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Zhang X, Lou Y, Zheng D, Lu J, Qi D. Quantitative proteomic analysis reveals the effects of mu opioid agonists on HT22 cells. Front Pharmacol 2023; 13:1022449. [PMID: 36699066 PMCID: PMC9868271 DOI: 10.3389/fphar.2022.1022449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction: At present, the mu opioid receptor is the most important neuroaesthetics receptor in anesthesiology research, and the damage that it does to the nervous system is unknown. Methods: We investigated the effects of loperamide, an agonist of the mu opioid receptor, on protein expression in HT22 cells using stable isotope labeling of amino acids in cell culture (SILAC), immobilized metal affinity chromatography (IMAC) enrichment, and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 7,823 proteins were identified. Results and Discussion: Bioinformatic analysis revealed that mu opioid receptor agonism can induce distinct changes in the proteome of HT22 cells. These findings improve our understanding of narcotic drugs.
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Affiliation(s)
- Xutong Zhang
- Department of Anesthesiology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yani Lou
- Department of Anesthesiology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dongxu Zheng
- Department of Anesthesiology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jialin Lu
- Department of Anesthesiology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dansi Qi
- Department of Pathology, Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China,*Correspondence: Dansi Qi,
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2
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Song B, Liu D, Greco TM, Cristea IM. Post-translational modification control of viral DNA sensors and innate immune signaling. Adv Virus Res 2021; 109:163-199. [PMID: 33934827 PMCID: PMC8489191 DOI: 10.1016/bs.aivir.2021.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vertebrate innate immune system confers host cells with mechanisms to protect against both evolutionarily ancient pathogens and newly emerging pathogenic strains. Innate immunity relies on the host cell's ability to distinguish between self and pathogen-derived molecules. To achieve this, the innate immune system uses germline encoded receptors called pattern recognition receptors (PRRs), which recognize various molecular signatures, including nucleic acids, proteins, lipids, glycans and glycolipids. Among these molecules, the recognition of pathogenic, mislocalized, or damaged DNA by cellular protein receptors, commonly called DNA sensors, represents a major surveillance pathway for initiating immune signaling. The ability of cells to temporally regulate DNA sensor activation and subsequent signal termination is critical for effective immune signaling. These same mechanisms are also co-opted by pathogens to promote their replication. Therefore, there is significant interest in understanding DNA sensor regulatory networks during microbial infections and autoimmune disease. One emerging aspect of DNA sensor regulation is through post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, ADP-ribosylation, SUMOylation, methylation, deamidation, glutamylation. In this chapter, we discuss how PTMs have been shown to positively or negatively impact DNA sensor functions via diverse mechanisms, including direct regulation of enzymatic activity, protein-protein and protein-DNA interactions, protein translocations and protein turnover. In addition, we highlight the ability of virus-induced PTMs to promote immune evasion. We also discuss the recent evidence linking PTMs on DNA sensors with human diseases and more broadly, highlight promising directions for future research on PTM-mediated regulation of DNA sensor-dependent immune signaling.
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Affiliation(s)
- Bokai Song
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Dawei Liu
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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Sürmen MG, Sürmen S, Ali A, Musharraf SG, Emekli N. Phosphoproteomic strategies in cancer research: a minireview. Analyst 2020; 145:7125-7149. [PMID: 32996481 DOI: 10.1039/d0an00915f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the cellular processes is central to comprehend disease conditions and is also true for cancer research. Proteomic studies provide significant insight into cancer mechanisms and aid in the diagnosis and prognosis of the disease. Phosphoproteome is one of the most studied complements of the whole proteome given its importance in the understanding of cellular processes such as signaling and regulations. Over the last decade, several new methods have been developed for phosphoproteome analysis. A significant amount of these efforts pertains to cancer research. The current use of powerful analytical instruments in phosphoproteomic approaches has paved the way for deeper and sensitive investigations. However, these methods and techniques need further improvements to deal with challenges posed by the complexity of samples and scarcity of phosphoproteins in the whole proteome, throughput and reproducibility. This review aims to provide a comprehensive summary of the variety of steps used in phosphoproteomic methods applied in cancer research including the enrichment and fractionation strategies. This will allow researchers to evaluate and choose a better combination of steps for their phosphoproteome studies.
