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Ji D, Hu C, Ning J, Ying X, Zhang H, Zhang B, Liu B, Liu Q, Ji W, Zhang R. N 6-methyladenosine mediates Nrf2 protein expression involved in PM2.5-induced pulmonary fibrosis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114755. [PMID: 36917877 DOI: 10.1016/j.ecoenv.2023.114755] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/10/2022] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
It has been reported that particulate matter with an aerodynamic diameter of <2.5 µm (PM2.5) could induce epithelial-mesenchymal transition (EMT)- and extracellular matrix (ECM)-related pulmonary fibrosis (PF). The transcription factor Nrf2 alleviated PM2.5-induced PF by antagonizing oxidative stress. The N6-methyladenosine (m6A) modification plays a significant role in the stress response. However, the effect of m6A modification on the mechanisms of Nrf2-mediated defense against PM2.5-induced PF remained unknown. Here, we explored the role and the underlying molecular mechanisms of m6A methylation of Nrf2 mRNA in PM2.5-induced PF. We established filtered air (FA), unfiltered air (UA), and concentrated PM2.5 air (CA) group mice model and 0, 50, and 100 μg/mL PM2.5-treated 16HBE cell models. The extent of lung fibrosis in mice and fibrosis indicators were detected by histopathological analysis, immunohistochemical staining and western blotting. The molecular mechanism of m6A-modified Nrf2 was demonstrated by m6A-methylated RNA immunoprecipitation (MeRIP), RNA immunoprecipitation (RIP), qRT-PCR and T3 ligase-based PCR. Our data showed that PM2.5 exposure for 16 weeks could induce pulmonary fibrosis and activate Nrf2 signaling pathway. m6A methyltransferase METTL3 was upregulated after PM2.5 treatment in vivo and in vitro. Moreover, METTL3 mediated m6A modification of Nrf2 mRNA and promoted Nrf2 translation in mice and 16HBE cells after PM2.5 exposure. Mechanistically, three m6A-modified sites (1317, 1376 and 935; numbered relative to the first nucleotide of 3'UTR) of Nrf2 mRNA were identified in PM2.5-treatment 16HBE cells. Furthermore, the m6A binding proteins YTHDF1/IGF2BP1 promoted Nrf2 translation by binding to m6A residues of Nrf2 mRNA. Our results revealed the mechanism of m6A mediated Nrf2 signaling pathway against oxidative stress, which affected the development of PM2.5-induced PF.
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Affiliation(s)
- Ding Ji
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang 050017, PR China; Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Chenxi Hu
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang 050017, PR China; Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Jie Ning
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Xiaoling Ying
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Haiqing Zhang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Bohan Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Bixia Liu
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Qingping Liu
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Weidong Ji
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China.
| | - Rong Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang 050017, PR China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang 050017, PR China.
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2
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Regulation of Metastasis in Ewing Sarcoma. Cancers (Basel) 2022; 14:cancers14194902. [PMID: 36230825 PMCID: PMC9563756 DOI: 10.3390/cancers14194902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Ewing sarcoma (EwS) is a type of bone and soft tissue tumor in children and adolescents. Over 85% of cases are caused by the expression of fusion protein EWSR1-FLI1 generated by chromosome translocation. Acting as a potent chimeric oncoprotein, EWSR1-FLI1 binds to chromatin, changes the epigenetic states, and thus alters the expression of a large set of genes. Several studies have revealed that the expression level of EWSR1-FLI1 is variable and dynamic within and across different EwS cell lines and primary tumors, leading to tumoral heterogeneity. Cells with high EWSR1-FLI1 expression (EWSR1-FLI1-high) proliferate in an exponential manner, whereas cells with low EWSR1-FLI1 expression (EWSR1-FLI1-low) tend to have a strong propensity to migrate, invade, and metastasize. Metastasis is the leading cause of cancer-related deaths. The continuous evolution of EwS research has revealed some of the molecular underpinnings of this dissemination process. In this review, we discuss the molecular signatures that contribute to metastasis.
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3
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Hamon L, Budkina K, Pastré D. YB-1 Structure/Function Relationship in the Packaging of mRNPs and Consequences for Translation Regulation and Stress Granule Assembly in Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S20-S93. [PMID: 35501984 DOI: 10.1134/s0006297922140036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
From their synthesis in the nucleus to their degradation in the cytoplasm, all mRNAs have the same objective, which is to translate the DNA-stored genetic information into functional proteins at the proper time and location. To this end, many proteins are generally associated with mRNAs as soon as transcription takes place in the nucleus to organize spatiotemporal regulation of the gene expression in cells. Here we reviewed how YB-1 (YBX1 gene), one of the major mRNA-binding proteins in the cytoplasm, packaged mRNAs into either compact or extended linear nucleoprotein mRNPs. Interestingly the structural plasticity of mRNPs coordinated by YB-1 could provide means for the contextual regulation of mRNA translation. Posttranslational modification of YB-1, notably in the long unstructured YB-1 C-terminal domain (CTD), and/or the protein partners of YB-1 may play a key role in activation/inactivation of mRNPs in the cells notably in response to cellular stress.
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Affiliation(s)
- Loïc Hamon
- SABNP, UnivEvry, INSERM U1204, Université Paris-Saclay, Evry, 91025, France.
| | - Karina Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - David Pastré
- SABNP, UnivEvry, INSERM U1204, Université Paris-Saclay, Evry, 91025, France.
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4
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Somasekharan SP, Saxena N, Zhang F, Beraldi E, Huang J, Gentle C, Fazli L, Thi M, Sorensen P, Gleave M. Regulation of AR mRNA translation in response to acute AR pathway inhibition. Nucleic Acids Res 2021; 50:1069-1091. [PMID: 34939643 PMCID: PMC8789049 DOI: 10.1093/nar/gkab1247] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
We report a new mechanism of androgen receptor (AR) mRNA regulation and cytoprotection in response to AR pathway inhibition (ARPI) stress in prostate cancer (PCA). AR mRNA translation is coordinately regulated by RNA binding proteins, YTHDF3 and G3BP1. Under ambient conditions m6A-modified AR mRNA is bound by YTHDF3 and translationally stimulated, while m6A-unmodified AR mRNA is bound by G3BP1 and translationally repressed. When AR-regulated PCA cell lines are subjected to ARPI stress, m6A-modified AR mRNA is recruited from actively translating polysomes (PSs) to RNA-protein stress granules (SGs), leading to reduced AR mRNA translation. After ARPI stress, m6A-modified AR mRNA liquid–liquid phase separated with YTHDF3, while m6A-unmodified AR mRNA phase separated with G3BP1. Accordingly, these AR mRNA messages form two distinct YTHDF3-enriched or G3BP1-enriched clusters in SGs. ARPI-induced SG formation is cell-protective, which when blocked by YTHDF3 or G3BP1 silencing increases PCA cell death in response to ARPI stress. Interestingly, AR mRNA silencing also delays ARPI stress-induced SG formation, highlighting its supportive role in triggering this stress response. Our results define a new mechanism for stress adaptive cell survival after ARPI stress involving SG-regulated translation of AR mRNA, mediated by m6A RNA modification and their respective regulatory proteins.
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Affiliation(s)
- Syam Prakash Somasekharan
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Neetu Saxena
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Fan Zhang
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Eliana Beraldi
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Jia Ni Huang
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Christina Gentle
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Ladan Fazli
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Marisa Thi
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Poul H Sorensen
- British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, British Columbia, Canada and Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
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Ying X, Liu B, Yuan Z, Huang Y, Chen C, Jiang X, Zhang H, Qi D, Yang S, Lin S, Luo J, Ji W. METTL1-m 7 G-EGFR/EFEMP1 axis promotes the bladder cancer development. Clin Transl Med 2021; 11:e675. [PMID: 34936728 PMCID: PMC8694502 DOI: 10.1002/ctm2.675] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The posttranscriptional modifications of transfer RNA (tRNA) are critical for all aspects of the tRNA function and have been implicated in the tumourigenesis and progression of many human cancers. By contrast, the biological functions of methyltransferase-like 1 (METTL1)-regulated m7 G tRNA modification in bladder cancer (BC) remain obscure. RESULTS In this research, we show that METTL1 was highly expressed in BC, and its level was correlated with poor patient prognosis. Silencing METTL1 suppresses the proliferation, migration and invasion of BC cells in vitro and in vivo. Multi-omics analysis reveals that METTL1-mediated m7 G tRNA modification altered expression of certain target genes, including EGFR/EFEMP1. Mechanistically, METTL1 regulates the translation of EGFR/EFEMP1 via modifying certain tRNAs. Furthermore, forced expression of EGFR/EFEMP1 partially rescues the effect of METTL1 deletion on BC cells. CONCLUSIONS Our findings demonstrate the oncogenic role of METTL1 and the pathological significance of the METTL1-m7 G-EGFR/EFEMP1 axis in the BC development, thus providing potential therapeutic targets for the BC treatment.
