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Zhou YT, Li S, Du SL, Zhao JH, Cai YQ, Zhang ZQ. The multifaceted role of macrophage mitophagy in SiO 2-induced pulmonary fibrosis: A brief review. J Appl Toxicol 2024. [PMID: 38644760 DOI: 10.1002/jat.4612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/23/2024]
Abstract
Prolonged exposure to environments with high concentrations of crystalline silica (CS) can lead to silicosis. Macrophages play a crucial role in the pathogenesis of silicosis. In the process of silicosis, silica (SiO2) invades alveolar macrophages (AMs) and induces mitophagy which usually exists in three states: normal, excessive, and/or deficiency. Different mitophagy states lead to corresponding toxic responses, including successful macrophage repair, injury, necrosis, apoptosis, and even pulmonary fibrosis. This is a complex process accompanied by various cytokines. Unfortunately, the details have not been fully systematically summarized. Therefore, it is necessary to elucidate the role of macrophage mitophagy in SiO2-induced pulmonary fibrosis by systematic analysis on the literature reports. In this review, we first summarized the current data on the macrophage mitophagy in the development of SiO2-induced pulmonary fibrosis. Then, we introduce the molecular mechanism on how SiO2-induced mitophagy causes pulmonary fibrosis. Finally, we focus on introducing new therapies based on newly developed mitophagy-inducing strategies. We conclude that macrophage mitophagy plays a multifaceted role in the progression of SiO2-induced pulmonary fibrosis, and reprogramming the macrophage mitophagy state accordingly may be a potential means of preventing and treating pulmonary fibrosis.
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Affiliation(s)
- Yu-Ting Zhou
- Department of Public Health, Shandong First Medical University, Jinan, China
- Department of Public Health, Jining Medical University, Jining, China
| | - Shuang Li
- Department of Public Health, Jining Medical University, Jining, China
| | - Shu-Ling Du
- Department of Public Health, Jining Medical University, Jining, China
| | - Jia-Hui Zhao
- Department of Public Health, Jining Medical University, Jining, China
| | | | - Zhao-Qiang Zhang
- Department of Public Health, Jining Medical University, Jining, China
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Morin L, Lecureur V, Lescoat A. Results from omic approaches in rat or mouse models exposed to inhaled crystalline silica: a systematic review. Part Fibre Toxicol 2024; 21:10. [PMID: 38429797 PMCID: PMC10905840 DOI: 10.1186/s12989-024-00573-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/26/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Crystalline silica (cSiO2) is a mineral found in rocks; workers from the construction or denim industries are particularly exposed to cSiO2 through inhalation. cSiO2 inhalation increases the risk of silicosis and systemic autoimmune diseases. Inhaled cSiO2 microparticles can reach the alveoli where they induce inflammation, cell death, auto-immunity and fibrosis but the specific molecular pathways involved in these cSiO2 effects remain unclear. This systematic review aims to provide a comprehensive state of the art on omic approaches and exposure models used to study the effects of inhaled cSiO2 in mice and rats and to highlight key results from omic data in rodents also validated in human. METHODS The protocol of systematic review follows PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Eligible articles were identified in PubMed, Embase and Web of Science. The search strategy included original articles published after 1990 and written in English which included mouse or rat models exposed to cSiO2 and utilized omic approaches to identify pathways modulated by cSiO2. Data were extracted and quality assessment was based on the SYRCLE's Risk of Bias tool for animal studies. RESULTS Rats and male rodents were the more used models while female rodents and autoimmune prone models were less studied. Exposure of animals were both acute and chronic and the timing of outcome measurement through omics approaches were homogeneously distributed. Transcriptomic techniques were more commonly performed while proteomic, metabolomic and single-cell omic methods were less utilized. Immunity and inflammation were the main domains modified by cSiO2 exposure in lungs of mice and rats. Less than 20% of the results obtained in rodents were finally verified in humans. CONCLUSION Omic technics offer new insights on the effects of cSiO2 exposure in mice and rats although the majority of data still need to be validated in humans. Autoimmune prone model should be better characterised and systemic effects of cSiO2 need to be further studied to better understand cSiO2-induced autoimmunity. Single-cell omics should be performed to inform on pathological processes induced by cSiO2 exposure.
