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Dabsan S, Twito G, Biadsy S, Igbaria A. Less is better: various means to reduce protein load in the endoplasmic reticulum. FEBS J 2024. [PMID: 38865586 DOI: 10.1111/febs.17201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/08/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
The endoplasmic reticulum (ER) is an important organelle that controls the intracellular and extracellular environments. The ER is responsible for folding almost one-third of the total protein population in the eukaryotic cell. Disruption of ER-protein folding is associated with numerous human diseases, including metabolic disorders, neurodegenerative diseases, and cancer. During ER perturbations, the cells deploy various mechanisms to increase the ER-folding capacity and reduce ER-protein load by minimizing the number of substrates entering the ER to regain homeostasis. These mechanisms include signaling pathways, degradation mechanisms, and other processes that mediate the reflux of ER content to the cytosol. In this review, we will discuss the recent discoveries of five different ER quality control mechanisms, including the unfolded protein response (UPR), ER-associated-degradation (ERAD), pre-emptive quality control, ER-phagy and ER to cytosol signaling (ERCYS). We will discuss the roles of these processes in decreasing ER-protein load and inter-mechanism crosstalk.
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Affiliation(s)
- Salam Dabsan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Gal Twito
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Suma Biadsy
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Aeid Igbaria
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Lyu Z, Genereux JC. Quantitative Measurement of Transthyretin Mistargeting by Proximity Labeling and Parallel Reaction Monitoring. FRONTIERS IN CHEMICAL BIOLOGY 2023; 2:1288188. [PMID: 38173467 PMCID: PMC10764115 DOI: 10.3389/fchbi.2023.1288188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Proximity labeling is a powerful approach for characterizing subcellular proteomes. We recently demonstrated that proximity labeling can be used to identify mistrafficking of secretory proteins, such as occurs during pre-emptive quality control (pre-QC) following endoplasmic reticulum (ER) stress. This assay depends on protein quantification by immunoblotting and densitometry, which sometimes suffers from poor sensitivity. Here, we integrate parallel reaction monitoring (PRM) mass spectrometry to enable a more quantitative platform, and assess how chemical ER stressors impact pre-QC of the model secretory protein transthyretin in HEK293T cells. We find that some drug treatments affect labeling efficiency, which can be controlled for by normalizing to APEX2 auto-labeling. While some chemical ER stress inducers including Brefeldin A and thapsigargin induce pre-QC, tunicamycin and dithiothreitol do not, indicating ER stress alone is not sufficient. This finding contrasts with the canonical model of pre-QC induction, and establishes the utility of our platform.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Joseph C. Genereux
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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Guo Z, Jiang P, Dong Q, Zhang Y, Xu K, Zhai Y, He F, Tian C, Sun A. RNF149 Promotes HCC Progression through Its E3 Ubiquitin Ligase Activity. Cancers (Basel) 2023; 15:5203. [PMID: 37958377 PMCID: PMC10648572 DOI: 10.3390/cancers15215203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) accounts for over 80% of cases among liver cancer, with high incidence and poor prognosis. Thus, it is of valuable clinical significance for discovery of potential biomarkers and drug targets for HCC. In this study, based on the proteomic profiling data of paired early-stage HCC samples, we found that RNF149 was strikingly upregulated in tumor tissues and correlated with poor prognosis in HCC patients, which was further validated by IHC staining experiments of an independent HCC cohort. Consistently, overexpression of RNF149 significantly promoted cell proliferation, migration, and invasion of HCC cells. We further proved that RNF149 stimulated HCC progression via its E3 ubiquitin ligase activity, and identified DNAJC25 as its new substrate. In addition, bioinformatics analysis showed that high expression of RNF149 was correlated with immunosuppressive tumor microenvironment (TME), indicating its potential role in immune regulation of HCC. These results suggest that RNF149 could exert protumor functions in HCC in dependence of its E3 ubiquitin ligase activity, and might be a potential prognostic marker and therapeutic target for HCC treatment.
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Affiliation(s)
- Zhaoyu Guo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
| | - Pei Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
- International Academy of Phronesis Medicine, Guangzhou 510005, China
| | - Qian Dong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
| | - Yiming Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Kaikun Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
- International Academy of Phronesis Medicine, Guangzhou 510005, China
| | - Yuanjun Zhai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
- International Academy of Phronesis Medicine, Guangzhou 510005, China
| | - Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Aihua Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (Z.G.); (P.J.); (Q.D.); (Y.Z.); (K.X.); (Y.Z.); (F.H.)
- Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
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Lyu Z, Genereux JC. Quantitative Measurement of Secretory Protein Mistargeting by Proximity Labeling and Parallel Reaction Monitoring. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549095. [PMID: 37503147 PMCID: PMC10370094 DOI: 10.1101/2023.07.19.549095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Proximity labeling is a powerful approach for characterizing subcellular proteomes. We recently demonstrated that proximity labeling can be used to identify mistrafficking of secretory proteins, such as occurs during pre-emptive quality control (pre-QC) following endoplasmic reticulum (ER) stress. This assay depends on protein quantification by immunoblotting and densitometry, which is only semi-quantitative and suffers from poor sensitivity. Here, we integrate parallel reaction monitoring mass spectrometry to enable a more quantitative platform for ER import. PRM as opposed to densitometry improves quantification of transthyretin mistargeting while also achieving at least a ten-fold gain in sensitivity. The multiplexing of PRM also enabled us to evaluate a series of normalization approaches, revealing that normalization to auto-labeled APEX2 peroxidase is necessary to account for drug treatment-dependent changes in labeling efficiency. We apply this approach to systematically characterize the relationship between chemical ER stressors and ER pre-QC induction in HEK293T cells. Using dual-FLAG-tagged transthyretin (FLAGTTR) as a model secretory protein, we find that Brefeldin A treatment as well as ER calcium depletion cause pre-QC, while tunicamycin and dithiothreitol do not, indicating ER stress alone is not sufficient. This finding contrasts with the canonical model of pre-QC induction, and establishes the utility of our platform.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521
| | - Joseph C. Genereux
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521
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