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Affiliation(s)
- Xiaoling Ying
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
- Department of UrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Bixia Liu
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Zusen Yuan
- Department of UrologyMinimally Invasive Surgery centerGuangdong Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510230China
| | - Yapeng Huang
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
- Department of UrologyMinimally Invasive Surgery centerGuangdong Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510230China
| | - Cong Chen
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Xu Jiang
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Haiqing Zhang
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Defeng Qi
- Department of UrologyMinimally Invasive Surgery centerGuangdong Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510230China
| | - Shulan Yang
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Shuibin Lin
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Junhang Luo
- Department of UrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Weidong Ji
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
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Somasekharan SP, Gleave M. SARS-CoV-2 nucleocapsid protein interacts with immunoregulators and stress granules and phase separates to form liquid droplets. FEBS Lett 2021; 595:2872-2896. [PMID: 34780058 PMCID: PMC8652540 DOI: 10.1002/1873-3468.14229] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 12/16/2022]
Abstract
The current work investigated SARS‐CoV‐2 Nucleocapsid (NCAP or N protein) interactors in A549 human lung cancer cells using a SILAC‐based mass spectrometry approach. NCAP interactors included proteins of the stress granule (SG) machinery and immunoregulators. NCAP showed specific interaction with the SG proteins G3BP1, G3BP2, YTHDF3, USP10 and PKR, and translocated to SGs following oxidative stress and heat shock. Treatment of recombinant NCAP with RNA isolated from A549 cells exposed to oxidative stress‐stimulated NCAP to undergo liquid–liquid phase separation (LLPS). RNA degradation using RNase A treatment completely blocked the LLPS property of NCAP as well as its SG association. The RNA intercalator mitoxantrone also disrupted NCAP assembly in vitro and in cells. This study provides insight into the biological processes and biophysical properties of the SARS‐CoV‐2 NCAP.
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Affiliation(s)
- Syam Prakash Somasekharan
- Department of Urologic Sciences, Faculty of Medicine, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Martin Gleave
- Department of Urologic Sciences, Faculty of Medicine, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
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7
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SILAC-based quantitative MS approach reveals Withaferin A regulated proteins in prostate cancer. J Proteomics 2021; 247:104334. [PMID: 34298187 DOI: 10.1016/j.jprot.2021.104334] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/30/2021] [Accepted: 07/16/2021] [Indexed: 01/06/2023]
Abstract
Withaferin A (WA) is a steroidal lactone extracted from Withania somnifera, commonly known as Ashwagandha. WA has several therapeutic benefits. The current study aims to identify proteins that are potentially regulated by WA in prostate cancer (PCA) cells. We used a SILAC-based proteomic approach to analyze the expression of proteins in response to WA treatment at 4 h and 24 h time points in three PCA cell lines: 22Rv1, DU-145, and LNCaP. Ontology analysis suggested that prolonged treatment with WA upregulated the expression of proteins involved in stress-response pathways. Treatment with WA increased oxidative stress, reduced global mRNA translation, and elevated the expression of cytoprotective stress granule (SG) protein G3BP1. WA treatment also enhanced the formation of SGs. The elevated expression of G3BP1 and the formation of SGs might constitute a mechanism of cytoprotection in PCA cells. Knockdown of G3BP1 blocked SG formation and enhanced the efficacy of WA to reduce PCA cell survival. SIGNIFICANCE: Withaferin A, a steroidal lactone, extracted from Withania somnifera is a promising anti-cancer drug. Using a SILAC-based quantitative proteomic approach, we identified proteins changed by WA-treatment at 4 h and 24 h in three prostate cancer (PCA) cell lines. WA-treatment induced the expression of proteins involved in apoptosis and reduced the expression of proteins involved in cell growth at 4 h. WA-treatment for 24 h enhanced the expression of proteins involved in stress response pathways. WA-treated cells exhibited increased oxidative stress, reduced mRNA translation and enhanced SG formation. PCA is characterized by higher metabolic rate and increased oxidative stress. PCA with a higher stress tolerance can effectively adapt to anti-cancer treatment stress, leading to drug resistance and cellular protection. Enhancing the level of oxidative stress along with inhibition of corresponding cytoprotective stress response pathways is a feasible option to prevent PCA from getting adapted to treatment stress. WA-treatment induced oxidative stress, in combination with blocking SGs by G3BP1 targeting, offers a therapeutic strategy to reduce PCA cell survival.
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8
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Somasekharan SP, Zhang F, Saxena N, Huang JN, Kuo IC, Low C, Bell R, Adomat H, Stoynov N, Foster L, Gleave M, Sorensen PH. G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress. Nucleic Acids Res 2020; 48:6855-6873. [PMID: 32406909 PMCID: PMC7337521 DOI: 10.1093/nar/gkaa376] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 04/20/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022] Open
Abstract
Cells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Sequestration of mRNAs by RNA binding proteins (RBPs) into RNA granules reduces their translation, but it remains unclear whether RBPs also function in partitioning of specific transcripts to polysomes (PSs) to guide selective translation and stress adaptation in cancer. To study transcript partitioning under cell stress, we catalogued mRNAs enriched in prostate carcinoma PC-3 cell PSs, as defined by polysome fractionation and RNA sequencing (RNAseq), and compared them to mRNAs complexed with the known SG-nucleator protein, G3BP1, as defined by spatially-restricted enzymatic tagging and RNAseq. By comparing these compartments before and after short-term arsenite-induced oxidative stress, we identified three major categories of transcripts, namely those that were G3BP1-associated and PS-depleted, G3BP1-dissociated and PS-enriched, and G3BP1-associated but also PS-enriched. Oxidative stress profoundly altered the partitioning of transcripts between these compartments. Under arsenite stress, G3BP1-associated and PS-depleted transcripts correlated with reduced expression of encoded mitochondrial proteins, PS-enriched transcripts that disassociated from G3BP1 encoded cell cycle and cytoprotective proteins whose expression increased, while transcripts that were both G3BP1-associated and PS-enriched encoded proteins involved in diverse stress response pathways. Therefore, G3BP1 guides transcript partitioning to reprogram mRNA translation and support stress adaptation.
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Affiliation(s)
| | - Fan Zhang
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Neetu Saxena
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Jia Ni Huang
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - I-Chih Kuo
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Caitlin Low
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Robert Bell
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Hans Adomat
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Nikolay Stoynov
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard Foster
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | | | - Poul H Sorensen
- Vancouver Prostate Centre, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
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Kosnopfel C, Sinnberg T, Sauer B, Niessner H, Muenchow A, Fehrenbacher B, Schaller M, Mertens PR, Garbe C, Thakur BK, Schittek B. Tumour Progression Stage-Dependent Secretion of YB-1 Stimulates Melanoma Cell Migration and Invasion. Cancers (Basel) 2020; 12:cancers12082328. [PMID: 32824741 PMCID: PMC7464723 DOI: 10.3390/cancers12082328] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/10/2020] [Accepted: 08/16/2020] [Indexed: 12/16/2022] Open
Abstract
Secreted factors play an important role in intercellular communication. Therefore, they are not only indispensable for the regulation of various physiological processes but can also decisively advance the development and progression of tumours. In the context of inflammatory disease, Y-box binding protein 1 (YB-1) is actively secreted and the extracellular protein promotes cell proliferation and migration. In malignant melanoma, intracellular YB-1 expression increases during melanoma progression and represents an unfavourable prognostic marker. Here, we show active secretion of YB-1 from melanoma cells as opposed to benign cells of the skin. Intriguingly, YB-1 secretion correlates with the stage of melanoma progression and depends on a calcium- and ATP-dependent non-classical secretory pathway leading to the occurrence of YB-1 in the extracellular space as a free protein. Along with an elevated YB-1 secretion of melanoma cells in the metastatic growth phase, extracellular YB-1 exerts a stimulating effect on melanoma cell migration, invasion, and tumourigenicity. Collectively, these data suggest that secreted YB-1 plays a functional role in melanoma cell biology, stimulating metastasis, and may serve as a novel biomarker in malignant melanoma that reflects tumour aggressiveness.