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Affiliation(s)
- Laura Morin
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en sante, environnement et travail), UMR_S 1085, 35000, Rennes, France
| | - Valérie Lecureur
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en sante, environnement et travail), UMR_S 1085, 35000, Rennes, France.
| | - Alain Lescoat
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en sante, environnement et travail), UMR_S 1085, 35000, Rennes, France
- Department of Internal Medicine, Rennes University Hospital, 35000, Rennes, France
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Wang Z, Yadav V, Chen X, Zhang S, Yuan X, Li H, Ma J, Zhang Y, Yang J, Zhang X, Wei C. Multi-Omics Analysis Reveals Intricate Gene Networks Involved in Female Development in Melon. Int J Mol Sci 2023; 24:16905. [PMID: 38069227 PMCID: PMC10706797 DOI: 10.3390/ijms242316905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Sexual differentiation is an important developmental phenomenon in cucurbits that directly affects fruit yield. The natural existence of multiple flower types in melon offers an inclusive structure for studying the molecular basis of sexual differentiation. The current study aimed to identify and characterize the molecular network involved in sex determination and female development in melon. Male and female pools separated by the F2 segregated generation were used for sequencing. The comparative multi-omics data revealed 551 DAPs and 594 DEGs involved in multiple pathways of melon growth and development, and based on functional annotation and enrichment analysis, we summarized four biological process modules, including ethylene biosynthesis, flower organ development, plant hormone signaling, and ubiquitinated protein metabolism, that are related to female development. Furthermore, the detailed analysis of the female developmental regulatory pathway model of ethylene biosynthesis, signal transduction, and target gene regulation identified some important candidates that might have a crucial role in female development. Two CMTs ((cytosine-5)-methyltransferase), one AdoHS (adenosylhomocysteinase), four ACSs (1-aminocyclopropane-1-carboxylic acid synthase), three ACOs (ACC oxidase), two ARFs (auxin response factor), four ARPs (auxin-responsive protein), and six ERFs (Ethylene responsive factor) were identified based on various female developmental regulatory models. Our data offer new and valuable insights into female development and hold the potential to offer a deeper comprehension of sex differentiation mechanisms in melon.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.W.); (V.Y.); (X.C.); (S.Z.); (X.Y.); (H.L.); (J.M.); (Y.Z.); (J.Y.)
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.W.); (V.Y.); (X.C.); (S.Z.); (X.Y.); (H.L.); (J.M.); (Y.Z.); (J.Y.)
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Wang RJ, Li W, Liu SN, Wang SY, Jiang P, Wang ZQ, Zhang X. Integrated transcriptomic and proteomic analyses of plerocercoid and adult Spirometra mansoni reveal potential important pathways in the development of the medical tapeworm. Parasit Vectors 2023; 16:316. [PMID: 37670335 PMCID: PMC10481575 DOI: 10.1186/s13071-023-05941-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Spirometra mansoni can parasitize animals and humans through food and water, causing parasitic zoonosis. Knowledge of the developmental process of S. mansoni is crucial for effective treatment; thus, it is important to characterize differential and specific proteins and pathways associated with parasite development. METHODS In this study, we performed a comparative proteomic analysis of the plerocercoid and adult stages using a tandem mass tag-based quantitative proteomic approach. Additionally, integrated transcriptomic and proteomic analyses were conducted to obtain the full protein expression profiles of different life cycle stages of the tapeworm. RESULTS Approximately 1166 differentially expressed proteins (DEPs) were identified in adults versus plerocercoids, of which 641 DEPs were upregulated and 525 were downregulated. Gene Ontology (GO), Clusters of Orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most DEPs related to genetic information processing and metabolism of energy in adults seem to be more activated. In the plerocercoid stage, compared to metabolism, genetic information processing appears more dynamic. Protein-protein interaction (PPI) revealed six key proteins (phosphomannomutase, glutathione transferase, malate dehydrogenase, cytoplasmic, 40S ribosomal protein S15, ribosomal protein L15 and 60S acidic ribosomal protein P2) that may play active roles in the growth and development of S. mansoni. Finally, the combination of transcriptomic and proteomic data suggested that three pathways (ubiquitin-mediated proteolysis, phagosome and spliceosome) and five proteins closely related to these pathways might have a significant influence in S. mansoni. CONCLUSIONS These findings contribute to increasing the knowledge on the protein expression profiles of S. mansoni and provide new insights into functional studies on the molecular mechanisms of the neglected medical tapeworm.
