of Development & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China.
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10
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Carlson KR, Georgiadis MM, Tameire F, Staschke KA, Wek RC. Activation of Gcn2 by small molecules designed to be inhibitors. J Biol Chem 2023; 299:104595. [PMID: 36898579 PMCID: PMC10124904 DOI: 10.1016/j.jbc.2023.104595] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
The integrated stress response (ISR) is an important mechanism by which cells confer protection against environmental stresses. Central to the ISR is a collection of related protein kinases that monitor stress conditions, such as Gcn2 (EIF2AK4) that recognizes nutrient limitations, inducing phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Gcn2 phosphorylation of eIF2 lowers bulk protein synthesis, conserving energy and nutrients, coincident with preferential translation of stress-adaptive gene transcripts, such as that encoding the Atf4 transcriptional regulator. While Gcn2 is central for cell protection to nutrient stress and its depletion in humans leads to pulmonary disorders, Gcn2 can also contribute to the progression of cancers and facilitate neurological disorders during chronic stress. Consequently, specific ATP-competitive inhibitors of Gcn2 protein kinase have been developed. In this study, we report that one such Gcn2 inhibitor, Gcn2iB, can activate Gcn2, and we probe the mechanism by which this activation occurs. Low concentrations of Gcn2iB increase Gcn2 phosphorylation of eIF2 and enhance Atf4 expression and activity. Of importance, Gcn2iB can activate Gcn2 mutants devoid of functional regulatory domains or with certain kinase domain substitutions derived from Gcn2-deficient human patients. Other ATP-competitive inhibitors can also activate Gcn2, although there are differences in their mechanisms of activation. These results provide a cautionary note about the pharmacodynamics of eIF2 kinase inhibitors in therapeutic applications. Compounds designed to be kinase inhibitors that instead directly activate Gcn2, even loss of function variants, may provide tools to alleviate deficiencies in Gcn2 and other regulators of the ISR.
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Affiliation(s)
- Kenneth R Carlson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Millie M Georgiadis
- 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
| | | | - 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
| | - 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.
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11
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Stern AD, Smith GR, Santos LC, Sarmah D, Zhang X, Lu X, Iuricich F, Pandey G, Iyengar R, Birtwistle MR. Relating individual cell division events to single-cell ERK and Akt activity time courses. Sci Rep 2022; 12:18077. [PMID: 36302844 PMCID: PMC9613772 DOI: 10.1038/s41598-022-23071-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/25/2022] [Indexed: 02/01/2023] Open
Abstract
Biochemical correlates of stochastic single-cell fates have been elusive, even for the well-studied mammalian cell cycle. We monitored single-cell dynamics of the ERK and Akt pathways, critical cell cycle progression hubs and anti-cancer drug targets, and paired them to division events in the same single cells using the non-transformed MCF10A epithelial line. Following growth factor treatment, in cells that divide both ERK and Akt activities are significantly higher within the S-G2 time window (~ 8.5-40 h). Such differences were much smaller in the pre-S-phase, restriction point window which is traditionally associated with ERK and Akt activity dependence, suggesting unappreciated roles for ERK and Akt in S through G2. Simple metrics of central tendency in this time window are associated with subsequent cell division fates. ERK activity was more strongly associated with division fates than Akt activity, suggesting Akt activity dynamics may contribute less to the decision driving cell division in this context. We also find that ERK and Akt activities are less correlated with each other in cells that divide. Network reconstruction experiments demonstrated that this correlation behavior was likely not due to crosstalk, as ERK and Akt do not interact in this context, in contrast to other transformed cell types. Overall, our findings support roles for ERK and Akt activity throughout the cell cycle as opposed to just before the restriction point, and suggest ERK activity dynamics may be more important than Akt activity dynamics for driving cell division in this non-transformed context.