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Affiliation(s)
- Corinna Kosnopfel
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
- Department of Dermatology, University Hospital Würzburg, 97080 Würzburg, Germany
- Correspondence: (C.K.); (B.S.); Tel.: +49-931-20126778 (C.K.); +49-7071-29-80832 (B.S.)
| | - Tobias Sinnberg
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
| | - Birgit Sauer
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
| | - Heike Niessner
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
| | - Alina Muenchow
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
| | - Birgit Fehrenbacher
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
| | - Martin Schaller
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
| | - Peter R. Mertens
- Department of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany;
| | - Claus Garbe
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
| | - Basant Kumar Thakur
- Department of Pediatric Hematology and Oncology, University Hospital Essen, 45147 Essen, Germany;
| | - Birgit Schittek
- Department of Dermatology, University of Tübingen, 72076 Tübingen, Germany; (T.S.); (B.S.); (H.N.); (A.M.); (B.F.); (M.S.); (C.G.)
- Correspondence: (C.K.); (B.S.); Tel.: +49-931-20126778 (C.K.); +49-7071-29-80832 (B.S.)
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10
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Lindsey ML, Gundry RL. Secrets of Cardiac Remodeling Revealed in the Secretome. Circulation 2020; 141:1645-1647. [PMID: 32421415 DOI: 10.1161/circulationaha.120.046042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Merry L Lindsey
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha (M.L.L., R.L.G.).,Research Service, Nebraska-Western Iowa Health Care System, Omaha, NE (M.L.L.)
| | - Rebekah L Gundry
- Research Service, Nebraska-Western Iowa Health Care System, Omaha, NE (M.L.L.)
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11
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Niu W, Luo Y, Zhou Y, Li M, Wu C, Duan Y, Wang H, Fan S, Li Z, Xiong W, Li X, Li G, Ren C, Li H, Zhou M. BRD7 suppresses invasion and metastasis in breast cancer by negatively regulating YB1-induced epithelial-mesenchymal transition. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:30. [PMID: 32028981 PMCID: PMC7006413 DOI: 10.1186/s13046-019-1493-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/26/2019] [Indexed: 01/02/2023]
Abstract
Background BRD7 is a tumor suppressor known to inhibit cell proliferation and cell cycle progression and initiate apoptosis in breast cancer. However, the function and underlying molecular events of BRD7 in tumor invasion and metastasis in breast cancer are not fully understood. Methods BRD7 expression was assessed in two stable cell lines MDA231 and MCF7 with BRD7 overexpression and one stable cell line MDA231 with BRD7 interference using qRT-PCR and western blotting. CCK8 assay was used to examine the proliferation ability of MDA231 and MCF7 cells. Scratch wound healing assay was used to evaluate cell migration in MDA231 and MCF7 cells. Both Matrigel and three-dimensional invasion assays were performed to investigate the cell invasion ability after BRD7 overexpression or silencing or YB1 restoration in MDA231 and MCF7 cells. The potential interacting proteins of BRD7 were screened using co-immunoprecipitation combined with mass spectrometry and verified by co-immunoprecipitation in HEK293T cells. Additionally, we confirmed the specific binding region between BRD7 and YB1 in HEK293T cells by constructing a series of deletion mutants of BRD7 and YB1 respectively. Finally, xenograft and metastatic mouse models using MDA231 cells were established to confirm the effect of BRD7 on tumor growth and metastasis. Results Here, the results of a series of assays in vitro indicated that BRD7 has the ability to inhibit the mobility, migration and invasion of breast cancer cells. In addition, YB1 was identified as a novel interacting protein of BRD7, and BRD7 was found to associate with the C-terminus of YB1 via its N-terminus. BRD7 decreases the expression of YB1 through negatively regulating YB1 phosphorylation at Ser102, thereby promoting its proteasomal degradation. Furthermore, gene set enrichment analysis revealed that epithelial-mesenchymal transition (EMT) is the common change occurring with altered expression of either BRD7 or YB1 and that BRD7 represses mesenchymal genes and activates epithelial genes. Moreover, restoring the expression of YB1 antagonized the inhibitory effect of BRD7 on tumorigenicity, EMT, invasiveness and metastasis through a series of in vitro and in vivo experiments. Additionally, BRD7 expression was negatively correlated with the level of YB1 in breast cancer patients. The combination of low BRD7 and high YB1 expression was significantly associated with poor prognosis, distant metastasis and advanced TNM stage. Conclusions Collectively, these findings uncover that BRD7 blocks tumor growth, migration and metastasis by negatively regulating YB1-induced EMT, providing new insights into the mechanism by which BRD7 contributes to the progression and metastasis of breast cancer.
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Affiliation(s)
- Weihong Niu
- The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410013, People's Republic of China.,Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Yanwei Luo
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Yao Zhou
- The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410013, People's Republic of China.,Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Mengna Li
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Chunchun Wu
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Yumei Duan
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Heran Wang
- The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410013, People's Republic of China.,Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Songqing Fan
- The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Zheng Li
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China.,High Resolution Mass Spectrometry Laboratory of Advanced Research Center, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Wei Xiong
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Xiaoling Li
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Guiyuan Li
- The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410013, People's Republic of China.,Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Caiping Ren
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China. .,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China.
| | - Hui Li
- The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China.
| | - Ming Zhou
- The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410013, People's Republic of China. .,Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410078, People's Republic of China. .,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan, 410078, People's Republic of China.
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12
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El‐Naggar AM, Somasekharan SP, Wang Y, Cheng H, Negri GL, Pan M, Wang XQ, Delaidelli A, Rafn B, Cran J, Zhang F, Zhang H, Colborne S, Gleave M, Mandinova A, Kedersha N, Hughes CS, Surdez D, Delattre O, Wang Y, Huntsman DG, Morin GB, Sorensen PH. Class I HDAC inhibitors enhance YB-1 acetylation and oxidative stress to block sarcoma metastasis. EMBO Rep 2019; 20:e48375. [PMID: 31668005 PMCID: PMC6893361 DOI: 10.15252/embr.201948375] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/29/2019] [Accepted: 10/06/2019] [Indexed: 12/13/2022] Open
Abstract
Outcomes for metastatic Ewing sarcoma and osteosarcoma are dismal and have not changed for decades. Oxidative stress attenuates melanoma metastasis, and melanoma cells must reduce oxidative stress to metastasize. We explored this in sarcomas by screening for oxidative stress sensitizers, which identified the class I HDAC inhibitor MS-275 as enhancing vulnerability to reactive oxygen species (ROS) in sarcoma cells. Mechanistically, MS-275 inhibits YB-1 deacetylation, decreasing its binding to 5'-UTRs of NFE2L2 encoding the antioxidant factor NRF2, thereby reducing NFE2L2 translation and synthesis of NRF2 to increase cellular ROS. By global acetylomics, MS-275 promotes rapid acetylation of the YB-1 RNA-binding protein at lysine-81, blocking binding and translational activation of NFE2L2, as well as known YB-1 mRNA targets, HIF1A, and the stress granule nucleator, G3BP1. MS-275 dramatically reduces sarcoma metastasis in vivo, but an MS-275-resistant YB-1K81-to-alanine mutant restores metastatic capacity and NRF2, HIF1α, and G3BP1 synthesis in MS-275-treated mice. These studies describe a novel function for MS-275 through enhanced YB-1 acetylation, thus inhibiting YB-1 translational control of key cytoprotective factors and its pro-metastatic activity.
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Affiliation(s)
- Amal M El‐Naggar
- Department of Pathology & Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
- Department of PathologyFaculty of MedicineMenoufia UniversityShibin El KomEgypt
| | | | - Yemin Wang
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | | | | | - Melvin Pan
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | - Xue Qi Wang
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | - Alberto Delaidelli
- Department of Pathology & Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | - Bo Rafn
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | - Jordan Cran
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | - Fan Zhang
- Vancouver Prostate CentreVancouverBCCanada
| | - Haifeng Zhang
- Department of Pathology & Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | | | | | - Anna Mandinova
- Brigham and Women's HospitalHarvard UniversityBostonMAUSA
| | - Nancy Kedersha
- Massachusetts General HospitalHarvard UniversityBostonMAUSA
| | - Christopher S Hughes
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | | | | | | | - David G Huntsman
- Department of Pathology & Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
| | - Gregg B Morin
- Michael Smith Genome Sciences CentreVancouverBCCanada
| | - Poul H Sorensen
- Department of Pathology & Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Department of Molecular Oncology, BC Cancerpart of the Provincial Health Services AuthorityVancouverBCCanada
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13
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Ma Y, Yates JR. Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications? Expert Rev Proteomics 2018; 15:545-554. [PMID: 30005169 PMCID: PMC6329588 DOI: 10.1080/14789450.2018.1500902] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells. Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs). AHA-NSPs can be coupled to biotin via CuAAC-mediated click-chemistry and enriched using avidin-based affinity purification. Thus, AHA-containing proteins or peptides can be enriched and efficiently separated from the whole proteome. In this review, we describe the development of mass spectrometry (MS) based AHA strategies and discuss their potential to measure proteins involved in immune response, secretome, gut microbiome, and proteostasis as well as their potential for clinical uses. Expert commentary: AHA strategies have been used to identify synthesis activity and to compare two biological conditions in various biological model organisms. In combination with instrument development, improved sample preparation and fractionation strategies, MS-based AHA strategies have the potential for broad application, and the methods should translate into clinical use.