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Affiliation(s)
- Mustafa Gani Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Saime Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Syed Ghulam Musharraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Nesrin Emekli
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
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4
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Valdés A, Bergström Lind S. Mass Spectrometry-Based Analysis of Time-Resolved Proteome Quantification. Proteomics 2019; 20:e1800425. [PMID: 31652013 DOI: 10.1002/pmic.201800425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/20/2019] [Indexed: 11/09/2022]
Abstract
The aspect of time is essential in biological processes and thus it is important to be able to monitor signaling molecules through time. Proteins are key players in cellular signaling and they respond to many stimuli and change their expression in many time-dependent processes. Mass spectrometry (MS) is an important tool for studying proteins, including their posttranslational modifications and their interaction partners-both in qualitative and quantitative ways. In order to distinguish the different trends over time, proteins, modification sites, and interacting proteins must be compared between different time points, and therefore relative quantification is preferred. In this review, the progress and challenges for MS-based analysis of time-resolved proteome dynamics are discussed. Further, aspects on model systems, technologies, sampling frequencies, and presentation of the dynamic data are discussed.
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Affiliation(s)
- Alberto Valdés
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, 28871, Alcalá de Henares, Madrid, Spain
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, 75124, Uppsala, Sweden
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5
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Ren L, Li C, Shao W, Lin W, He F, Jiang Y. TiO2 with Tandem Fractionation (TAFT): An Approach for Rapid, Deep, Reproducible, and High-Throughput Phosphoproteome Analysis. J Proteome Res 2017; 17:710-721. [DOI: 10.1021/acs.jproteome.7b00520] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Liangliang Ren
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
| | - Chaoying Li
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
| | - Wenli Shao
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
- Graduate
School, Anhui Medical University, Hefei 230032, China
| | - Weiran Lin
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
| | - Fuchu He
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
| | - Ying Jiang
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
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Wang Z, Liu X, Ni SQ, Zhang J, Zhang X, Ahmad HA, Gao B. Weak magnetic field: A powerful strategy to enhance partial nitrification. WATER RESEARCH 2017; 120:190-198. [PMID: 28486170 DOI: 10.1016/j.watres.2017.04.058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/24/2017] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
Partial nitrification (PN) combined with anaerobic ammonium oxidation process has been recognized as a promising technology for the removal of nitrogenous contaminants from wastewater. This research aimed to investigate the potential of external magnetic field for enhancing the PN process in short and long term laboratory-scale experiments. Different strength magnetic fields (0, 5, 10, 15, 20 and 25 mT) were evaluated in short-term batch tests and 5 mT magnetic field was found to have better ability to increase the activities of aerobic ammonium oxidizing bacteria (AOB) of PN consortium. Long-term effect of magnetic field on PN consortium was studied with 5 mT magnetic field. The results demonstrated that the positive effect of magnetic field on PN process could also be testified at all of the four stages. Furthermore, a decrease of bacterial diversity was noted with the increase of magnetic field strength. Relative abundance of Nitrosomonadaceae decreased significantly (p < 0.01) from 13.9% in RCK to 12.9% in R5mT and 5.5% in R25mT. Functional genes forecast based on KEGG database indicated that the expressions of functional genes related to signal transduction and cell motility in 5 mT environment were higher expressed compared with no magnetic field addition and high magnetic field addition. The existence of 5 mT magnetic field didn't increase the abundance of AOB but increased the activity of AOB by increasing the rate of free ammonia into the interior of microbial cells. Addition of magnetic field couldn't change the final state of PN process according to the hypothesis proposed in this article. These findings indicated that the weak magnetic field was useful and reliable for the fast start-up of PN process since it was proved as a simple and convenient approach to enhance AOB activity.
