1
|
Liu YY, Wang RJ, Ru SS, Gao F, Liu W, Zhang X. Comparative analysis of phosphorylated proteomes between plerocercoid and adult Spirometra mansoni reveals phosphoproteomic profiles of the medical tapeworm. Parasit Vectors 2024; 17:371. [PMID: 39217359 PMCID: PMC11366163 DOI: 10.1186/s13071-024-06454-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Plerocercoid larvae of the tapeworm Spirometra mansoni can infect both humans and animals, leading to severe parasitic zoonosis worldwide. Despite ongoing research efforts, our understanding of the developmental process of S. mansoni remains inadequate. To better characterize posttranslational regulation associated with parasite growth, development, and reproduction, a comparative phosphoproteomic study was conducted on the plerocercoid and adult stages of S. mansoni. METHODS In this study, site-specific phosphoproteomic analysis was conducted via 4D label-free quantitative analysis technology to obtain primary information about the overall phosphorylation status of plerocercoids and adults. RESULTS A total of 778 differentially abundant proteins (DAPs) were detected between adults and plerocercoids, of which 704 DAPs were upregulated and only 74 were downregulated. DAPs involved in metabolic activity were upregulated in plerocercoid larvae compared with adults, whereas DAPs associated with binding were upregulated in adults. Gene Ontology (GO) and Kyoto Encyclopedia of Genes (KEGG) analyses indicated that most DAPs involved in signal transduction and environmental information processing pathways were highly active in adults. DAPs upregulated in the plerocercoid group were enriched mainly in metabolic activities. The kinases PKACA, GSK3B, and smMLCK closely interact, suggesting potential active roles in the growth and development of S. mansoni. CONCLUSIONS The dataset presented in this study offers a valuable resource for forthcoming research on signaling pathways as well as new insights into functional studies on the molecular mechanisms of S. mansoni.
Collapse
Affiliation(s)
- Yong Yan Liu
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Department of Clinical Microbiology, The People's Hospital of Xixian, Xinyang, 464300, Henan, China
| | - Rui Jie Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Si Si Ru
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fei Gao
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Wei Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| | - Xi Zhang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| |
Collapse
|
2
|
Duan X, Zhang Y, Huang X, Ma X, Gao H, Wang Y, Xiao Z, Huang C, Wang Z, Li B, Yang W, Wang Y. GreenPhos, a universal method for in-depth measurement of plant phosphoproteomes with high quantitative reproducibility. MOLECULAR PLANT 2024; 17:199-213. [PMID: 38018035 DOI: 10.1016/j.molp.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/08/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
Protein phosphorylation regulates a variety of important cellular and physiological processes in plants. In-depth profiling of plant phosphoproteomes has been more technically challenging than that of animal phosphoproteomes. This is largely due to the need to improve protein extraction efficiency from plant cells, which have a dense cell wall, and to minimize sample loss resulting from the stringent sample clean-up steps required for the removal of a large amount of biomolecules interfering with phosphopeptide purification and mass spectrometry analysis. To this end, we developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis, rice, tomato, and Chlamydomonas reinhardtii, enabling in-depth identification with high quantitative reproducibility of about 11 000 phosphosites, the greatest depth achieved so far with single liquid chromatography-mass spectrometry (LC-MS) runs operated in a data-dependent acquisition (DDA) mode. The mainstay features of the method are the minimal sample loss achieved through elimination of sample clean-up before protease digestion and of desalting before phosphopeptide enrichment and hence the dramatic increases of time- and cost-effectiveness. The method, named GreenPhos, combined with single-shot LC-MS, enabled in-depth quantitative identification of Arabidopsis phosphoproteins, including differentially phosphorylated spliceosomal proteins, at multiple time points during salt stress and a number of kinase substrate motifs. GreenPhos is expected to serve as a universal method for purification of plant phosphopeptides, which, if samples are further fractionated and analyzed by multiple LC-MS runs, could enable measurement of plant phosphoproteomes with an unprecedented depth using a given mass spectrometry technology.