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Affiliation(s)
- Alan D Stern
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luis C Santos
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deepraj Sarmah
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Xiang Zhang
- School of Computing, Clemson University, Clemson, SC, USA
| | - Xiaoming Lu
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | | | - Gaurav Pandey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc R Birtwistle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
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12
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El-Megiri N, Mostafa YM, Ahmed A, Mehanna ET, El-Azab MF, Alshehri F, Alahdal H, El-Sayed NM. Pioglitazone Ameliorates Hippocampal Neurodegeneration, Disturbances in Glucose Metabolism and AKT/mTOR Signaling Pathways in Pentyelenetetrazole-Kindled Mice. Pharmaceuticals (Basel) 2022; 15:ph15091113. [PMID: 36145334 PMCID: PMC9506442 DOI: 10.3390/ph15091113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Disturbance of glucose metabolism, nerve growth factor (NGF) and m-TOR signaling have been associated with the pathophysiology of epilepsy. Pioglitazone (PGZ) is an anti-diabetic drug that shows a protective effect in neurodegenerative diseases including epilepsy; however, its exact mechanism is not fully elucidated. The present study aimed to investigate the potential neuroprotective effect of PGZ in pentylenetetrazole (PTZ) kindled seizure in mice. Swiss male albino mice were randomly distributed into four groups, each having six mice. Group 1 was considered the control. Epilepsy was induced by PTZ (35 mg/kg i.p.) thrice a week for a total of 15 injections in all other groups. Group 2 was considered the untreated PTZ group while Group 3 and Group 4 were treated by PGZ prior to PTZ injection at two dose levels (5 and 10 mg/kg p.o., respectively). Seizure activity was evaluated after each PTZ injection according to the Fischer and Kittner scoring system. At the end of the experiment, animals were sacrificed under deep anesthesia and the hippocampus was isolated for analysis of glucose transporters by RT-PCR, nerve growth factor (NGF) by ELISA and mTOR by western blotting, in addition to histopathological investigation. The PTZ-treated group showed a significant rise in seizure score, NGF and m-TOR hyperactivation, along with histological abnormalities compared to the control group. Treatment with PGZ demonstrated a significant decrease in NGF, seizure score, m-TOR, GLUT-1 and GLUT-3 in comparison to the PTZ group. In addition, improvement of histological features was observed in both PGZ treated groups. These findings suggest that PGZ provides its neuroprotective effect through modulating m-TOR signaling, glucose metabolism and NGF levels.
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Affiliation(s)
- Nada El-Megiri
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Yasser M. Mostafa
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Badr University, Badr 11829, Egypt
| | - Amal Ahmed
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Eman T. Mehanna
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (E.T.M.); (N.M.E.-S.)
| | - Mona F. El-Azab
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Fatma Alshehri
- Department of Biology, College of Sciences, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Hadil Alahdal
- Department of Biology, College of Sciences, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Norhan M. El-Sayed
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (E.T.M.); (N.M.E.-S.)
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13
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Farooq Z, Kusuma F, Burke P, Dufour CR, Lee D, Tabatabaei N, Toboz P, Radovani E, Greenblatt J, Rehman J, Class J, Khoutorsky A, Fonseca BD, Richner JM, Mercier E, Bourque G, Giguère V, Subramaniam AR, Han J, Tahmasebi S. The amino acid sensor GCN2 suppresses Terminal Oligopyrimidine (TOP) mRNA translation via La-related Protein 1 (LARP1). J Biol Chem 2022; 298:102277. [PMID: 35863436 PMCID: PMC9396407 DOI: 10.1016/j.jbc.2022.102277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
La-related protein 1 (LARP1) has been identified as a key translational inhibitor of terminal oligopyrimidine (TOP) mRNAs downstream of the nutrient sensing protein kinase complex, mTORC1. LARP1 exerts this inhibitory effect on TOP mRNA translation by binding to the mRNA cap and the adjacent 5′TOP motif, resulting in the displacement of the cap-binding protein eIF4E from TOP mRNAs. However, the involvement of additional signaling pathway in regulating LARP1-mediated inhibition of TOP mRNA translation is largely unexplored. In the present study, we identify a second nutrient sensing kinase GCN2 that converges on LARP1 to control TOP mRNA translation. Using chromatin-immunoprecipitation followed by massive parallel sequencing (ChIP-seq) analysis of activating transcription factor 4 (ATF4), an effector of GCN2 in nutrient stress conditions, in WT and GCN2 KO mouse embryonic fibroblasts, we determined that LARP1 is a GCN2-dependent transcriptional target of ATF4. Moreover, we identified GCN1, a GCN2 activator, participates in a complex with LARP1 on stalled ribosomes, suggesting a role for GCN1 in LARP1-mediated translation inhibition in response to ribosome stalling. Therefore, our data suggest that the GCN2 pathway controls LARP1 activity via two mechanisms: ATF4-dependent transcriptional induction of LARP1 mRNA and GCN1-mediated recruitment of LARP1 to stalled ribosomes.