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Affiliation(s)
- Yuanhui Ma
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
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14
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Marciano R, Leprivier G, Rotblat B. Puromycin labeling does not allow protein synthesis to be measured in energy-starved cells. Cell Death Dis 2018; 9:39. [PMID: 29348556 PMCID: PMC5833866 DOI: 10.1038/s41419-017-0056-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Ran Marciano
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Gabriel Leprivier
- Clinic for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Barak Rotblat
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.
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15
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Sekine E, Schmidt N, Gaboriau D, O’Hare P. Spatiotemporal dynamics of HSV genome nuclear entry and compaction state transitions using bioorthogonal chemistry and super-resolution microscopy. PLoS Pathog 2017; 13:e1006721. [PMID: 29121649 PMCID: PMC5697887 DOI: 10.1371/journal.ppat.1006721] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/21/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
We investigated the spatiotemporal dynamics of HSV genome transport during the initiation of infection using viruses containing bioorthogonal traceable precursors incorporated into their genomes (HSVEdC). In vitro assays revealed a structural alteration in the capsid induced upon HSVEdC binding to solid supports that allowed coupling to external capture agents and demonstrated that the vast majority of individual virions contained bioorthogonally-tagged genomes. Using HSVEdC in vivo we reveal novel aspects of the kinetics, localisation, mechanistic entry requirements and morphological transitions of infecting genomes. Uncoating and nuclear import was observed within 30 min, with genomes in a defined compaction state (ca. 3-fold volume increase from capsids). Free cytosolic uncoated genomes were infrequent (7-10% of the total uncoated genomes), likely a consequence of subpopulations of cells receiving high particle numbers. Uncoated nuclear genomes underwent temporal transitions in condensation state and while ICP4 efficiently associated with condensed foci of initial infecting genomes, this relationship switched away from residual longer lived condensed foci to increasingly decondensed genomes as infection progressed. Inhibition of transcription had no effect on nuclear entry but in the absence of transcription, genomes persisted as tightly condensed foci. Ongoing transcription, in the absence of protein synthesis, revealed a distinct spatial clustering of genomes, which we have termed genome congregation, not seen with non-transcribing genomes. Genomes expanded to more decondensed forms in the absence of DNA replication indicating additional transitional steps. During full progression of infection, genomes decondensed further, with a diffuse low intensity signal dissipated within replication compartments, but frequently with tight foci remaining peripherally, representing unreplicated genomes or condensed parental strands of replicated DNA. Uncoating and nuclear entry was independent of proteasome function and resistant to inhibitors of nuclear export. Together with additional data our results reveal new insight into the spatiotemporal dynamics of HSV genome uncoating, transport and organisation.
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Affiliation(s)
- Eiki Sekine
- Section of Virology, Department of Medicine, Imperial College, St Mary’s Medical School, London, United Kingdom
| | - Nora Schmidt
- Section of Virology, Department of Medicine, Imperial College, St Mary’s Medical School, London, United Kingdom
| | - David Gaboriau
- Department of Medicine, Facility for Imaging by Light Microscopy, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Peter O’Hare
- Section of Virology, Department of Medicine, Imperial College, St Mary’s Medical School, London, United Kingdom
- * E-mail:
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16
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Stastna M, Gottlieb RA, Van Eyk JE. Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications. Expert Rev Proteomics 2017; 14:529-543. [PMID: 28532181 DOI: 10.1080/14789450.2017.1333424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation. The methods that identify both regulatory proteins associated with translational components and newly synthesized proteins are discussed. Expert commentary: Emerging proteomic approaches make it possible to monitor protein dynamics in cells, tissues and whole animals. The ability to detect alteration in protein abundance soon after their synthesis enables earlier recognition of disease causing factors and candidates to prevent/rectify disease phenotype.
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Affiliation(s)
- Miroslava Stastna
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,c Institute of Analytical Chemistry of the Czech Academy of Sciences, v. v. i ., Brno , Czech Republic
| | - Roberta A Gottlieb
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer E Van Eyk
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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17
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Kar AN, Vargas JNS, Chen CY, Kowalak JA, Gioio AE, Kaplan BB. Molecular determinants of cytochrome C oxidase IV mRNA axonal trafficking. Mol Cell Neurosci 2017; 80:32-43. [PMID: 28161363 DOI: 10.1016/j.mcn.2017.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 01/10/2017] [Accepted: 01/29/2017] [Indexed: 01/17/2023] Open
Abstract
In previous studies, we identified a putative 38-nucleotide stem-loop structure (zipcode) in the 3' untranslated region of the cytochrome c oxidase subunit IV (COXIV) mRNA that was necessary and sufficient for the axonal localization of the message in primary superior cervical ganglion (SCG) neurons. However, little is known about the proteins that interact with the COXIV-zipcode and regulate the axonal trafficking and local translation of the COXIV message. To identify proteins involved in the axonal transport of the COXIV mRNA, we used the biotinylated 38-nucleotide COXIV RNA zipcode as bait in the affinity purification of COXIV zipcode binding proteins. Gel-shift assays of the biotinylated COXIV zipcode indicated that the putative stem-loop structure functions as a nucleation site for the formation of ribonucleoprotein complexes. Mass spectrometric analysis of the COXIV zipcode ribonucleoprotein complex led to the identification of a large number RNA binding proteins, including fused in sarcoma/translated in liposarcoma (FUS/TLS), and Y-box protein 1 (YB-1). Validation experiments, using western analyses, confirmed the presence of the candidate proteins in the COXIV zipcode affinity purified complexes obtained from SCG axons. Immunohistochemical studies show that FUS, and YB-1 are present in SCG axons. Importantly, RNA immunoprecipitation studies show that FUS, and YB-1 interact with endogenous axonal COXIV transcripts. siRNA-mediated downregulation of the candidate proteins FUS and YB-1 expression in the cell-bodies diminishes the levels of COXIV mRNA in the axon, suggesting functional roles for these proteins in the axonal trafficking of COXIV mRNA.
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Affiliation(s)
- Amar N Kar
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Jose Norberto S Vargas
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Cai-Yun Chen
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey A Kowalak
- NIMH-NINDS Clinical Proteomics Unit, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Anthony E Gioio
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Barry B Kaplan
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
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Gebert J, Schnölzer M, Warnken U, Kopitz J. Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression. Methods Enzymol 2016; 585:295-327. [PMID: 28109436 DOI: 10.1016/bs.mie.2016.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Inactivating mutations in single genes can trigger, prevent, promote, or alleviate diseases. Identifying such disease-related genes is a main pillar of medical research. Since proteins play a crucial role in mediating these effects, their impact on the diseased cells' proteome including posttranslational modifications has to be elucidated for a detailed understanding of the role of these genes in the disease process. In complex disorders, like cancer, several genes contribute to the disease process, thereby hampering the assignment of a proteomic change to the corresponding causative gene. To enable comprehensive screening for the impact of inactivation of a gene, e.g., loss of a tumor suppressor in cancer, on the cellular proteome, we present a strategy based on combination of three technologies that is recombinase-mediated cassette exchange, click chemistry, and mass spectrometry. The methodology is exemplified by the analysis of the proteomic changes induced by the loss of a tumor suppressor gene in colorectal cancer cells. To demonstrate the applicability to screen for posttranslational modification changes, we also describe the analysis of protein glycosylation changes caused by the tumor suppressor inactivation. In principle, this strategy can be applied to analyze the effects of any gene of interest on protein expression as well as posttranslational modification by glycosylation. Moreover adaptation of the strategy to an appropriate cell culture model has the potential for application on a broad range of diseases where the disease-promoting mutations have been identified.