Collapse
Affiliation(s)
- Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Gao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongshu Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bolong Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang Yang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
3
|
Li Y, Zhang Z, Jiang S, Xu F, Tulum L, Li K, Liu S, Li S, Chang L, Liddell M, Tu F, Gu X, Carmichael PL, White A, Peng S, Zhang Q, Li J, Zuo T, Kukic P, Xu P. Using transcriptomics, proteomics and phosphoproteomics as new approach methodology (NAM) to define biological responses for chemical safety assessment. CHEMOSPHERE 2023; 313:137359. [PMID: 36427571 DOI: 10.1016/j.chemosphere.2022.137359] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Omic-based technologies are of particular interest and importance for hazard identification and health risk characterization of chemicals. Their application in the new approach methodologies (NAMs) anchored on cellular toxicity pathways is based on the premise that any apical health endpoint change must be underpinned by some alterations at the omic levels. In the present study we examined the cellular responses to two chemicals, caffeine and coumarin, by generating and integrating multi-omic data from multi-dose and multi-time point transcriptomic, proteomic and phosphoproteomic experiments. We showed that the methodology presented here was able to capture the complete chain of events from the first chemical-induced changes at the phosphoproteome level, to changes in gene expression, and lastly to changes in protein abundance, each with vastly different points of departure (PODs). In HepG2 cells we found that the metabolism of lipids and general cellular stress response to be the dominant biological processes in response to caffeine and coumarin exposure, respectively. The phosphoproteomic changes were detected early in time, at very low doses and provided a fast, adaptive cellular response to chemical exposure with 7-37-fold lower points of departure comparing to the transcriptomics. Changes in protein abundance were found much less frequently than transcriptomic changes. While challenges remain, our study provides strong and novel evidence supporting the notion that these three omic technologies can be used in an integrated manner to facilitate a more complete understanding of pathway perturbations and POD determinations for risk assessment of chemical exposures.
Collapse
Affiliation(s)
- Yuan Li
- Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Songhao Jiang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Feng Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Liz Tulum
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Kaixuan Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Shu Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Suzhen Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Mark Liddell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Fengjuan Tu
- Unilever Research & Development Centre Shanghai, Shanghai, 200335, China
| | - Xuelan Gu
- Unilever Research & Development Centre Shanghai, Shanghai, 200335, China
| | - Paul Lawford Carmichael
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Andrew White
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Shuangqing Peng
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Jin Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Tao Zuo
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China.
| | - Predrag Kukic
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - Ping Xu
- Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China.
| |
Collapse
|
4
|
Recent advances in metal oxide affinity chromatography materials for phosphoproteomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
5
|
Chen B, Sun L, Zeng G, Shen Z, Wang K, Yin L, Xu F, Wang P, Ding Y, Nie Q, Wu Q, Zhang Z, Xia J, Lin J, Luo Y, Cai J, Krausz KW, Zheng R, Xue Y, Zheng MH, Li Y, Yu C, Gonzalez FJ, Jiang C. Gut bacteria alleviate smoking-related NASH by degrading gut nicotine. Nature 2022; 610:562-568. [PMID: 36261549 PMCID: PMC9589931 DOI: 10.1038/s41586-022-05299-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/31/2022] [Indexed: 01/04/2023]
Abstract
Tobacco smoking is positively correlated with non-alcoholic fatty liver disease (NAFLD)1-5, but the underlying mechanism for this association is unclear. Here we report that nicotine accumulates in the intestine during tobacco smoking and activates intestinal AMPKα. We identify the gut bacterium Bacteroides xylanisolvens as an effective nicotine degrader. Colonization of B. xylanisolvens reduces intestinal nicotine concentrations in nicotine-exposed mice, and it improves nicotine-exacerbated NAFLD progression. Mechanistically, AMPKα promotes the phosphorylation of sphingomyelin phosphodiesterase 3 (SMPD3), stabilizing the latter and therefore increasing intestinal ceramide formation, which contributes to NAFLD progression to non-alcoholic steatohepatitis (NASH). Our results establish a role for intestinal nicotine accumulation in NAFLD progression and reveal an endogenous bacterium in the human intestine with the ability to metabolize nicotine. These findings suggest a possible route to reduce tobacco smoking-exacerbated NAFLD progression.