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Affiliation(s)
- Zeenat Farooq
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Fedho Kusuma
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Phillip Burke
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Catherine R Dufour
- Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Duckgue Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Phoenix Toboz
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Jacob Class
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Arkady Khoutorsky
- Department of Anesthesia and Faculty of Dentistry, McGill University, Montreal, QC H3A 0G1, Canada
| | | | - Justin M Richner
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Eloi Mercier
- Canadian Centre for Computational Genomics, and McGill University and Genome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, and McGill University and Genome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Vincent Giguère
- Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jaeseok Han
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea.
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA.
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14
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Flores ME, McNamara-Bordewick NK, Lovinger NL, Snow JW. Halofuginone triggers a transcriptional program centered on ribosome biogenesis and function in honey bees. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 139:103667. [PMID: 34626768 DOI: 10.1016/j.ibmb.2021.103667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/19/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
We previously found that pharmacological inhibition of prolyl-tRNA synthetase by halofuginone has potent activity against Nosema ceranae, an important pathogen of honey bees. However, we also observed that prolyl-tRNA synthetase inhibition is toxic to bees, suggesting further work is necessary to make this a feasible therapeutic strategy. As expected, we found that pharmacological inhibition of prolyl-tRNA synthetase activity resulted in robust induction of select canonical ATF4 target genes in honey bees. However, our understanding of this and other cellular stress responses in general in honey bees is incomplete. Thus, we used RNAseq to identify novel changes in gene expression after halofuginone treatment and observed induction of genes involved in ribosome biogenesis, translation, tRNA synthesis, and ribosome-associated quality control (RQC). These results suggest that halofuginone, potentially acting through the Integrated Stress Response (ISR), promotes a transcriptional response to ribosome functional impairment in honey bees rather than the response designed to oppose amino acid limitation, which has been observed in other organisms after ISR induction. In support of this idea, we found that cycloheximide (CHX) administration also induced all tested target genes, indicating that this gene expression program could be induced by ribosome stalling in addition to tRNA synthetase inhibition. Only a subset of halofuginone-induced genes was upregulated by Unfolded Protein Response (UPR) induction, suggesting that mode of activation and cross-talk with other cellular signaling pathways significantly influence ISR function and cellular response to its activation. Future work will focus on understanding how the apparently divergent transcriptional output of the ISR in honey bees impacts the health and disease of this important pollinator species.
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Affiliation(s)
| | | | | | - Jonathan W Snow
- Biology Department, Barnard College, New York, NY, 10027, USA.
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15
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Perzanowska O, Majewski M, Strenkowska M, Głowala P, Czarnocki-Cieciura M, Mazur M, Kowalska J, Jemielity J. Nucleotide-decorated AuNPs as probes for nucleotide-binding proteins. Sci Rep 2021; 11:15741. [PMID: 34344911 PMCID: PMC8333360 DOI: 10.1038/s41598-021-94983-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/12/2021] [Indexed: 12/01/2022] Open
Abstract
Gold nanoparticles (AuNPs) decorated with biologically relevant molecules have variety of applications in optical sensing of bioanalytes. Coating AuNPs with small nucleotides produces particles with high stability in water, but functionality-compatible strategies are needed to uncover the full potential of this type of conjugates. Here, we demonstrate that lipoic acid-modified dinucleotides can be used to modify AuNPs surfaces in a controllable manner to produce conjugates that are stable in aqueous buffers and biological mixtures and capable of interacting with nucleotide-binding proteins. Using this strategy we obtained AuNPs decorated with 7-methylguanosine mRNA 5' cap analogs and showed that they bind cap-specific protein, eIF4E. AuNPs decorated with non-functional dinucleotides also interacted with eIF4E, albeit with lower affinity, suggesting that eIF4E binding to cap-decorated AuNPs is partially mediated by unspecific ionic interactions. This issue was overcome by applying lipoic-acid-Tris conjugate as a charge-neutral diluting molecule. Tris-Lipo-diluted cap-AuNPs conjugates interacted with eIF4E in fully specific manner, enabling design of functional tools. To demonstrate the potential of these conjugates in protein sensing, we designed a two-component eIF4E sensing system consisting of cap-AuNP and 4E-BP1-AuNP conjugates, wherein 4E-BP1 is a short peptide derived from 4E-BP protein that specifically binds eIF4E at a site different to that of the 5' cap. This system facilitated controlled aggregation, in which eIF4E plays the role of the agent that crosslinks two types of AuNP, thereby inducing a naked-eye visible absorbance redshift. The reported AuNPs-nucleotide conjugation method based on lipoic acid affinity for gold, can be harnessed to obtain other types of nucleotide-functionalized AuNPs, thereby paving the way to studying other nucleotide-binding proteins.