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Affiliation(s)
- J Gebert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - U Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - J Kopitz
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Kariminia A, Ivison SM, Leung VM, Sung S, Couto N, Rozmus J, Rolf N, Narendran A, Dunn SE, Reid GSD, Schultz KR. Y-box-binding protein 1 contributes to IL-7-mediated survival signaling in B-cell precursor acute lymphoblastic leukemia. Oncol Lett 2016; 13:497-505. [PMID: 28123588 DOI: 10.3892/ol.2016.5437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/27/2016] [Indexed: 11/06/2022] Open
Abstract
Y-box-binding protein 1 (YB-1) is a regulatory protein that is associated with drug resistance and relapse in solid tumors. As YB-1 mediates some of its activity through growth factor receptor signaling dysregulation, the present study compared the expression of YB-1 and interleukin 7 (IL-7) receptor α (IL-7Rα) in pediatric B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) and normal BCP cells. The expression levels of IL-7Rα and YB-1 were higher in relapsed vs. diagnostic samples of primary BCP ALL; however, co-expression was also observed in a minor BCP cell population in samples from healthy donors. Functional crosstalk between YB-1 and IL-7R was detected: Overexpression of YB-1 increased surface levels of IL-7R in B cells, and the stimulation of BCP ALL cell lines and primary samples by IL-7 activated YB-1 by phosphorylation at S102 in a phosphatidylinositol 3-kinase-independent and MEK1/2-dependent manner. Targeted knockdown of YB-1 reduced IL-7-mediated protection against rapamycin, and an inhibitor of MEK1/2 potentiated rapamycin-mediated killing in the presence of IL-7. These data establish a novel link between two well-characterized pro-survival factors in acute leukemia, and suggest that YB-1 inhibition may represent a novel therapeutic strategy for increasing sensitivity to chemotherapy in patients with refractory acute B-cell leukemia.
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Affiliation(s)
- Amina Kariminia
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Sabine M Ivison
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Vivian M Leung
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Susanna Sung
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Nicole Couto
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Jacob Rozmus
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Nina Rolf
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Aru Narendran
- Division of Pediatric Oncology, Alberta Children's Hospital, Calgary, AB T2N 4N1, Canada
| | - Sandra E Dunn
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Gregor S D Reid
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Kirk R Schultz
- Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE. Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay. Mol Cell Proteomics 2016; 15:1584-97. [PMID: 26896796 DOI: 10.1074/mcp.m115.054056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/31/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) has originally been described as a surveillance mechanism to inhibit the expression of mRNAs with truncated open reading frames (ORFs) and to contribute to the fidelity of gene expression. It is now recognized that NMD also controls the expression of physiological genes with "intact" mRNA. Stress can decrease NMD efficiency and thus increase the mRNA levels of physiological NMD targets. As stress can also inhibit translation, the net outcome for shaping the proteome is difficult to predict. We have thus analyzed de novo protein synthesis in response to NMD inhibition or the induction of mild endoplasmic reticulum (ER) stress by treatment of cells with the reducing agent dithiotreitol (DTT). For this purpose, we combined pulsed azidohomoalanine (AHA) and stable isotope labeling by amino acids in cell culture (SILAC). Labeled proteins were purified by click chemistry-based covalent coupling to agarose beads, trypsinized, fractionated, and analyzed by mass spectrometry (MS). We find that mild ER stress up-regulates the de novo synthesis of components of all three branches of the unfolded protein response (PERK, IRE1 and ATF6) without increasing eIF2α phosphorylation or impairing of protein translation. In contrast, inhibition of NMD induces de novo protein synthesis of downstream targets of the PERK and IRE1 pathways, whereas we could not detect regulation of ATF6-responsive genes. These data thus support a model that implicates a positive feedback loop of ER stress inhibiting NMD efficiency which further promotes the ER stress response in a branch-specific manner.
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Affiliation(s)
- Jana Sieber
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Christian Hauer
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany; ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | - Madhuri Bhuvanagiri
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Stefan Leicht
- ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Gabriele Neu-Yilik
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Matthias W Hentze
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas E Kulozik
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany;
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21
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Kenney JW, Genheden M, Moon KM, Wang X, Foster LJ, Proud CG. Eukaryotic elongation factor 2 kinase regulates the synthesis of microtubule-related proteins in neurons. J Neurochem 2015; 136:276-84. [PMID: 26485687 PMCID: PMC4843953 DOI: 10.1111/jnc.13407] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/10/2015] [Accepted: 10/14/2015] [Indexed: 12/11/2022]
Abstract
Modulation of the elongation phase of protein synthesis is important for numerous physiological processes in both neurons and other cell types. Elongation is primarily regulated via eukaryotic elongation factor 2 kinase (eEF2K). However, the consequence of altering eEF2K activity on the synthesis of specific proteins is largely unknown. Using both pharmacological and genetic manipulations of eEF2K combined with two protein‐labeling techniques, stable isotope labeling of amino acids in cell culture and bio‐orthogonal non‐canonical amino acid tagging, we identified a subset of proteins whose synthesis is sensitive to inhibition of eEF2K in murine primary cortical neurons. Gene ontology (GO) analyses indicated that processes related to microtubules are particularly sensitive to eEF2K inhibition. Our findings suggest that eEF2K likely contributes to neuronal function by regulating the synthesis of microtubule‐related proteins.
Modulation of the elongation phase of protein synthesis is important for numerous physiological processes in neurons. Here, using labeling of new proteins coupled with proteomic techniques in primary cortical neurons, we find that the synthesis of microtubule‐related proteins is up‐regulated by inhibition of elongation. This suggests that translation elongation is a key regulator of cytoskeletal dynamics in neurons.
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Affiliation(s)
- Justin W Kenney
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Maja Genheden
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Kyung-Mee Moon
- Centre for High-throughput Biology and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Xuemin Wang
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Leonard J Foster
- Centre for High-throughput Biology and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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22
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Schmidt N, Hennig T, Serwa RA, Marchetti M, O'Hare P. Remote Activation of Host Cell DNA Synthesis in Uninfected Cells Signaled by Infected Cells in Advance of Virus Transmission. J Virol 2015; 89:11107-15. [PMID: 26311877 PMCID: PMC4621119 DOI: 10.1128/jvi.01950-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/21/2015] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Viruses modulate cellular processes and metabolism in diverse ways, but these are almost universally studied in the infected cell itself. Here, we study spatial organization of DNA synthesis during multiround transmission of herpes simplex virus (HSV) using pulse-labeling with ethynyl nucleotides and cycloaddition of azide fluorophores. We report a hitherto unknown and unexpected outcome of virus-host interaction. Consistent with the current understanding of the single-step growth cycle, HSV suppresses host DNA synthesis and promotes viral DNA synthesis in spatially segregated compartments within the cell. In striking contrast, during progressive rounds of infection initiated at a single cell, we observe that infection induces a clear and pronounced stimulation of cellular DNA replication in remote uninfected cells. This induced DNA synthesis was observed in hundreds of uninfected cells at the extended border, outside the perimeter of the progressing infection. Moreover, using pulse-chase analysis, we show that this activation is maintained, resulting in a propagating wave of host DNA synthesis continually in advance of infection. As the virus reaches and infects these activated cells, host DNA synthesis is then shut off and replaced with virus DNA synthesis. Using nonpropagating viruses or conditioned medium, we demonstrate a paracrine effector of uninfected cell DNA synthesis in remote cells continually in advance of infection. These findings have significant implications, likely with broad applicability, for our understanding of the ways in which virus infection manipulates cell processes not only in the infected cell itself but also now in remote uninfected cells, as well as of mechanisms governing host DNA synthesis. IMPORTANCE We show that during infection initiated by a single particle with progressive cell-cell virus transmission (i.e., the normal situation), HSV induces host DNA synthesis in uninfected cells, mediated by a virus-induced paracrine effector. The field has had no conception that this process occurs, and the work changes our interpretation of virus-host interaction during advancing infection and has implications for understanding controls of host DNA synthesis. Our findings demonstrate the utility of chemical biology techniques in analysis of infection processes, reveal distinct processes when infection is examined in multiround transmission versus single-step growth curves, and reveal a hitherto-unknown process in virus infection, likely relevant for other viruses (and other infectious agents) and for remote signaling of other processes, including transcription and protein synthesis.