Collapse
Affiliation(s)
- Bo Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Guangyi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Zhe Shen
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Kai Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Limin Yin
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology, Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Feng Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Pengcheng Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Yong Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Qing Wu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Zhiwei Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Jialin Xia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China.,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China.,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China
| | - Yuhong Luo
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Cai
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kristopher W Krausz
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ruimao Zheng
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, China
| | - Yanxue Xue
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, China
| | - Ming-Hua Zheng
- NAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China. .,Key Laboratory of Diagnosis and Treatment for The Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, China.
| | - Yang Li
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology, Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China.
| | - Chaohui Yu
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China. .,Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China. .,Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing, China. .,The Key Laboratory of Molecular Cardiovascular Science, Peking University, Ministry of Education, Beijing, China.
| |
Collapse
|
6
|
James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
Collapse
Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
Collapse
Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
| |
Collapse
|
7
|
Comprehensive Evaluation of Different TiO2-Based Phosphopeptide Enrichment and Fractionation Methods for Phosphoproteomics. Cells 2022; 11:cells11132047. [PMID: 35805136 PMCID: PMC9265536 DOI: 10.3390/cells11132047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Protein phosphorylation is an essential post-translational modification that regulates multiple cellular processes. Due to their low stoichiometry and ionization efficiency, it is critical to efficiently enrich phosphopeptides for phosphoproteomics. Several phosphopeptide enrichment methods have been reported; however, few studies have comprehensively compared different TiO2-based phosphopeptide enrichment methods using complex proteomic samples. Here, we compared four TiO2-based phosphopeptide enrichment methods that used four non-phosphopeptide excluders (glutamic acid, lactic acid, glycolic acid, and DHB). We found that these four TiO2-based phosphopeptide enrichment methods had different enrichment specificities and that phosphopeptides enriched by the four methods had different physicochemical characteristics. More importantly, we discovered that phosphopeptides had a higher deamidation ratio than peptides from cell lysate and that phosphopeptides enriched using the glutamic acid method had a higher deamidation ratio than the other three methods. We then compared two phosphopeptide fractionation methods: ammonia- or TEA-based high pH reversed-phase (HpH-RP). We found that fewer phosphopeptides, especially multi-phosphorylated peptides, were identified using the ammonia-based method than using the TEA-based method. Therefore, the TEA-based HpH-RP fractionation method performed better than the ammonia method. In conclusion, we comprehensively evaluated different TiO2-based phosphopeptide enrichment and fractionation methods, providing a basis for selecting the proper protocols for comprehensive phosphoproteomics.
Collapse
|
8
|
Urban J. A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis. Anal Chim Acta 2022; 1199:338857. [DOI: 10.1016/j.aca.2021.338857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
|
9
|
A global phosphoproteomics analysis of adult Fasciola gigantica by LC-MS/MS. Parasitol Res 2022; 121:623-631. [PMID: 34985596 PMCID: PMC8727970 DOI: 10.1007/s00436-021-07422-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/29/2021] [Indexed: 12/05/2022]
Abstract
Protein phosphorylation plays key roles in a variety of essential cellular processes. Fasciola gigantica is a tropical liver fluke causing hepatobiliary disease fascioliasis, leading to human health threats and heavy economic losses. Although the genome and protein kinases of F. gigantica provided new insights to understand the molecular biology and etiology of this parasite, there is scant knowledge of protein phosphorylation events in F. gigantica. In this study, we characterized the global phosphoproteomics of adult F. gigantica by phosphopeptide enrichment-based LC–MS/MS, a high-throughput analysis to maximize the detection of a large repertoire of phosphoproteins and phosphosites. A total of 1030 phosphopeptides with 1244 phosphosites representing 635 F. gigantica phosphoproteins were identified. The phosphoproteins were involved in a wide variety of biological processes including cellular, metabolic, and single-organism processes. Meanwhile, these proteins were found predominantly in cellular components like membranes and organelles with molecular functions of binding (51.3%) and catalytic activity (40.6%). The KEGG annotation inferred that the most enriched pathways of the phosphoproteins included tight junction, spliceosome, and RNA transport (each one contains 15 identified proteins). Combining the reports in other protozoa and helminths, the phosphoproteins identified in this work play roles in metabolic regulation and signal transduction. To our knowledge, this work performed the first global phosphoproteomics analysis of adult F. gigantica, which provides valuable information for development of intervention strategies for fascioliasis.