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Affiliation(s)
- Rui Jie Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Wen Li
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Shi Nan Liu
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Si Yao Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Peng Jiang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhong Quan Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xi Zhang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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Chen D, Chen C, Guo C, Zhang H, Liang Y, Cheng Y, Qu H, Wa Y, Zhang C, Guan C, Qian J, Gu R. The regulation of simulated artificial oro-gastrointestinal transit stress on the adhesion of Lactobacillus plantarum S7. Microb Cell Fact 2023; 22:170. [PMID: 37660047 PMCID: PMC10474686 DOI: 10.1186/s12934-023-02174-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 08/09/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND Oro-gastrointestinal stress in the digestive tract is the main stress to which orally administered probiotics are exposed. The regulation of oro-gastrointestinal transit (OGT) stress on the adhesion and survival of probiotics under continuous exposure to simulated salivary-gastric juice-intestinal juice was researched in this study. RESULTS Lactobacillus plantarum S7 had a higher survival rate after exposure to simulated OGT1 (containing 0.15% bile salt) stress and OGT2 (containing 0.30% bile salt) stress. The adhesion ability of L. plantarum S7 was significantly increased by OGT1 stress (P < 0.05) but was not changed significantly by OGT2 stress (P > 0.05), and this trend was also observed in terms of the thickness of the surface material of L. plantarum S7 cells. The expression of surface proteins of L. plantarum S7, such as the 30 S ribosomal proteins, mucus-binding protein and S-layer protein, was significantly downregulated by OGT stress (P < 0.05); meanwhile, the expression of moonlight proteins, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycorate kinase (PGK), beta-phosphoglucomutase (PGM1), GroEL and glucose-6-phosphate isomerase (PGI), was significantly upregulated (P < 0.05). However, the upregulation of GAPDH, PGK, PGM1 and PGI mediated by OGT1 stress was greater than those mediated by OGT2 stress. The quorum sensing pathway of L. plantarum S7 was changed significantly by OGT stress compared with no OGT stress cells (P < 0.05), and the expression of Luxs in the pathway was significantly upregulated by OGT1 stress (P < 0.05). The ABC transportation pathway was significantly altered by OGT1 stress (P < 0.05), of which the expression of the peptide ABC transporter substrate-binding protein and energy-coupling factor transporter ATP-binding protein EcfA was significantly upregulated by OGT stress (P < 0.05). The glycolide metabolism pathway was significantly altered by OGT1 stress compared with that in response to OGT2 stress (P < 0.05). CONCLUSION L. plantarum S7 had a strong ability to resist OGT stress, which was regulated by the proteins and pathways related to OGT stress. The adhesion ability of L. plantarum S7 was enhanced after continuous exposure to OGT1 stress, making it a potential probiotic with a promising future for application.
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Affiliation(s)
- Dawei Chen
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
- Jiangsu Yuhang Food Technology Co., Ltd, Yancheng, 224000, Jiangsu, China
| | - Chunmeng Chen
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Congcong Guo
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Hui Zhang
- Yangzhou Hospital of Traditional Chinese Medicine, Yangzhou, 225127, Jiangsu, China
| | - Yating Liang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Yue Cheng
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Hengxian Qu
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Yunchao Wa
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Chenchen Zhang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Chengran Guan
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Jianya Qian
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China
| | - Ruixia Gu
- College of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China.
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, 225127, Jiangsu, China.