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Affiliation(s)
- Nora Schmidt
- Section of Virology, St. Mary's Medical School, Imperial College, London, United Kingdom
| | - Thomas Hennig
- Section of Virology, St. Mary's Medical School, Imperial College, London, United Kingdom
| | - Remigiusz A Serwa
- Section of Virology, St. Mary's Medical School, Imperial College, London, United Kingdom Department of Chemistry, Imperial College London, London, United Kingdom
| | - Magda Marchetti
- Section of Virology, St. Mary's Medical School, Imperial College, London, United Kingdom Department of Technology and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Peter O'Hare
- Section of Virology, St. Mary's Medical School, Imperial College, London, United Kingdom
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23
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Debarba JA, Monteiro KM, Moura H, Barr JR, Ferreira HB, Zaha A. Identification of Newly Synthesized Proteins by Echinococcus granulosus Protoscoleces upon Induction of Strobilation. PLoS Negl Trop Dis 2015; 9:e0004085. [PMID: 26393918 PMCID: PMC4578768 DOI: 10.1371/journal.pntd.0004085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/25/2015] [Indexed: 12/21/2022] Open
Abstract
Background The proteins responsible for the key molecular events leading to the structural changes between the developmental stages of Echinococcus granulosus remain unknown. In this work, azidohomoalanine (AHA)-specific labeling was used to identify proteins expressed by E. granulosus protoscoleces (PSCs) upon the induction of strobilar development. Methodology/Principal Findings The in vitro incorporation of AHA with different tags into newly synthesized proteins (NSPs) by PSCs was analyzed using SDS-PAGE and confocal microscopy. The LC-MS/MS analysis of AHA-labeled NSPs by PSCs undergoing strobilation allowed for the identification of 365 proteins, of which 75 were differentially expressed in comparison between the presence or absence of strobilation stimuli and 51 were expressed exclusively in either condition. These proteins were mainly involved in metabolic, regulatory and signaling processes. Conclusions/Significance After the controlled-labeling of proteins during the induction of strobilar development, we identified modifications in protein expression. The changes in the metabolism and the activation of control and signaling pathways may be important for the correct parasite development and be target for further studies. In the life cycle of the parasite Echinococcus granulosus, hydatid cysts produce the pre-adult form, which has the ability to either differentiate into an adult worm (strobilation) or dedifferentiate into a secondary hydatid cyst. We used different protein tags that allowed for the visualization and purification of proteins produced specifically after the induction of strobilar development to identify proteins that might be involved in this process (temporally controlled and context-dependent). As a result, we found proteins that are involved in important processes during development, such as energy metabolism, control pathways and cellular communication. We believe that these results will be useful for the development of scientific approaches to controlling and preventing cystic hydatid disease.
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Affiliation(s)
- João Antonio Debarba
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Biologia Molecular de Cestódeos, and Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Karina Mariante Monteiro
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Biologia Molecular de Cestódeos, and Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Hercules Moura
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John R. Barr
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Henrique Bunselmeyer Ferreira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Biologia Molecular de Cestódeos, and Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Arnaldo Zaha
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Biologia Molecular de Cestódeos, and Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
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24
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Kretov DA, Curmi PA, Hamon L, Abrakhi S, Desforges B, Ovchinnikov LP, Pastré D. mRNA and DNA selection via protein multimerization: YB-1 as a case study. Nucleic Acids Res 2015; 43:9457-73. [PMID: 26271991 PMCID: PMC4627072 DOI: 10.1093/nar/gkv822] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/29/2015] [Indexed: 12/16/2022] Open
Abstract
Translation is tightly regulated in cells for keeping adequate protein levels, this task being notably accomplished by dedicated mRNA-binding proteins recognizing a specific set of mRNAs to repress or facilitate their translation. To select specific mRNAs, mRNA-binding proteins can strongly bind to specific mRNA sequences/structures. However, many mRNA-binding proteins rather display a weak specificity to short and redundant sequences. Here we examined an alternative mechanism by which mRNA-binding proteins could inhibit the translation of specific mRNAs, using YB-1, a major translation regulator, as a case study. Based on a cooperative binding, YB-1 forms stable homo-multimers on some mRNAs while avoiding other mRNAs. Via such inhomogeneous distribution, YB-1 can selectively inhibit translation of mRNAs on which it has formed stable multimers. This novel mechanistic view on mRNA selection may be shared by other proteins considering the elevated occurrence of multimerization among mRNA-binding proteins. Interestingly, we also demonstrate how, by using the same mechanism, YB-1 can form multimers on specific DNA structures, which could provide novel insights into YB-1 nuclear functions in DNA repair and multi-drug resistance.
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Affiliation(s)
- Dmitry A Kretov
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Patrick A Curmi
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Loic Hamon
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Sanae Abrakhi
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Bénédicte Desforges
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
| | - Lev P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - David Pastré
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204 and Université Evry-Val d'Essonne, Evry, 91025 France
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25
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Erdmann I, Marter K, Kobler O, Niehues S, Abele J, Müller A, Bussmann J, Storkebaum E, Ziv T, Thomas U, Dieterich DC. Cell-selective labelling of proteomes in Drosophila melanogaster. Nat Commun 2015; 6:7521. [PMID: 26138272 PMCID: PMC4507001 DOI: 10.1038/ncomms8521] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 05/16/2015] [Indexed: 01/06/2023] Open
Abstract
The specification and adaptability of cells rely on changes in protein composition. Nonetheless, uncovering proteome dynamics with cell-type-specific resolution remains challenging. Here we introduce a strategy for cell-specific analysis of newly synthesized proteomes by combining targeted expression of a mutated methionyl-tRNA synthetase (MetRS) with bioorthogonal or fluorescent non-canonical amino-acid-tagging techniques (BONCAT or FUNCAT). Substituting leucine by glycine within the MetRS-binding pocket (MetRSLtoG) enables incorporation of the non-canonical amino acid azidonorleucine (ANL) instead of methionine during translation. Newly synthesized proteins can thus be labelled by coupling the azide group of ANL to alkyne-bearing tags through ‘click chemistry'. To test these methods for applicability in vivo, we expressed MetRSLtoG cell specifically in Drosophila. FUNCAT and BONCAT reveal ANL incorporation into proteins selectively in cells expressing the mutated enzyme. Cell-type-specific FUNCAT and BONCAT, thus, constitute eligible techniques to study protein synthesis-dependent processes in complex and behaving organisms. Mutated tRNA synthetases can incorporate non-canonical amino acids into proteins. Erdmann et al. exploit this property to metabolically label newly synthesized proteins in selected cell types in Drosophila, and demonstrate their detection using proteomics (BONCAT) and fluorescence imaging (FUNCAT).
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Affiliation(s)
- Ines Erdmann
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Kathrin Marter
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Oliver Kobler
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Sven Niehues
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Julia Abele
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Anke Müller
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Julia Bussmann
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Erik Storkebaum
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Tamar Ziv
- Smoler Proteomics Center, Faculty of Biology, Technion, Haifa 32000, Israel
| | - Ulrich Thomas
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Daniela C Dieterich
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany [3] Center for Behavioral Brain Sciences, Magdeburg 39118, Germany
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26
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El-Naggar AM, Veinotte CJ, Cheng H, Grunewald TGP, Negri GL, Somasekharan SP, Corkery DP, Tirode F, Mathers J, Khan D, Kyle AH, Baker JH, LePard NE, McKinney S, Hajee S, Bosiljcic M, Leprivier G, Tognon CE, Minchinton AI, Bennewith KL, Delattre O, Wang Y, Dellaire G, Berman JN, Sorensen PH. Translational Activation of HIF1α by YB-1 Promotes Sarcoma Metastasis. Cancer Cell 2015; 27:682-97. [PMID: 25965573 DOI: 10.1016/j.ccell.2015.04.003] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 02/28/2015] [Accepted: 04/10/2015] [Indexed: 12/27/2022]
Abstract
Metastatic dissemination is the leading cause of death in cancer patients, which is particularly evident for high-risk sarcomas such as Ewing sarcoma, osteosarcoma, and rhabdomyosarcoma. Previous research identified a crucial role for YB-1 in the epithelial-to-mesenchymal transition (EMT) and metastasis of epithelial malignancies. Based on clinical data and two distinct animal models, we now report that YB-1 is also a major metastatic driver in high-risk sarcomas. Our data establish YB-1 as a critical regulator of hypoxia-inducible factor 1α (HIF1α) expression in sarcoma cells. YB-1 enhances HIF1α protein expression by directly binding to and activating translation of HIF1A messages. This leads to HIF1α-mediated sarcoma cell invasion and enhanced metastatic capacity in vivo, highlighting a translationally regulated YB-1-HIF1α axis in sarcoma metastasis.