Collapse
|
10
|
Liu SY, Ikegami K. Nuclear lamin phosphorylation: an emerging role in gene regulation and pathogenesis of laminopathies. Nucleus 2021; 11:299-314. [PMID: 33030403 PMCID: PMC7588210 DOI: 10.1080/19491034.2020.1832734] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Decades of studies have established that nuclear lamin polymers form the nuclear lamina, a protein meshwork that supports the nuclear envelope structure and tethers heterochromatin to the nuclear periphery. Much less is known about unpolymerized nuclear lamins in the nuclear interior, some of which are now known to undergo specific phosphorylation. A recent finding that phosphorylated lamins bind gene enhancer regions offers a new hypothesis that lamin phosphorylation may influence transcriptional regulation in the nuclear interior. In this review, we discuss the regulation, localization, and functions of phosphorylated lamins. We summarize kinases that phosphorylate lamins in a variety of biological contexts. Our discussion extends to laminopathies, a spectrum of degenerative disorders caused by lamin gene mutations, such as cardiomyopathies and progeria. We compare the prevailing hypothesis for laminopathy pathogenesis based on lamins’ function at the nuclear lamina with an emerging hypothesis based on phosphorylated lamins’ function in the nuclear interior.
Collapse
Affiliation(s)
- Sunny Yang Liu
- Department of Pediatrics, The University of Chicago , Chicago, Illinois, USA
| | - Kohta Ikegami
- Department of Pediatrics, The University of Chicago , Chicago, Illinois, USA.,Division of Molecular and Cardiovascular Biology, Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio, USA
| |
Collapse
|
11
|
Cao L, Wang Z, Zhang D, Li X, Hou C, Ren C. Phosphorylation of myosin regulatory light chain at Ser17 regulates actomyosin dissociation. Food Chem 2021; 356:129655. [PMID: 33831832 DOI: 10.1016/j.foodchem.2021.129655] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 11/19/2022]
Abstract
Phosphorylation of myosin regulatory light chain (MRLC) can regulate muscle contraction and thus affect actomyosin dissociation and meat quality. The objective of this study was to explore the mechanism by how MRLC phosphorylation regulates actomyosin dissociation and thus develop strategies for improving meat quality. Here, the phosphorylation status of MRLC was modulated by myosin light chain kinase and myosin light chain kinase inhibitor. MRLC phosphorylation at Ser17 decreased the kinetic energy and total energy of actomyosin, thus stabilized the structure, facilitating the interaction between myosin and actin; this was one possible way that MRLC phosphorylation at Ser17 negatively affects actomyosin dissociation. Moreover, MRLC phosphorylation at Ser17 was beneficial to the formation of ionic bonds, hydrogen bonds, and hydrophobic interaction between myosin and actin, and was the second possible way that MRLC phosphorylation at Ser17 negatively affects actomyosin dissociation.
Collapse
Affiliation(s)
- Lichuang Cao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China; Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg C, Denmark.
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
| | - Xin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Chengli Hou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Chi Ren
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| |
Collapse
|
12
|
Safabakhsh S, Panwar P, Barichello S, Sangha SS, Hanson PJ, Van Petegem F, Laksman Z. THE ROLE OF PHOSPHORYLATION IN ATRIAL FIBRILLATION: A FOCUS ON MASS SPECTROMETRY APPROACHES. Cardiovasc Res 2021; 118:1205-1217. [PMID: 33744917 DOI: 10.1093/cvr/cvab095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/16/2021] [Indexed: 11/14/2022] Open
Abstract
Atrial fibrillation (AF) is the most common arrhythmia worldwide. It is associated with significant increases in morbidity in the form of stroke and heart failure, and a doubling in all-cause mortality. The pathophysiology of AF is incompletely understood, and this has contributed to a lack of effective treatments and disease-modifying therapies. An important cellular process that may explain how risk factors give rise to AF includes post-translational modification (PTM) of proteins. As the most commonly occurring PTM, protein phosphorylation is especially relevant. Although many methods exist for studying protein phosphorylation, a common and highly resolute technique is mass spectrometry (MS). This review will discuss recent evidence surrounding the role of protein phosphorylation in the pathogenesis of AF. MS-based technology to study phosphorylation and uses of MS in other areas of medicine such as oncology will also be presented. Based on these data, future goals and experiments will be outlined that utilize MS technology to better understand the role of phosphorylation in AF and elucidate its role in AF pathophysiology. This may ultimately allow for the development of more effective AF therapies.