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Zhang L, Wu F, Fan C, Huang S, Ma Y, Chen S, Zhang J, Jiang H. Quantitative phosphoproteomic analysis of mice with liver fibrosis by DIA mass spectrometry analysis with PRM verification. J Proteomics 2023; 271:104768. [PMID: 36336261 DOI: 10.1016/j.jprot.2022.104768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Liver fibrosis (LF), commonly associated with chronic liver diseases, is a major public health problem worldwide. Protein phosphorylation is not only an important form of protein modification in organisms but also the most important mechanism to regulate and control the activity and function of proteins, affecting the occurrence and development of many diseases. However, comprehensive phosphoproteomic profiling in LF has not been fully elucidated. In this study, data-independent acquisition (DIA) was used to analyse the phosphoproteomics of mice with LF. A total of 553 phosphopeptides (representing 440 phosphoproteins) had significant phosphorylation levels. Among these phosphoproteins, 49 were upregulated and 401 were downregulated, and 5 phosphoserine (P-Ser) motifs and 2 phosphothreonine (P-Thr) motifs were conserved in LF. GO and KEGG pathway enrichment analyses identified 769 significant GO terms and 49 significant KEGG pathways. Four phosphorylated proteins were selected for parallel reaction monitoring (PRM) verification, and the results were consistent with DIA data. Together, there were significantly different phosphoproteomic profiles in LF, suggesting that protein phosphorylation was related to the occurrence and progression of LF, which could pave the way for further investigation into the related regulatory mechanisms. SIGNIFICANCE: LF is a necessary stage in the development of chronic liver disease to liver cirrhosis and has attracted wide attention. To the best of our knowledge, there are few reports on the phosphorylated proteomics of LF. In this study, DIA and PRM techniques were used to study the liver tissue of mice induced by CCl4. The results showed that phosphorylation had a significant effect on the activity and function of proteins, and the PRM results were consistent with the trend observed in DIA analysis. This study will help to better reveal the relationship of phosphorylated proteins in LF and lay a foundation for further study of related regulatory mechanisms.
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Affiliation(s)
- Lili Zhang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Furong Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Shaopeng Huang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Yanzhen Ma
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Sen Chen
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Jiafu Zhang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
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Pan H, Yu Q, Qian C, Shao H, Li Y, Lou Y. Effects of Electron Beam Irradiation on Portunus trituberculatus Based on Tandem-Mass Tag-Based Quantitative Proteomic Analysis. Journal of Aquatic Food Product Technology 2022. [DOI: 10.1080/10498850.2022.2119117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Huijuan Pan
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, P R China
| | - Qi Yu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, P R China
| | - Chenru Qian
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, P R China
| | - Haitao Shao
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, P R China
| | - Yongyong Li
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, P R China
| | - Yongjiang Lou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, P R China
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Xu D, Zhu X, Ren J, Huang S, Xiao Z, Jiang H, Tan Y. Quantitative proteomic analysis of cervical cancer based on TMT-labeled quantitative proteomics. J Proteomics 2022; 252:104453. [PMID: 34915198 DOI: 10.1016/j.jprot.2021.104453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022]
Abstract
Cervical cancer is the second most common gynecological malignancy, which immensely threatens the well-being of women. However, the pathogenesis of cervical cancer is still unclear. Using tandem mass tags-labeled quantitative proteomic technology and bioinformatics tools, we analyzed the exfoliated cervical cells from the normal and cervical cancer groups to establish a cancer-specific protein profile, thereby identifying key proteins related to cervical oncogenesis. When compared with the normal group, a total of 351 differentially expressed proteins were identified in the cervical cancer group, including 247 up-regulated and 104 down-regulated proteins. Gene ontology function annotation revealed that the differentially expressed proteins were mainly involved in the single-multicellular organism process, multicellular organismal process, and negative regulation of biological process. These proteins were discerned to play a role in the extracellular membrane-bounded organelle, exosome of cell components, protein binding, structural molecule activity, and enzyme binding of molecular functions. The results of Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment proved that these differentially expressed proteins were mainly involved in PI3K - Akt, ECM-receptor interaction, complement and coagulation cascades, and other signaling pathways. Particularly, peroxiredoxin-2 may be involved in cervical tumor oncogenesis through inhibition of apoptosis signaling. SIGNIFICANCE: In this study, we determined that the proteins of the cervical cancer group exhibited qualitative and quantitative changes, and a total of 351 differentially expressed proteins were identified. The functions and signaling pathways of these differentially expressed proteins have laid a theoretical foundation for elucidating the molecular mechanism of cervical cancer.
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Affiliation(s)
- Dianqin Xu
- Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Xiaoyu Zhu
- Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Ji Ren
- School of Laboratory Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Shan Huang
- School of Laboratory Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Ziwen Xiao
- Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Hongmei Jiang
- School of Laboratory Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yujie Tan
- Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, China; School of Laboratory Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China.