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Affiliation(s)
- Olga Perzanowska
- Division of Biophysics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097, Warsaw, Poland
| | - Maciej Majewski
- Division of Biophysics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093, Warsaw, Poland
| | - Malwina Strenkowska
- Division of Biophysics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093, Warsaw, Poland
| | - Paulina Głowala
- Faculty of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland
| | - Mariusz Czarnocki-Cieciura
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland
| | - Maciej Mazur
- Faculty of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093, Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097, Warsaw, Poland.
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16
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Dmitriev SE, Vladimirov DO, Lashkevich KA. A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis. BIOCHEMISTRY (MOSCOW) 2021; 85:1389-1421. [PMID: 33280581 PMCID: PMC7689648 DOI: 10.1134/s0006297920110097] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic ribosome and cap-dependent translation are attractive targets in the antitumor, antiviral, anti-inflammatory, and antiparasitic therapies. Currently, a broad array of small-molecule drugs is known that specifically inhibit protein synthesis in eukaryotic cells. Many of them are well-studied ribosome-targeting antibiotics that block translocation, the peptidyl transferase center or the polypeptide exit tunnel, modulate the binding of translation machinery components to the ribosome, and induce miscoding, premature termination or stop codon readthrough. Such inhibitors are widely used as anticancer, anthelmintic and antifungal agents in medicine, as well as fungicides in agriculture. Chemicals that affect the accuracy of stop codon recognition are promising drugs for the nonsense suppression therapy of hereditary diseases and restoration of tumor suppressor function in cancer cells. Other compounds inhibit aminoacyl-tRNA synthetases, translation factors, and components of translation-associated signaling pathways, including mTOR kinase. Some of them have antidepressant, immunosuppressive and geroprotective properties. Translation inhibitors are also used in research for gene expression analysis by ribosome profiling, as well as in cell culture techniques. In this article, we review well-studied and less known inhibitors of eukaryotic protein synthesis (with the exception of mitochondrial and plastid translation) classified by their targets and briefly describe the action mechanisms of these compounds. We also present a continuously updated database (http://eupsic.belozersky.msu.ru/) that currently contains information on 370 inhibitors of eukaryotic protein synthesis.
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Affiliation(s)
- S E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - D O Vladimirov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - K A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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17
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Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. Nat Methods 2021; 18:507-519. [PMID: 33963355 PMCID: PMC8148648 DOI: 10.1038/s41592-021-01128-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/26/2021] [Indexed: 02/03/2023]
Abstract
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP-RNA interactions. STAMP does not rely on ultraviolet cross-linking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP-specific and cell-type-specific RNA-protein interactions for multiple RBPs and cell types in single, pooled experiments. Pairing STAMP with long-read sequencing yields RBP target sites in an isoform-specific manner. Finally, Ribo-STAMP leverages small ribosomal subunits to measure transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP-RNA interactomes and translational landscapes with unprecedented cellular resolution.
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18
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Build-UPS and break-downs: metabolism impacts on proteostasis and aging. Cell Death Differ 2021; 28:505-521. [PMID: 33398091 PMCID: PMC7862225 DOI: 10.1038/s41418-020-00682-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/30/2022] Open
Abstract
Perturbation of metabolism elicits cellular stress which profoundly modulates the cellular proteome and thus protein homeostasis (proteostasis). Consequently, changes in the cellular proteome due to metabolic shift require adaptive mechanisms by molecular protein quality control. The mechanisms vitally controlling proteostasis embrace the entire life cycle of a protein involving translational control at the ribosome, chaperone-assisted native folding, and subcellular sorting as well as proteolysis by the proteasome or autophagy. While metabolic imbalance and proteostasis decline have been recognized as hallmarks of aging and age-associated diseases, both processes are largely considered independently. Here, we delineate how proteome stability is governed by insulin/IGF1 signaling (IIS), mechanistic target of Rapamycin (TOR), 5′ adenosine monophosphate-activated protein kinase (AMPK), and NAD-dependent deacetylases (Sir2-like proteins known as sirtuins). This comprehensive overview is emphasizing the regulatory interconnection between central metabolic pathways and proteostasis, indicating the relevance of shared signaling nodes as targets for future therapeutic interventions. ![]()
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19
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Mateju D, Eichenberger B, Voigt F, Eglinger J, Roth G, Chao JA. Single-Molecule Imaging Reveals Translation of mRNAs Localized to Stress Granules. Cell 2020; 183:1801-1812.e13. [PMID: 33308477 DOI: 10.1016/j.cell.2020.11.010] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/14/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022]
Abstract
Cellular stress leads to reprogramming of mRNA translation and formation of stress granules (SGs), membraneless organelles consisting of mRNA and RNA-binding proteins. Although the function of SGs remains largely unknown, it is widely assumed they contain exclusively non-translating mRNA. Here, we re-examine this hypothesis using single-molecule imaging of mRNA translation in living cells. Although we observe non-translating mRNAs are preferentially recruited to SGs, we find unequivocal evidence that mRNAs localized to SGs can undergo translation. Our data indicate that SG-associated translation is not rare, and the entire translation cycle (initiation, elongation, and termination) can occur on SG-localized transcripts. Furthermore, translating mRNAs can be observed transitioning between the cytosol and SGs without changing their translational status. Together, these results demonstrate that mRNA localization to SGs is compatible with translation and argue against a direct role for SGs in inhibition of protein synthesis.