Collapse
Affiliation(s)
- Sina Safabakhsh
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pankaj Panwar
- AbCellera Biologicals Inc., Vancouver, British Columbia, Canada
| | - Scott Barichello
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarabjit S Sangha
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, British Columbia, Canada.,Molecular Cardiac Physiology Group, Departments of Biomedical Physiology and Kinesiology and Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada
| | - Paul J Hanson
- UBC Heart Lung Innovation Centre, Vancouver, British Columbia, Canada.,UBC Department of Pathology and Laboratory Medicine, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zachary Laksman
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
13
|
Juarez-Escobar J, Elizalde-Contreras JM, Loyola-Vargas VM, Ruiz-May E. A Phosphoproteomic Analysis Pipeline for Peels of Tropical Fruits. Methods Mol Biol 2021; 2139:179-196. [PMID: 32462587 DOI: 10.1007/978-1-0716-0528-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Phosphorylation is a posttranslational reversible modification related to signaling and regulatory mechanisms. Protein phosphorylation is linked to structural changes that modulate protein activity, interaction, or localization and therefore the cell signaling pathways. The use of techniques for phosphoprotein enrichment along with mass spectrometry has become a powerful tool for the characterization of signal transduction in model organisms. However, limited efforts have focused on the establishment of protocols for the analysis of the phosphoproteome in nonmodel organisms such as tropical fruits. This chapter describes a potential pipeline for sample preparation and enrichment of phosphorylated proteins/peptides before MS analysis of peels of some species of tropical fruits.
Collapse
Affiliation(s)
- Janet Juarez-Escobar
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán (CICY), Mérida, Yucatán, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Liu W, Tang H, Abuzeid AMI, Tan L, Wang A, Wan X, Zhang H, Liu Y, Li G. Protein phosphorylation networks in spargana of Spirometra erinaceieuropaei revealed by phosphoproteomic analysis. Parasit Vectors 2020; 13:248. [PMID: 32404185 PMCID: PMC7218563 DOI: 10.1186/s13071-020-04119-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/06/2020] [Indexed: 01/07/2023] Open
Abstract
Background Sparganosis caused by Spirometra erinaceieuropaei spargana is a zoonotic parasitic infection that has been reported in many countries, including China, Japan, Thailand and Korea, as well as European countries and the USA. The biological and clinical significance of the parasite have previously been reported. Although the genomic and transcriptomic analysis of S. erinaceieuropaei provided insightful views about the development and pathogenesis of this species, little knowledge has been acquired in terms of post-translational regulation that is essential for parasite growth, development and reproduction. Here, we performed site-specific phosphoproteomic profiling, with an aim to obtain primary information about the global phosphorylation status of spargana. Results A total of 3228 phosphopeptides and 3461 phosphorylation sites were identified in 1758 spargana proteins. The annotated phosphoproteins were involved in a variety of biological pathways, including cellular (28%), metabolic (20%) and single-organism (17%) processes. The functional enrichment of phosphopeptides by Gene Ontology analysis indicated that most spargana phosphoproteins were related to the cytoskeleton cellular compartment, signaling molecular function, and a variety of biological processes, including a molecular function regulator, guanyl-nucleotide exchange factor activity, protein kinase activities, and calcium ion binding. The highly enriched pathways of phosphorylation proteins include the phosphatidylinositol signaling system, phagosome, endocytosis, inositol phosphate metabolism, terpenoid backbone biosynthesis, and peroxisome. Domain analysis identified an EF-hand domain and pleckstrin homology domain among the key domains. Conclusions To our knowledge, this study performed the first global phosphoproteomic analysis of S. erinaceieuropaei. The dataset reported herein provides a valuable resource for future studies on the signaling pathways of this important zoonotic parasite.![]()
Collapse
Affiliation(s)
- Wei Liu
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China.,The Key Laboratory of Animal Vaccine & Protein Engineering, Changsha, 410128, Hunan, People's Republic of China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, People's Republic of China
| | - Asmaa M I Abuzeid
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Lei Tan
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China.,The Key Laboratory of Animal Vaccine & Protein Engineering, Changsha, 410128, Hunan, People's Republic of China
| | - Aibing Wang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China.,The Key Laboratory of Animal Vaccine & Protein Engineering, Changsha, 410128, Hunan, People's Republic of China
| | - Xueping Wan
- Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA, 30912, USA
| | - Haoji Zhang
- College of Life Science and Engineering, Foshan University, Foshan, 528225, Guangdong Province, People's Republic of China
| | - Yisong Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China. .,Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA, 30912, USA.