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Bo C, Zhang J, Sai L, Du Z, Yu G, Li C, Li M, Peng C, Jia Q, Shao H. Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats. BMC Pulm Med 2022; 22:13. [PMID: 34991559 DOI: 10.1186/s12890-021-01807-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/13/2021] [Indexed: 11/10/2022] Open
Abstract
Background Silicosis is a systemic disease characterized by persistent inflammation and incurable pulmonary fibrosis. Although great effort has been made to understand the pathogenesis of the disease, molecular mechanism underlying silicosis is not fully elucidated. This study was aimed to explore proteomic and transcriptomic changes in rat model of silicosis. Methods Twenty male Wistar rats were randomly divided into two groups with 10 rats in each group. Rats in the model group were intratracheally instilled with 50 mg/mL silicon dioxide (1 mL per rat) and rats in the control group were treated with 1.0 mL saline (1 mL per rat). Twenty-eight days later, transcriptomic analysis by microarray and tandem mass tags (TMT)-based proteomic analysis were performed to reveal the expression of mRNAs and proteins in lung tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to analyze the altered genes and proteins. The integrated analysis was performed between transcriptome and proteome. The data were further verified by RT-qPCR and parallel reaction monitoring (PRM). Results In total, 1769 differentially expressed genes (DEGs) and 650 differentially expressed proteins (DEPs) were identified between the silicosis model and control groups. The integrated analysis showed 250 DEPs were correlated to the corresponding DEGs (cor-DEPs-DEGs), which were mainly enriched in phagosome, leukocyte transendothelial migration, complement and coagulation cascades and cellular adhesion molecule (CAM). These pathways are interrelated and converged at common points to produce an effect. GM2a, CHI3L1, LCN2 and GNAI1 are involved in the extracellular matrix (ECM) and inflammation contributing to fibrosis. Conclusion Our comprehensive transcriptome and proteome data provide new insights into the mechanisms of silicosis and helpful information for more targeted prevention and treatment of silicosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01807-w.
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Zhang D, Liu T, Sheng J, Lv S, Ren L. TMT-Based Quantitative Proteomic Analysis Reveals the Physiological Regulatory Networks of Embryo Dehydration Protection in Lotus ( Nelumbo nucifera). Front Plant Sci 2021; 12:792057. [PMID: 34975978 PMCID: PMC8718645 DOI: 10.3389/fpls.2021.792057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Lotus is an aquatic plant that is sensitive to water loss, but its seeds are longevous after seed embryo dehydration and maturation. The great difference between the responses of vegetative organs and seeds to dehydration is related to the special protective mechanism in embryos. In this study, tandem mass tags (TMT)-labeled proteomics and parallel reaction monitoring (PRM) technologies were used to obtain novel insights into the physiological regulatory networks during lotus seed dehydration process. Totally, 60,266 secondary spectra and 32,093 unique peptides were detected. A total of 5,477 proteins and 815 differentially expressed proteins (DEPs) were identified based on TMT data. Of these, 582 DEPs were continuously downregulated and 228 proteins were significantly up-regulated during the whole dehydration process. Bioinformatics and protein-protein interaction network analyses indicated that carbohydrate metabolism (including glycolysis/gluconeogenesis, galactose, starch and sucrose metabolism, pentose phosphate pathway, and cell wall organization), protein processing in ER, DNA repair, and antioxidative events had positive responses to lotus embryo dehydration. On the contrary, energy metabolism (metabolic pathway, photosynthesis, pyruvate metabolism, fatty acid biosynthesis) and secondary metabolism (terpenoid backbone, steroid, flavonoid biosynthesis) gradually become static status during lotus embryo water loss and maturation. Furthermore, non-enzymatic antioxidants and pentose phosphate pathway play major roles in antioxidant protection during dehydration process in lotus embryo. Abscisic acid (ABA) signaling and the accumulation of oligosaccharides, late embryogenesis abundant proteins, and heat shock proteins may be the key factors to ensure the continuous dehydration and storage tolerance of lotus seed embryo. Stress physiology detection showed that H2O2 was the main reactive oxygen species (ROS) component inducing oxidative stress damage, and glutathione and vitamin E acted as the major antioxidant to maintain the REDOX balance of lotus embryo during the dehydration process. These results provide new insights to reveal the physiological regulatory networks of the protective mechanism of embryo dehydration in lotus.
