Xinyu Cheng, Li Kang, Jinfang Liu, Qingye Wang, Zhenpeng Zhang, Li Zhang, Yuping Xie, Lei Chang, Daobing Zeng, Lantian Tian, Lingqiang Zhang, Ping Xu, Yanchang Li
{"title":"蛋白质组学和磷酸化蛋白质组学揭示了肝纤维化的激酶失调和潜在的治疗方法。","authors":"Xinyu Cheng, Li Kang, Jinfang Liu, Qingye Wang, Zhenpeng Zhang, Li Zhang, Yuping Xie, Lei Chang, Daobing Zeng, Lantian Tian, Lingqiang Zhang, Ping Xu, Yanchang Li","doi":"10.1016/j.mcpro.2025.100991","DOIUrl":null,"url":null,"abstract":"<p><p>Liver fibrosis is the initial stage of most liver diseases, and it is also a pathological process involving the liver in the late stages of many metabolic diseases. Therefore, it is important to systematically understand the pathological mechanism of liver fibrosis and seek therapeutic approaches for intervention and treatment of liver fibrosis. Disordered proteins and their post-translational modifications, such as phosphorylation, play vital roles in the occurrence and development of liver fibrosis. However, the regulatory mechanisms that govern this process remain poorly understood. In this study, we analyzed and quantified the liver proteome and phosphoproteome of CCl<sub>4</sub>-induced early liver fibrosis model in mice. Proteomic analysis revealed that the pathways involved in extracellular matrix (ECM) recombination, collagen formation, metabolism and other related disorders, and protein phosphorylation modification pathways were also significantly enriched. In addition, western blotting and phosphoproteomics demonstrated that phosphorylation levels were elevated in the context of liver fibrosis. A total of 13,152 phosphosites were identified, with 952 sites increased while only 156 ones decreased. Furthermore, the upregulated phosphorylation sites, which exhibited no change at the proteome level mainly shared a common [xxxSPxxx] motif. Consequently, the kinases-substrates analysis ascertained the overactive kinases of these up-regulated substrates, which ultimately led to the identification of 13 significantly altered kinases within this dataset. These kinases were mainly catalogued into the STE, CMGC, and CAMK kinase families. Among them, STK4, GSK3α and CDK11B were subsequently validated though cellular and animal experiments, and the results demonstrated that their inhibitors could effectively reduce the activation of hepatic stellate cells and ECM production. 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Proteomics and phosphoproteomics revealed dysregulated kinases and potential therapy for liver fibrosis.
Liver fibrosis is the initial stage of most liver diseases, and it is also a pathological process involving the liver in the late stages of many metabolic diseases. Therefore, it is important to systematically understand the pathological mechanism of liver fibrosis and seek therapeutic approaches for intervention and treatment of liver fibrosis. Disordered proteins and their post-translational modifications, such as phosphorylation, play vital roles in the occurrence and development of liver fibrosis. However, the regulatory mechanisms that govern this process remain poorly understood. In this study, we analyzed and quantified the liver proteome and phosphoproteome of CCl4-induced early liver fibrosis model in mice. Proteomic analysis revealed that the pathways involved in extracellular matrix (ECM) recombination, collagen formation, metabolism and other related disorders, and protein phosphorylation modification pathways were also significantly enriched. In addition, western blotting and phosphoproteomics demonstrated that phosphorylation levels were elevated in the context of liver fibrosis. A total of 13,152 phosphosites were identified, with 952 sites increased while only 156 ones decreased. Furthermore, the upregulated phosphorylation sites, which exhibited no change at the proteome level mainly shared a common [xxxSPxxx] motif. Consequently, the kinases-substrates analysis ascertained the overactive kinases of these up-regulated substrates, which ultimately led to the identification of 13 significantly altered kinases within this dataset. These kinases were mainly catalogued into the STE, CMGC, and CAMK kinase families. Among them, STK4, GSK3α and CDK11B were subsequently validated though cellular and animal experiments, and the results demonstrated that their inhibitors could effectively reduce the activation of hepatic stellate cells and ECM production. These kinases may represent potential therapeutic targets for liver fibrosis, and their inhibitors may serve as promising anti- hepatic fibrosis drugs.
期刊介绍:
The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. MCP will publish manuscripts that report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life. Manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action.
The journal also emphasizes articles that describe innovative new computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data.
Scope:
-Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights
-Novel experimental and computational technologies
-Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes
-Pathway and network analyses of signaling that focus on the roles of post-translational modifications
-Studies of proteome dynamics and quality controls, and their roles in disease
-Studies of evolutionary processes effecting proteome dynamics, quality and regulation
-Chemical proteomics, including mechanisms of drug action
-Proteomics of the immune system and antigen presentation/recognition
-Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease
-Clinical and translational studies of human diseases
-Metabolomics to understand functional connections between genes, proteins and phenotypes