| | - Guoqing Li
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| |
Collapse
|
16
|
Dai L, Sun Z, Zhou P. Modification of Luffa Sponge for Enrichment of Phosphopeptides. Int J Mol Sci 2019; 21:ijms21010101. [PMID: 31877829 PMCID: PMC6982136 DOI: 10.3390/ijms21010101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
The enrichment technique is crucial to the comprehensive analysis of protein phosphorylation. In this work, a facile, green and efficient synthetic method was set up for quaternization of luffa sponge. The resultant luffa sponge showed strong anion-exchange characteristics and a high adsorption ability for phosphate ions. Along with the unique physical properties, e.g., tenacity and porous texture, quaternized luffa sponge was demonstrated to be a well-suited solid-phase extraction (SPE) material. The quaternized luffa sponge-based SPE method was simple, cost-effective and convenient in operation, and was successfully applied to the capture of phosphopeptides from protein digests. The enrichment approach exhibited exceptionally high selectivity, sensitivity and strong anti-interference ability. Four phosphopeptides were still detected by using the digest mixture of β-casein and bovine serum albumin with a molar ratio of 1:100. 21 phosphopeptides were identified from the tryptic digest of non-fat milk.
Collapse
|
17
|
Diao S, Yang H, Cao Y, Yang D, Fan Z. IGF2 enhanced the osteo-/dentinogenic and neurogenic differentiation potentials of stem cells from apical papilla. J Oral Rehabil 2019; 47 Suppl 1:55-65. [PMID: 31291686 DOI: 10.1111/joor.12859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/27/2022]
Abstract
OBJECTIVES In dental tissue engineering, niche is important for maintaining stem cell function and regenerating the dental tissues. However, there is limited knowledge for the growth factors in niche to maintain the function of stem cells. In this study, we investigated the effect of IGF2, a growth factor in stem cells from apical papilla (SCAPs) niche, on differentiation and proliferation potentials of SCAPs. MATERIALS AND METHODS Recombinant human IGF2 protein (rhIGF2) was used. Cell counting kit-8 assay, Carboxyfluorescein succinimidyl ester assay, alkaline phosphatase (ALP) activity, Alizarin Red staining, quantitative calcium analysis, immunofluorescence staining and real-time RT-PCR were performed to investigate the cell proliferation and differentiation potentials of SCAPs. And proteomic analysis was used to identify the differential secreted proteins. RESULTS By ALP activity assay, we found that 5 ng/mL rhIGF2 might be the optimal concentration for treatment. Then, Alizarin Red staining, quantitative calcium analysis and osteogenesis-related gene expression results showed that 5 ng/mL rhIGF2 could enhance the osteo-/dentinogenic differentiation potentials in SCAPs. Immunofluorescence staining and real-time RT-PCR results showed that neurogenic markers were significantly induced by 5 ng/mL rhIGF2 in SCAPs. Then, CCK-8 assay and CFSE assay results showed that 5 ng/mL rhIGF2 could enhance the cell proliferation in SCAPs. Furthermore, proteomic analysis showed that IGF2 could induce some secreted proteins which function related to the osteogenesis, neurogenesis and cell proliferation. CONCLUSIONS Our results identified that IGF2 might be the potential mediator in niche to promote SCAP function and dental tissue regeneration.