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Affiliation(s)
- Di Zhang
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Liu
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangyuan Sheng
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Lv
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Li Ren
- Institute for Agri-Food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Abstract
Lysosomes are the main degradative organelles of almost all eukaryotic cells. They fulfil a crucial function in cellular homeostasis, and impairments in lysosomal function are connected to a continuously increasing number of pathological conditions. In recent years, lysosomes are furthermore emerging as control centers of cellular metabolism, and major regulators of cellular signaling were shown to be activated at the lysosomal surface. To date, >300 proteins were demonstrated to be located in/at the lysosome, and the lysosomal proteome and interactome is constantly growing. For the identification of these proteins, and their involvement in cellular mechanisms or disease progression, mass spectrometry (MS)-based proteomics has proven its worth in a large number of studies. In this review, we are recapitulating the application of MS-based approaches for the investigation of the lysosomal proteome, and their application to a diverse set of research questions. Numerous strategies were applied for the enrichment of lysosomes or lysosomal proteins and their identification by MS-based methods. This allowed for the characterization of the lysosomal proteome, the investigation of lysosome-related disorders, the utilization of lysosomal proteins as biomarkers for diseases, and the characterization of lysosome-related cellular mechanisms. While these >60 studies provide a comprehensive picture of the lysosomal proteome across several model organisms and pathological conditions, various proteomics approaches have not been applied to lysosomes yet, and a large number of questions are still left unanswered.
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Affiliation(s)
- Pathma Muthukottiappan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Nussallee 11, 53115 Bonn, Germany.
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Nussallee 11, 53115 Bonn, Germany.
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12
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Abstract
Mass spectrometry (MS) is a powerful technique for protein identification, quantification and characterization that is widely applied in biochemical studies, and which can provide data on the quantity, structural integrity and post-translational modifications of proteins. It is therefore a versatile and widely used analytic tool for quality control of biopharmaceuticals, especially in quantifying host-cell protein impurities, identifying post-translation modifications and structural characterization of biopharmaceutical proteins. Here, we summarize recent advances in MS-based analyses of these key quality attributes of the biopharmaceutical development and manufacturing processes.
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13
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Abstract
OBJECTIVES To explore the circulating metabolites and related pathways in silicosis and asbestosis exposure to different mineral dust. METHODS Plasma of 30 silicosis, 30 asbestosis, and 20 healthy controls was analyzed using liquid chromatography-mass spectrometry. Metabolic networks and the relevance of the identified metabolic derangements were explored. RESULTS Compared with healthy controls, 37 and 39 dysregulated plasma metabolites were found in silicosis and asbestosis, respectively, of which the levels of 22 metabolites differed. Three major pathways were identified, among which arginine and proline metabolism was identified as the most closely related metabolic pathway. CONCLUSIONS The types and quantities of up-regulated metabolites including lipids, amino acids, and carnitines differed between silicosis and asbestosis. Pathways inducing lung fibrosis were common to mineral dust exposure, while pathways related to oxidative stress and tumorigenesis differed between silicosis and asbestosis.
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Affiliation(s)
- Mi Zhou
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Workers' Stadium South Road, Chao-Yang District, Beijing 100020, China (Zhou, Xue, Fan, Wu, Ma, Ye), Department of Occupational Diseases and Chemical Poisoning, the Fifth People's Hospital of Suzhou, the Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Xiang-Cheng District, Suzhou 215131, Jiangsu Province, China (Zhou)
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14
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Xie T, Guo J, Jiang Y, Li L, Jiang L, Wei Y. Screening differentially expressed proteins of coronary heart disease with congenital cold syndrome based on tandem mass tag (TMT) technology. Bioengineered 2021; 12:1338-1350. [PMID: 33904367 PMCID: PMC8806272 DOI: 10.1080/21655979.2021.1912546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In our previous studies, we discovered the congenital cold syndrome (CCS), which is characterized by 'qi deficiency and qi stagnation, mixed cold and heat.' And there is a type of syndrome with special incidence characteristic. However, the diagnosis of CCS still lacks an objective basis. In this study, we performed Tandem Mass Tag (TMT) based on quantitative proteomics technology to screen the significantly differentially expressed proteins (DEPs) in serum of patients with coronary heart disease (CHD) patients with CCS, patients with heart and kidney yang deficiency, and healthy people. A total of 22 DEPs (nine upregulated and 13 downregulated) were identified between patients with CCS and healthy subjects. Next, we performed GO and KEGG pathway enrichment analysis, we found the primary functions of DEPs of CCS were binding, catalytic activity, and molecular function regulator. These DEPs were mainly involved in important biological processes, such as cellular process, response to stimulus, localization, metabolic process, and biological regulation. The KEGG analysis revealed that the DEPs showed significant changes in fructose and mannose metabolism, Pentose phosphate pathway, and Arrhythmogenic right ventricular cardiomyopathy. After parallel reaction monitoring (PRM) verification, four upregulated target proteins (ALDOA, PCYOX1, Crisp3 and IGLV4-69) and three downregulated proteins (ALDOC, ADAMTSL-2 and C3) were accurately identified. These proteins were mainly related to immune response and glucose metabolism. These DEPs could be the marker proteins of coronary heart disease with CCS. This findings help to reveal the pathogenesis of CHD with CCS and provide potential therapeutic targets.