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Affiliation(s)
- Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Chansey J Veinotte
- Department of Pediatrics, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Hongwei Cheng
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Thomas G P Grunewald
- Laboratory for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Thalkirchner Strasse 36, 80337 Munich, Germany
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Syam Prakash Somasekharan
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Dale P Corkery
- Department of Pediatrics, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Franck Tirode
- INSERM U830, Laboratoire de génétique et biologie des cancers, Institut Curie, 75248 Paris, France
| | - Joan Mathers
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Debjit Khan
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Alastair H Kyle
- Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Jennifer H Baker
- Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Nancy E LePard
- Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Steven McKinney
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Shamil Hajee
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Momir Bosiljcic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Gabriel Leprivier
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Cristina E Tognon
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Andrew I Minchinton
- Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Kevin L Bennewith
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Integrative Oncology, Radiation Biology Unit, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada
| | - Olivier Delattre
- INSERM U830, Laboratoire de génétique et biologie des cancers, Institut Curie, 75248 Paris, France
| | - Yuzhuo Wang
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jason N Berman
- Department of Pediatrics, IWK Health Centre, Halifax, NS B3K 6R8, Canada; Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Pediatrics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC V5Z 1L3, Canada.
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27
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BDNF stimulation of protein synthesis in cortical neurons requires the MAP kinase-interacting kinase MNK1. J Neurosci 2015; 35:972-84. [PMID: 25609615 DOI: 10.1523/jneurosci.2641-14.2015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although the MAP kinase-interacting kinases (MNKs) have been known for >15 years, their roles in the regulation of protein synthesis have remained obscure. Here, we explore the involvement of the MNKs in brain-derived neurotrophic factor (BDNF)-stimulated protein synthesis in cortical neurons from mice. Using a combination of pharmacological and genetic approaches, we show that BDNF-induced upregulation of protein synthesis requires MEK/ERK signaling and the downstream kinase, MNK1, which phosphorylates eukaryotic initiation factor (eIF) 4E. Translation initiation is mediated by the interaction of eIF4E with the m(7)GTP cap of mRNA and with eIF4G. The latter interaction is inhibited by the interactions of eIF4E with partner proteins, such as CYFIP1, which acts as a translational repressor. We find that BDNF induces the release of CYFIP1 from eIF4E, and that this depends on MNK1. Finally, using a novel combination of BONCAT and SILAC, we identify a subset of proteins whose synthesis is upregulated by BDNF signaling via MNK1 in neurons. Interestingly, this subset of MNK1-sensitive proteins is enriched for functions involved in neurotransmission and synaptic plasticity. Additionally, we find significant overlap between our subset of proteins whose synthesis is regulated by MNK1 and those encoded by known FMRP-binding mRNAs. Together, our data implicate MNK1 as a key component of BDNF-mediated translational regulation in neurons.
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28
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Somasekharan SP, El-Naggar A, Leprivier G, Cheng H, Hajee S, Grunewald TGP, Zhang F, Ng T, Delattre O, Evdokimova V, Wang Y, Gleave M, Sorensen PH. YB-1 regulates stress granule formation and tumor progression by translationally activating G3BP1. ACTA ACUST UNITED AC 2015; 208:913-29. [PMID: 25800057 PMCID: PMC4384734 DOI: 10.1083/jcb.201411047] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
YB-1, which is upregulated in human sarcomas, controls the availability of the stress granule nucleator G3BP1 and thereby controls stress granule assembly. Under cell stress, global protein synthesis is inhibited to preserve energy. One mechanism is to sequester and silence mRNAs in ribonucleoprotein complexes known as stress granules (SGs), which contain translationally silent mRNAs, preinitiation factors, and RNA-binding proteins. Y-box binding protein 1 (YB-1) localizes to SGs, but its role in SG biology is unknown. We now report that YB-1 directly binds to and translationally activates the 5′ untranslated region (UTR) of G3BP1 mRNAs, thereby controlling the availability of the G3BP1 SG nucleator for SG assembly. YB-1 inactivation in human sarcoma cells dramatically reduces G3BP1 and SG formation in vitro. YB-1 and G3BP1 expression are highly correlated in human sarcomas, and elevated G3BP1 expression correlates with poor survival. Finally, G3BP1 down-regulation in sarcoma xenografts prevents in vivo SG formation and tumor invasion, and completely blocks lung metastasis in mouse models. Together, these findings demonstrate a critical role for YB-1 in SG formation through translational activation of G3BP1, and highlight novel functions for SGs in tumor progression.
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Affiliation(s)
- Syam Prakash Somasekharan
- Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Amal El-Naggar
- Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Gabriel Leprivier
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Hongwei Cheng
- Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Shamil Hajee
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Thomas G P Grunewald
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unit 830, Genetics and Biology of Cancers, Institute Curie Research Center, 75248 Paris, France
| | - Fan Zhang
- Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Olivier Delattre
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unit 830, Genetics and Biology of Cancers, Institute Curie Research Center, 75248 Paris, France
| | - Valentina Evdokimova
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Yuzhuo Wang
- Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Martin Gleave
- Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Department of Pathology and Laboratory Medicine and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
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Structure-function based molecular relationships in Ewing's sarcoma. BIOMED RESEARCH INTERNATIONAL 2015; 2015:798426. [PMID: 25688366 PMCID: PMC4320925 DOI: 10.1155/2015/798426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/30/2014] [Accepted: 10/14/2014] [Indexed: 02/07/2023]
Abstract
Ewing's Sarcoma Oncogene (ews) on chromosome 22q12 is encoding a ubiquitously expressed RNA-binding protein (EWS) with unknown function that is target of tumor-specific chromosomal translocations in Ewing's sarcoma family of tumors. A model of transcription complex was proposed in which the heterodimer Rpb4/7 binds to EAD, connecting it to Core RNA Pol II. The DNA-binding domain, provided by EFP, is bound to the promoter. Rpb4/7 binds RNA, stabilizing the transcription complex. The complex Rpb4/7 can stabilize the preinitiation complexes by converting the conformation of RNA Pol II. EWS may change its conformation, so that NTD becomes accessible. Two different mechanisms of interaction between EWS and RNA Pol II are proposed: (I) an intermolecular EWS-EWS interaction between two molecules, pushing conformation from “closed” to “open” state, or (II) an intramolecular interaction inside the molecule of EWS, pushing conformation of the molecule from “closed” to “open” state. The modified forms of EWS may interact with Pol II subunits hsRpb5 and hsRpb7. The EWS and EFPs binding partners are described schematically in a model, an attempt to link the transcription with the splicing. The proposed model helps to understand the functional molecular interactions in cancer, to find new partners and ways to treat cancer.
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30
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Zhang G, Bowling H, Hom N, Kirshenbaum K, Klann E, Chao MV, Neubert TA. In-depth quantitative proteomic analysis of de novo protein synthesis induced by brain-derived neurotrophic factor. J Proteome Res 2014; 13:5707-14. [PMID: 25271054 PMCID: PMC4261974 DOI: 10.1021/pr5006982] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Measuring the synthesis of new proteins
in the context of a much
greater number of pre-existing proteins can be difficult. To overcome
this obstacle, bioorthogonal noncanonical amino acid tagging (BONCAT)
can be combined with stable isotope labeling by amino acid in cell
culture (SILAC) for comparative proteomic analysis of de novo protein
synthesis (BONLAC). In the present study, we show that alkyne resin-based
isolation of l-azidohomoalanine (AHA)-labeled proteins using
azide/alkyne cycloaddition minimizes contamination from pre-existing
proteins. Using this approach, we isolated and identified 7414 BONCAT-labeled
proteins. The nascent proteome isolated by BONCAT was very similar
to the steady-state proteome, although transcription factors were
highly enriched by BONCAT. About 30% of the methionine residues were
replaced by AHA in our BONCAT samples, which allowed for identification
of methionine-containing peptides. There was no bias against low-methionine
proteins by BONCAT at the proteome level. When we applied the BONLAC
approach to screen for brain-derived neurotrophic factor (BDNF)-induced
protein synthesis, 53 proteins were found to be significantly changed
2 h after BDNF stimulation. Our study demonstrated that the newly
synthesized proteome, even after a short period of stimulation, can
be efficiently isolated by BONCAT and analyzed to a depth that is
similar to that of the steady-state proteome.