Collapse
Affiliation(s)
- Shu Diao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Pediatric dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Haoqing Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Yangyang Cao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Dongmei Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Pediatric dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| |
Collapse
|
18
|
Jiang Y, Sun A, Zhao Y, Ying W, Sun H, Yang X, Xing B, Sun W, Ren L, Hu B, Li C, Zhang L, Qin G, Zhang M, Chen N, Zhang M, Huang Y, Zhou J, Zhao Y, Liu M, Zhu X, Qiu Y, Sun Y, Huang C, Yan M, Wang M, Liu W, Tian F, Xu H, Zhou J, Wu Z, Shi T, Zhu W, Qin J, Xie L, Fan J, Qian X, He F. Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma. Nature 2019; 567:257-261. [PMID: 30814741 DOI: 10.1038/s41586-019-0987-8] [Citation(s) in RCA: 529] [Impact Index Per Article: 105.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 02/01/2019] [Indexed: 12/28/2022]
Abstract
Hepatocellular carcinoma is the third leading cause of deaths from cancer worldwide. Infection with the hepatitis B virus is one of the leading risk factors for developing hepatocellular carcinoma, particularly in East Asia1. Although surgical treatment may be effective in the early stages, the five-year overall rate of survival after developing this cancer is only 50-70%2. Here, using proteomic and phospho-proteomic profiling, we characterize 110 paired tumour and non-tumour tissues of clinical early-stage hepatocellular carcinoma related to hepatitis B virus infection. Our quantitative proteomic data highlight heterogeneity in early-stage hepatocellular carcinoma: we used this to stratify the cohort into the subtypes S-I, S-II and S-III, each of which has a different clinical outcome. S-III, which is characterized by disrupted cholesterol homeostasis, is associated with the lowest overall rate of survival and the greatest risk of a poor prognosis after first-line surgery. The knockdown of sterol O-acyltransferase 1 (SOAT1)-high expression of which is a signature specific to the S-III subtype-alters the distribution of cellular cholesterol, and effectively suppresses the proliferation and migration of hepatocellular carcinoma. Finally, on the basis of a patient-derived tumour xenograft mouse model of hepatocellular carcinoma, we found that treatment with avasimibe, an inhibitor of SOAT1, markedly reduced the size of tumours that had high levels of SOAT1 expression. The proteomic stratification of early-stage hepatocellular carcinoma presented in this study provides insight into the tumour biology of this cancer, and suggests opportunities for personalized therapies that target it.
Collapse
Affiliation(s)
- Ying Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Aihua Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yang Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Huichuan Sun
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinrong Yang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baocai Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Wei Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Liangliang Ren
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Bo Hu
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chaoying Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Li Zhang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Guangrong Qin
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Menghuan Zhang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Ning Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Manli Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yin Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jinan Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yan Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xiaodong Zhu
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Qiu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yanjun Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Cheng Huang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Meng Yan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wei Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Fang Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Huali Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jian Zhou
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhenyu Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Weimin Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery & Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China. .,College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China.