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Affiliation(s)
- Tingting Xie
- Changchun University of Chinese Medicine, College of traditional Chinese medicine, Changchun, China
| | - Jiajuan Guo
- Department of cardiovascular medicine, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Yanshu Jiang
- The first clinical hospital of Jilin Province Academy of Traditional Chinese Medicine, Department of orthopedic, Changchun, China
| | - Lijie Li
- Changchun University of Chinese Medicine, College of traditional Chinese medicine, Changchun, China
| | - Lihong Jiang
- Department of cardiovascular medicine, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Yan Wei
- Changchun University of Chinese Medicine, College of Basic Medicine, Changchun, China
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15
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Xue C, Wu N, Fan Y, Ma J, Ye Q. Distinct metabolic features in the plasma of patients with silicosis and dust-exposed workers in China: a case-control study. BMC Pulm Med 2021; 21:91. [PMID: 33731064 PMCID: PMC7971960 DOI: 10.1186/s12890-021-01462-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/09/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Silicosis is a progressive pneumoconiosis characterized by interstitial fibrosis following exposure to silica dust. The role of metabolic dysregulation in the pathogenesis of silicosis has not been investigated in detail. This study aimed to identify different metabolic features in the plasma of patients with silicosis and dust-exposed workers without silicosis in metabolomics studies. METHODS Patients with silicosis, dust-exposed workers (DEWs) without silicosis and age-matched healthy controls were recruited in a case-control study. The metabolomics analyses by ultra-high performance liquid chromatography-mass spectrometry were conducted. Distinct metabolic features (DMFs) were identified in the pilot study and were validated in the validation study. The enriched signalling pathways of these DMFs were determined. The ability of DMFs to discriminate among the groups was analysed through receiver operating characteristic (ROC) curves. The correlations between DMFs and clinical features were also explored. RESULTS Twenty-nine DMFs and 9 DMFs were detected and had the same trend in the pilot study and the validation study in the plasma of the DEW and silicosis groups, respectively. Sphingolipid metabolism was the major metabolic pathway in the DEWs, and arginine and proline metabolism was associated with silicosis. Twenty DMFs in the DEWs and 3 DMFs in the patients with silicosis showed a discriminatory ability with ROC curve analysis. The abundance of kynurenine was higher in Stage III silicosis than in Stage I or Stage II silicosis. L-arginine and kynurenine were both negatively correlated with the percentage of forced vital capacity predicted in silicosis. CONCLUSIONS Distinct metabolic features in the plasma of DEWs and the patients with silicosis were found to be different. Sphingolipid metabolism and arginine and proline metabolism were identified as the major metabolic pathway in the DEW and silicosis groups, respectively. L-arginine and kynurenine were correlated with the severity of silicosis.
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Affiliation(s)
- Changjiang Xue
- Department of Occupational Medicine and Toxicology, Clinical Centre for Interstitial Lung Diseases, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Workers' Stadium South Road, Chao-Yang District, Beijing, 100020, China
| | - Na Wu
- Department of Occupational Medicine and Toxicology, Clinical Centre for Interstitial Lung Diseases, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Workers' Stadium South Road, Chao-Yang District, Beijing, 100020, China
| | - Yali Fan
- Department of Occupational Medicine and Toxicology, Clinical Centre for Interstitial Lung Diseases, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Workers' Stadium South Road, Chao-Yang District, Beijing, 100020, China
| | - Jing Ma
- Department of Occupational Medicine and Toxicology, Clinical Centre for Interstitial Lung Diseases, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Workers' Stadium South Road, Chao-Yang District, Beijing, 100020, China
| | - Qiao Ye
- Department of Occupational Medicine and Toxicology, Clinical Centre for Interstitial Lung Diseases, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Workers' Stadium South Road, Chao-Yang District, Beijing, 100020, China.
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