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Affiliation(s)
- Daniel Mateju
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Bastian Eichenberger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jan Eglinger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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20
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TOP mRNPs: Molecular Mechanisms and Principles of Regulation. Biomolecules 2020; 10:biom10070969. [PMID: 32605040 PMCID: PMC7407576 DOI: 10.3390/biom10070969] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
The cellular response to changes in the surrounding environment and to stress requires the coregulation of gene networks aiming to conserve energy and resources. This is often achieved by downregulating protein synthesis. The 5’ Terminal OligoPyrimidine (5’ TOP) motif-containing mRNAs, which encode proteins that are essential for protein synthesis, are the primary targets of translational control under stress. The TOP motif is a cis-regulatory RNA element that begins directly after the m7G cap structure and contains the hallmark invariant 5’-cytidine followed by an uninterrupted tract of 4–15 pyrimidines. Regulation of translation via the TOP motif coordinates global protein synthesis with simultaneous co-expression of the protein components required for ribosome biogenesis. In this review, we discuss architecture of TOP mRNA-containing ribonucleoprotein complexes, the principles of their assembly, and the modes of regulation of TOP mRNA translation.
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21
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Multifaceted deregulation of gene expression and protein synthesis with age. Proc Natl Acad Sci U S A 2020; 117:15581-15590. [PMID: 32576685 DOI: 10.1073/pnas.2001788117] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis represents a major metabolic activity of the cell. However, how it is affected by aging and how this in turn impacts cell function remains largely unexplored. To address this question, herein we characterized age-related changes in both the transcriptome and translatome of mouse tissues over the entire life span. We showed that the transcriptome changes govern those in the translatome and are associated with altered expression of genes involved in inflammation, extracellular matrix, and lipid metabolism. We also identified genes that may serve as candidate biomarkers of aging. At the translational level, we uncovered sustained down-regulation of a set of 5'-terminal oligopyrimidine (5'-TOP) transcripts encoding protein synthesis and ribosome biogenesis machinery and regulated by the mTOR pathway. For many of them, ribosome occupancy dropped twofold or even more. Moreover, with age, ribosome coverage gradually decreased in the vicinity of start codons and increased near stop codons, revealing complex age-related changes in the translation process. Taken together, our results reveal systematic and multidimensional deregulation of protein synthesis, showing how this major cellular process declines with age.
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22
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Aliouat A, Hatin I, Bertin P, François P, Stierlé V, Namy O, Salhi S, Jean-Jean O. Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes. RNA Biol 2019; 17:227-239. [PMID: 31619139 PMCID: PMC6973328 DOI: 10.1080/15476286.2019.1674595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5ʹ leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.
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Affiliation(s)
- Affaf Aliouat
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pierre Bertin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pauline François
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Vérène Stierlé
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Samia Salhi
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
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23
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An H, Harper JW. Ribosome Abundance Control Via the Ubiquitin-Proteasome System and Autophagy. J Mol Biol 2019; 432:170-184. [PMID: 31195016 DOI: 10.1016/j.jmb.2019.06.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/13/2022]
Abstract
Ribosomes are central to the life of a cell, as they translate the genetic code into the amino acid language of proteins. Moreover, ribosomal abundance within the cell is coordinated with protein production required for cell function or processes such as cell division. As such, it is not surprising that these elegant machines are both highly regulated at the level of both their output of newly translated proteins but also at the level of ribosomal protein expression, ribosome assembly, and ribosome turnover. In this review, we focus on mechanisms that regulate ribosome abundance through both the ubiquitin-proteasome system and forms of autophagy referred to as "ribophagy." We discussed mechanisms employed in both yeast and mammalian cells, including the various machineries that are important for recognition and degradation of ribosomal components. In addition, we discussed controversies in the field and how the development of new approaches for examining flux through the proteasomal and autophagic systems in the context of a systematic inventory of ribosomal components is necessary to fully understand how ribosome abundance is controlled under various physiological conditions.