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | | |
Collapse
|
19
|
Liu B, Lu Y, Wang B, Yan Y, Liang H, Yang H. Facile Preparation of Hydrophilic Dual Functional Magnetic Metal-Organic Frameworks as a Platform for Proteomics Research. ChemistrySelect 2019. [DOI: 10.1002/slct.201803527] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Bin Liu
- School of Materials Science and Chemical Engineering; Ningbo University, Ningbo; Zhejiang 315211 P. R. China
| | - Yujie Lu
- School of Materials Science and Chemical Engineering; Ningbo University, Ningbo; Zhejiang 315211 P. R. China
| | - Baichun Wang
- School of Materials Science and Chemical Engineering; Ningbo University, Ningbo; Zhejiang 315211 P. R. China
| | - Yinghua Yan
- School of Materials Science and Chemical Engineering; Ningbo University, Ningbo; Zhejiang 315211 P. R. China
| | - Hongze Liang
- School of Materials Science and Chemical Engineering; Ningbo University, Ningbo; Zhejiang 315211 P. R. China
| | - Huayan Yang
- Key Laboratory of Green Chemical Media and Reactions; School of Chemistry and Chemical Engineering; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Ministry of Education; Henan Normal University; Xinxiang P. R. China
| |
Collapse
|
20
|
Yuan H, Jiang B, Zhao B, Zhang L, Zhang Y. Recent Advances in Multidimensional Separation for Proteome Analysis. Anal Chem 2018; 91:264-276. [DOI: 10.1021/acs.analchem.8b04894] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Huiming Yuan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Bo Jiang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Baofeng Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| |
Collapse
|
21
|
Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
Collapse
Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| |
Collapse
|
22
|
PhoPepMass: A database and search tool assisting human phosphorylation peptide identification from mass spectrometry data. J Genet Genomics 2018; 45:381-388. [PMID: 30055873 DOI: 10.1016/j.jgg.2018.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 11/20/2022]
Abstract
Protein phosphorylation, one of the most important protein post-translational modifications, is involved in various biological processes, and the identification of phosphorylation peptides (phosphopeptides) and their corresponding phosphorylation sites (phosphosites) will facilitate the understanding of the molecular mechanism and function of phosphorylation. Mass spectrometry (MS) provides a high-throughput technology that enables the identification of large numbers of phosphosites. PhoPepMass is designed to assist human phosphopeptide identification from MS data based on a specific database of phophopeptide masses and a multivariate hypergeometric matching algorithm. It contains 244,915 phosphosites from several public sources. Moreover, the accurate masses of peptides and fragments with phosphosites were calculated. It is the first database that provides a systematic resource for the query of phosphosites on peptides and their corresponding masses. This allows researchers to search certain proteins of which phosphosites have been reported, to browse detailed phosphopeptide and fragment information, to match masses from MS analyses with defined threshold to the corresponding phosphopeptide, and to compare proprietary phosphopeptide discovery results with results from previous studies. Additionally, a database search software is created and a "two-stage search strategy" is suggested to identify phosphopeptides from tandem mass spectra of proteomics data. We expect PhoPepMass to be a useful tool and a source of reference for proteomics researchers. PhoPepMass is available at https://www.scbit.org/phopepmass/index.html.
Collapse
|
23
|
Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA. Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. J Proteome Res 2018; 17:2226-2236. [PMID: 29734811 DOI: 10.1021/acs.jproteome.8b00217] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and, by inference, thousands of proteins from multiple samples in a single MS experiment. Accurate quantification demands a consistent and robust sample-preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of tandem mass tag (TMT)-labeled proteins and phosphopeptides that we have named the streamlined (SL)-TMT protocol. We describe a universally applicable strategy that requires minimal individual sample processing and permits the seamless addition of a phosphopeptide enrichment step ("mini-phos") with little deviation from the deep proteome analysis. To showcase our workflow, we profile the proteome of wild-type Saccharomyces cerevisiae yeast grown with either glucose or pyruvate as the carbon source. Here, we have established a streamlined TMT protocol that enables deep proteome and medium-scale phosphoproteome analysis.
Collapse
Affiliation(s)
- José Navarrete-Perea
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Qing Yu
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| |
Collapse
|
24
|
Liu H, Lian B. A guanidyl-functionalized TiO2 nanoparticle-anchored graphene nanohybrid for enhanced capture of phosphopeptides. RSC Adv 2018; 8:29476-29481. [PMID: 35547983 PMCID: PMC9084561 DOI: 10.1039/c8ra05006f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/13/2018] [Accepted: 08/12/2018] [Indexed: 12/31/2022] Open
Abstract
A novel TiO2-based MOAC hybrid nanomaterial was successfully synthesized and applied as a biofunctional adsorbent for selective enrichment of trace phosphopeptides.
Collapse
Affiliation(s)
- Hailong Liu
- College of Life Sciences
- Nanjing Normal University
- Nanjing
- China
- State Key Laboratory of Environmental Geochemistry
| | - Bin Lian
- College of Life Sciences
- Nanjing Normal University
- Nanjing
- China
| |
Collapse
|