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Affiliation(s)
- Guoan Zhang
- Department of Biochemistry and Molecular Pharmacology, ‡Departments of Cell Biology, Physiology, and Neuroscience and Psychiatry, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine , New York, New York 10016, United States
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31
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Au HHT, Jan E. Novel viral translation strategies. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:779-801. [PMID: 25045163 PMCID: PMC7169809 DOI: 10.1002/wrna.1246] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/03/2014] [Accepted: 05/08/2014] [Indexed: 01/06/2023]
Abstract
Viral genomes are compact and encode a limited number of proteins. Because they do not encode components of the translational machinery, viruses exhibit an absolute dependence on the host ribosome and factors for viral messenger RNA (mRNA) translation. In order to recruit the host ribosome, viruses have evolved unique strategies to either outcompete cellular transcripts that are efficiently translated by the canonical translation pathway or to reroute translation factors and ribosomes to the viral genome. Furthermore, viruses must evade host antiviral responses and escape immune surveillance. This review focuses on some recent major findings that have revealed unconventional strategies that viruses utilize, which include usurping the host translational machinery, modulating canonical translation initiation factors to specifically enhance or repress overall translation for the purpose of viral production, and increasing viral coding capacity. The discovery of these diverse viral strategies has provided insights into additional translational control mechanisms and into the viral host interactions that ensure viral protein synthesis and replication. WIREs RNA 2014, 5:779–801. doi: 10.1002/wrna.1246 This article is categorized under:
Translation > Translation Mechanisms Translation > Translation Regulation
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Affiliation(s)
- Hilda H T Au
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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32
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Bagert JD, Xie YJ, Sweredoski MJ, Qi Y, Hess S, Schuman EM, Tirrell DA. Quantitative, time-resolved proteomic analysis by combining bioorthogonal noncanonical amino acid tagging and pulsed stable isotope labeling by amino acids in cell culture. Mol Cell Proteomics 2014; 13:1352-8. [PMID: 24563536 DOI: 10.1074/mcp.m113.031914] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An approach to proteomic analysis that combines bioorthogonal noncanonical amino acid tagging (BONCAT) and pulsed stable isotope labeling with amino acids in cell culture (pSILAC) provides accurate quantitative information about rates of cellular protein synthesis on time scales of minutes. The method is capable of quantifying 1400 proteins produced by HeLa cells during a 30 min interval, a time scale that is inaccessible to isotope labeling techniques alone. Potential artifacts in protein quantification can be reduced to insignificant levels by limiting the extent of noncanonical amino acid tagging. We find no evidence for artifacts in protein identification in experiments that combine the BONCAT and pSILAC methods.
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Affiliation(s)
- John D Bagert
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
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HACE1 reduces oxidative stress and mutant Huntingtin toxicity by promoting the NRF2 response. Proc Natl Acad Sci U S A 2014; 111:3032-7. [PMID: 24516159 DOI: 10.1073/pnas.1314421111] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Oxidative stress plays a key role in late onset diseases including cancer and neurodegenerative diseases such as Huntington disease. Therefore, uncovering regulators of the antioxidant stress responses is important for understanding the course of these diseases. Indeed, the nuclear factor erythroid 2-related factor 2 (NRF2), a master regulator of the cellular antioxidative stress response, is deregulated in both cancer and neurodegeneration. Similar to NRF2, the tumor suppressor Homologous to the E6-AP Carboxyl Terminus (HECT) domain and Ankyrin repeat containing E3 ubiquitin-protein ligase 1 (HACE1) plays a protective role against stress-induced tumorigenesis in mice, but its roles in the antioxidative stress response or its involvement in neurodegeneration have not been investigated. To this end we examined Hace1 WT and KO mice and found that Hace1 KO animals exhibited increased oxidative stress in brain and that the antioxidative stress response was impaired. Moreover, HACE1 was found to be essential for optimal NRF2 activation in cells challenged with oxidative stress, as HACE1 depletion resulted in reduced NRF2 activity, stability, and protein synthesis, leading to lower tolerance against oxidative stress triggers. Strikingly, we found a reduction of HACE1 levels in the striatum of Huntington disease patients, implicating HACE1 in the pathology of Huntington disease. Moreover, ectopic expression of HACE1 in striatal neuronal progenitor cells provided protection against mutant Huntingtin-induced redox imbalance and hypersensitivity to oxidative stress, by augmenting NRF2 functions. These findings reveal that the tumor suppressor HACE1 plays a role in the NRF2 antioxidative stress response pathway and in neurodegeneration.
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Y-box binding protein 1--a prognostic marker and target in tumour therapy. Eur J Cell Biol 2013; 93:61-70. [PMID: 24461929 DOI: 10.1016/j.ejcb.2013.11.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/22/2013] [Accepted: 11/28/2013] [Indexed: 01/11/2023] Open
Abstract
Y-box binding protein 1 (YB-1) is a multifunctional protein involved in various cellular processes including both transcriptional and translational regulation of target gene expression. Significantly increased YB-1 levels have been reported in a number of human malignancies and shown to be associated with poor prognosis and disease recurrence. Indeed, YB-1 can act as a versatile oncoprotein playing an important role in tumour cell proliferation and progression. Consequently, YB-1 not only proves to be a good prognostic tumour marker, but also may be a promising emerging molecular target for the development of new therapeutical strategies. In this review, we discuss both the role of YB-1 in cancer and specifically in malignant melanoma as well as possible translations into the clinics derived thereof.
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Lyabin DN, Eliseeva IA, Ovchinnikov LP. YB-1 protein: functions and regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:95-110. [PMID: 24217978 DOI: 10.1002/wrna.1200] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/23/2013] [Accepted: 09/27/2013] [Indexed: 12/15/2022]
Abstract
The Y-box binding protein 1 (YB-1, YBX1) is a member of the family of DNA- and RNA-binding proteins with an evolutionarily ancient and conserved cold shock domain. It falls into a group of intrinsically disordered proteins that do not follow the classical rule 'one protein-one function' but introduce a novel principle stating that a disordered structure suggests many functions. YB-1 participates in a wide variety of DNA/RNA-dependent events, including DNA reparation, pre-mRNA transcription and splicing, mRNA packaging, and regulation of mRNA stability and translation. At the cell level, the multiple activities of YB-1 are manifested as its involvement in cell proliferation and differentiation, stress response, and malignant cell transformation. WIREs RNA 2014, 5:95-110. doi: 10.1002/wrna.1200 CONFLICT OF INTEREST: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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36
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Hinz FI, Dieterich DC, Schuman EM. Teaching old NCATs new tricks: using non-canonical amino acid tagging to study neuronal plasticity. Curr Opin Chem Biol 2013; 17:738-46. [PMID: 23938204 DOI: 10.1016/j.cbpa.2013.07.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/23/2013] [Indexed: 11/26/2022]
Abstract
The non-canonical amino acid labeling techniques BONCAT (bioorthogonal non-canonical amino acid tagging) and FUNCAT (fluorescent non-canonical amino acid tagging) enable the specific identification and visualization of newly synthesized proteins. Recently, these techniques have been applied to neuronal systems to elucidate protein synthesis dynamics during plasticity, identify stimulation-induced proteomes and subproteomes and to investigate local protein synthesis in specific subcellular compartments. The next generation of tools and applications, reviewed here, includes the development of new tags, the quantitative identification of newly synthesized proteins, the application of NCAT to whole animals, and the ability to genetically restrict NCAT labeling. These techniques will enable not only improved detection but also allow new scientific questions to be tackled.
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Affiliation(s)
- F I Hinz
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA; Max Planck Institute for Brain Research, D-60528 Frankfurt am Main, Germany
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37
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The eEF2 kinase confers resistance to nutrient deprivation by blocking translation elongation. Cell 2013; 153:1064-79. [PMID: 23706743 DOI: 10.1016/j.cell.2013.04.055] [Citation(s) in RCA: 311] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 11/13/2012] [Accepted: 04/30/2013] [Indexed: 01/11/2023]
Abstract
Metabolic adaptation is essential for cell survival during nutrient deprivation. We report that eukaryotic elongation factor 2 kinase (eEF2K), which is activated by AMP-kinase (AMPK), confers cell survival under acute nutrient depletion by blocking translation elongation. Tumor cells exploit this pathway to adapt to nutrient deprivation by reactivating the AMPK-eEF2K axis. Adaptation of transformed cells to nutrient withdrawal is severely compromised in cells lacking eEF2K. Moreover, eEF2K knockdown restored sensitivity to acute nutrient deprivation in highly resistant human tumor cell lines. In vivo, overexpression of eEF2K rendered murine tumors remarkably resistant to caloric restriction. Expression of eEF2K strongly correlated with overall survival in human medulloblastoma and glioblastoma multiforme. Finally, C. elegans strains deficient in efk-1, the eEF2K ortholog, were severely compromised in their response to nutrient depletion. Our data highlight a conserved role for eEF2K in protecting cells from nutrient deprivation and in conferring tumor cell adaptation to metabolic stress. PAPERCLIP:
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Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J. Experimental characterization of the human non-sequence-specific nucleic acid interactome. Genome Biol 2013; 14:R81. [PMID: 23902751 PMCID: PMC4053969 DOI: 10.1186/gb-2013-14-7-r81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022] Open
Abstract
Background The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported. Results We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function. Conclusions The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms.
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