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Affiliation(s)
- Heeseon An
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
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24
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Zhang S, Macias-Garcia A, Ulirsch JC, Velazquez J, Butty VL, Levine SS, Sankaran VG, Chen JJ. HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis. eLife 2019; 8:46976. [PMID: 31033440 PMCID: PMC6533081 DOI: 10.7554/elife.46976] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/26/2019] [Indexed: 12/05/2022] Open
Abstract
Iron and heme play central roles in the production of red blood cells, but the underlying mechanisms remain incompletely understood. Heme-regulated eIF2α kinase (HRI) controls translation by phosphorylating eIF2α. Here, we investigate the global impact of iron, heme, and HRI on protein translation in vivo in murine primary erythroblasts using ribosome profiling. We validate the known role of HRI-mediated translational stimulation of integratedstressresponse mRNAs during iron deficiency in vivo. Moreover, we find that the translation of mRNAs encoding cytosolic and mitochondrial ribosomal proteins is substantially repressed by HRI during iron deficiency, causing a decrease in cytosolic and mitochondrial protein synthesis. The absence of HRI during iron deficiency elicits a prominent cytoplasmic unfolded protein response and impairs mitochondrial respiration. Importantly, ATF4 target genes are activated during iron deficiency to maintain mitochondrial function and to enable erythroid differentiation. We further identify GRB10 as a previously unappreciated regulator of terminal erythropoiesis. Red blood cells use a molecule called hemoglobin to transport oxygen around the body. To make hemoglobin, cells require iron to build a component called heme. If an individual does not get enough iron in their diet, the body cannot produce enough red blood cells, or the cells lack hemoglobin. This condition is known as iron deficiency anemia, and it affects around one-third of the world’s population. Researchers did not know exactly how iron levels control red blood cell production, though several proteins had been identified to play important roles. Heme forms in the cell's mitochondria: the compartments in the cell that supply it with energy. When heme levels in a developing red blood cell are low, a protein called HRI reduces the production of many proteins, most importantly the proteins that make up hemoglobin. HRI also boosts the production of a protein called ATF4, which switches on a set of genes that help both the cell and its mitochondria to adapt to the lack of heme. In turn, HRI and ATF4 reduce the activity of a signaling pathway called mTORC1, which controls the production of proteins that help cells to grow and divide. To understand in more detail how iron and heme regulate the production of new red blood cells, Zhang et al. looked at immature red blood cells from the livers of developing mice. Some of the mice lacked the gene that produces HRI, and some experienced iron deficiency. Comparing gene activity in the different mice revealed that in the developing blood cells of iron-deficient mice, HRI largely reduces the rate of protein production in both the mitochondria and the wider cell. At the same time, the increased activity of ATF4 allows the mitochondria to carry on releasing energy and the cells to continue developing. Zhang et al. also found that a protein that inhibits the mTORC1 signaling pathway needs to be active for the new red blood cells to mature. Overall, the results suggest that drugs that activate HRI or block the activity of the mTORC1 pathway could help to treat anemia. The next step is to test the effects that such drugs have in anemic mice and cells from anemic people.
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Affiliation(s)
- Shuping Zhang
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Alejandra Macias-Garcia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, United States.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, United States
| | - Jason Velazquez
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Vincent L Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, United States
| | - Jane-Jane Chen
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
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25
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Li BB, Qian C, Roberts TM, Zhao JJ. Targeted Profiling of RNA Translation. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 125:e71. [PMID: 30346115 PMCID: PMC6326074 DOI: 10.1002/cpmb.71] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This unit describes a reverse transcription-quantitative PCR (RT-qPCR)-based method for gene-targeted measurement of RNA translation levels. The method includes washing and lysing cells with a buffer containing cycloheximide to enrich ribosomal accumulation at translation initiation sites (TIS), followed by enzymatic treatment to generate ribosomal footprints, reverse transcription targeted towards TIS of specific transcripts of interest to generate complementary DNA (cDNA), and qPCR to measure the abundance of these footprints. This method enables time- and cost-effective assessment of changes in translation levels across focused panels of genes and across numerous samples. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ben B Li
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Changli Qian
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Thomas M Roberts
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Jean J Zhao
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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