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Affiliation(s)
- Zhibin Wang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China; Institute of Marine Science and Technology, Shandong University, 250000, China
| | - Xiaolin Liu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | - Shou-Qing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China.
| | - Jian Zhang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | - Xu Zhang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | - Hafiz Adeel Ahmad
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | - Baoyu Gao
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
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7
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Zhang H, Ye J, Shi Z, Bu C, Bao F. Quantitative analyses of the global proteome and phosphoproteome reveal the different impacts of propofol and dexmedetomidine on HT22 cells. Sci Rep 2017; 7:46455. [PMID: 28418008 PMCID: PMC5394455 DOI: 10.1038/srep46455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 03/17/2017] [Indexed: 02/07/2023] Open
Abstract
Propofol and dexmedetomidine are both commonly used anaesthetics. Although they employ two different mechanisms to induce anaesthesia, both compounds influence the hippocampus and the HT22 cell line. HT22 cells are broadly used in neurobiological research. In this study, we assessed the effects of propofol and dexmedetomidine on signalling in HT22 cells. Using the SILAC (stable isotope labelling with amino acids in cell culture) labelling technique, IMAC (immobilized metal affinity chromatography) enrichment and high-resolution LC-MS/MS (liquid chromatography tandem mass spectrometry) analysis, we investigated the quantitative proteome and phosphoproteome in HT22 cells treated with propofol or dexmedetomidine. In total, 4,527 proteins and 6,824 phosphosites were quantified in cells treated with these two anaesthetics. With the assistance of intensive bioinformatics, the propofol and dexmedetomidine treatments were shown to induce distinct proteome and phosphoproteome profiles in HT22 cells. Consistent with our bioinformatics analysis, dexmedetomidine had a smaller effect than propofol on cell survival. These findings deepen our understanding of drug-induced anaesthesia.
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Affiliation(s)
- Honggang Zhang
- Department of Anesthesiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Juan Ye
- Department of Pediatrics, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Zhaomei Shi
- Jingjie PTM Biolab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Chen Bu
- Jingjie PTM Biolab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Fangping Bao
- Department of Anesthesiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
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8
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Wakabayashi M, Kyono Y, Sugiyama N, Ishihama Y. Extended Coverage of Singly and Multiply Phosphorylated Peptides from a Single Titanium Dioxide Microcolumn. Anal Chem 2015; 87:10213-21. [DOI: 10.1021/acs.analchem.5b01216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Masaki Wakabayashi
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yutaka Kyono
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
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Yue X, Schunter A, Hummon AB. Comparing multistep immobilized metal affinity chromatography and multistep TiO2 methods for phosphopeptide enrichment. Anal Chem 2015; 87:8837-44. [PMID: 26237447 PMCID: PMC4766865 DOI: 10.1021/acs.analchem.5b01833] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Phosphopeptide enrichment from complicated peptide mixtures is an essential step for mass spectrometry-based phosphoproteomic studies to reduce sample complexity and ionization suppression effects. Typical methods for enriching phosphopeptides include immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO2) beads, which have selective affinity and can interact with phosphopeptides. In this study, the IMAC enrichment method was compared with the TiO2 enrichment method, using a multistep enrichment strategy from whole cell lysate, to evaluate their abilities to enrich for different types of phosphopeptides. The peptide-to-beads ratios were optimized for both IMAC and TiO2 beads. Both IMAC and TiO2 enrichments were performed for three rounds to enable the maximum extraction of phosphopeptides from the whole cell lysates. The phosphopeptides that are unique to IMAC enrichment, unique to TiO2 enrichment, and identified with both IMAC and TiO2 enrichment were analyzed for their characteristics. Both IMAC and TiO2 enriched similar amounts of phosphopeptides with comparable enrichment efficiency. However, phosphopeptides that are unique to IMAC enrichment showed a higher percentage of multiphosphopeptides as well as a higher percentage of longer, basic, and hydrophilic phosphopeptides. Also, the IMAC and TiO2 procedures clearly enriched phosphopeptides with different motifs. Finally, further enriching with two rounds of TiO2 from the supernatant after IMAC enrichment or further enriching with two rounds of IMAC from the supernatant TiO2 enrichment does not fully recover the phosphopeptides that are not identified with the corresponding multistep enrichment.
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Affiliation(s)
- Xiaoshan Yue
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Alissa Schunter
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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