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Wang L, Zhou K, Wu Q, Zhu L, Hu Y, Yang X, Li D. Microanatomy of the metabolic associated fatty liver disease (MAFLD) by single-cell transcriptomics. J Drug Target 2023; 31:421-432. [PMID: 36847649 DOI: 10.1080/1061186x.2023.2185626] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
BACKGROUND Metabolic-associated fatty liver disease (MAFLD) is a major cause of liver disease worldwide and comprises non-alcoholic fatty liver (NAFL) and non-alcoholic steatohepatitis (NASH). Due to the high prevalence and poor prognosis of NASH, it is critical to identify and treat patients at risk. However, the aetiology and mechanisms remain largely unknown, warranting further analysis. METHODS We first identified differential genes in NASH by single-cell analysis of the GSE129516 dataset and conducted expression profiling data analysis of the GSE184019 dataset from the Gene Expression Omnibus (GEO) database. Then single-cell trajectory reconstruction and analysis, immune gene score, cellular communication, key gene screening, functional enrichment analysis, and immune microenvironment analysis were carried out. Finally, cell experiments were performed to verify the role of key genes in NASH. RESULTS We conducted transcriptome profiling of 30,038 single cells, including hepatocytes and non-hepatocytes from normal and steatosis adult mouse livers. Comparative analysis of hepatocytes and non-hepatocytes revealed pronounced heterogeneity as non-hepatocytes acted as major cell-communication hubs. The results showed that Hspa1b, Tfrc, Hmox1 and Map4k4 could effectively distinguish NASH tissues from normal samples. The results of scRNA-seq and qPCR indicated that the expression levels of hub genes in NASH were significantly higher than in normal cells or tissues. Further immune infiltration analysis showed significant differences in M2 macrophage distribution between healthy and metabolic-associated fatty liver samples. CONCLUSIONS Our results suggest that Hspa1b, Tfrc, Hmox1 and Map4k4 have huge prospects as diagnostic and prognostic biomarkers for NASH and may be potential therapeutic targets for NASH.
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Affiliation(s)
- Lijun Wang
- The Nanhua Affiliated Hospital, Department of Stomatology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Kebing Zhou
- Hunan Provincial Clinical Research Center for Metabolic Associated Fatty Liver Disease, The Nanhua Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Nanhua Affiliated Hospital, Department of General Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Nanhua Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Qing Wu
- Hunan Provincial Clinical Research Center for Metabolic Associated Fatty Liver Disease, The Nanhua Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Nanhua Affiliated Hospital, Department of General Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Lingping Zhu
- Hunan Provincial Clinical Research Center for Metabolic Associated Fatty Liver Disease, The Nanhua Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Nanhua Affiliated Hospital, Department of General Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yang Hu
- Hunan Provincial Clinical Research Center for Metabolic Associated Fatty Liver Disease, The Nanhua Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Nanhua Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xuefeng Yang
- Hunan Provincial Clinical Research Center for Metabolic Associated Fatty Liver Disease, The Nanhua Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Nanhua Affiliated Hospital, Department of General Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Nanhua Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Duo Li
- Hunan Provincial Clinical Research Center for Metabolic Associated Fatty Liver Disease, The Nanhua Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Nanhua Affiliated Hospital, Department of General Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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Zhu X, Zhang C, Shi M, Li H, Jiang X, Wang L. IL-6/STAT3-mediated autophagy participates in the development of age-related glomerulosclerosis. J Biochem Mol Toxicol 2021; 35:e22698. [PMID: 33393185 DOI: 10.1002/jbt.22698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 10/10/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022]
Abstract
The standard of age-related glomerulosclerosis is unclear. Both signal transducer and activator of transcription 3 (STAT3) and autophagy are involved in age-related kidney disease. Therefore, we aimed to explore the standard, as well as the potential mechanism(s). A total of 44 patients who underwent radical nephrectomy were enrolled. Pearson analysis was performed to investigate the parameters with ages. The patients were divided into the young- and aged-kidney groups. Kidney morphological changes were evaluated by histology staining, senescence was evaluated by senescence-associated-β-galactosidase (SA-β-gal) staining, and autophagosome was measured by transmission electron microscopy. Moreover, Western blot and/or immunohistochemistry were accomplished to assess the expression of p16, STAT3, and glycoprotein130 (GP130) and autophagy-related proteins. Furthermore, human glomerular mesangial cells were administrated with tocilizumab (TCZ) and/or IL-6, and then the above indexes were tested again. Sclerotic glomerular density and glomerular sclerosis rate were significantly higher in individuals more than 40 years old, and they were strongly correlated with ages. Moreover, the expression of p16, STAT3, GP130, and p62 was significantly increased, while LC3II and autophagosome were statistically decreased in the aged-kidney. Glomeruli were hardly to stain with SA-β-gal. For the in vitro experiments, we observed that IL-6 significantly increased p16, STAT3, GP130, and p62, induced higher SA-β-gal staining, while downregulated LC3II and autophagosome. Furthermore, TCZ statistically reversed the effects of IL-6 on the above expression of proteins. Glomerular sclerosis rate might be one standard for natural renal aging, and IL-6/STAT3-mediated autophagy may participate in the development of age-related glomerulosclerosis.
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Affiliation(s)
- Xinwang Zhu
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Congxiao Zhang
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China.,Blood Purification Center, The Fourth People's Hospital of Shenyang, Shenyang, China
| | - Mai Shi
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Huimin Li
- Department of Nephrology, The Fourth Hospital of China Medical University, Shenyang, China
| | - Xue Jiang
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Lining Wang
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
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Lu Y, Luo G, Zhu S, Wang X, Chen Y, Dong Z, Wang S, Ma J, Deng H, Wu D, Dong J. The different expression of glycogen phosphorylases in renal clear cell renal carcinoma and chromophobe renal carcinoma. Clin Proteomics 2020; 17:7. [PMID: 32127786 PMCID: PMC7043045 DOI: 10.1186/s12014-020-9270-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/30/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The various pathogenesis between Clear cell renal carcinoma (CCRCC) and Chromophobe renal carcinoma (CHRCC) contributes to the different tumor growth rate and metastasis. In this study, we explored the distinct proteomic profiles between these two cancers and found different expression of glycogen phosphorylases in two cancers. METHODS We explored novel targets by proteomics. Five CCRCC cases and five CHRCC cases were selected for tandem mass tag-labeling liquid chromatography-mass spectroscopy (LC-MS). Gene ontology and KEGG pathway were applied for bioinformatic analysis. Glycogen phosphorylases were detected by Western blotting. RESULTS CHRCC were younger, more commonly female, and had larger tumors compared to those with CCRCC. 101 differentially expressed proteins (DEPs) in CCRCC and 235 DEPs in CHRCC were detected by LC-MS. It was found that disruption of metabolic pathways, epithelial cell differentiation, and cell response were the common characters for two tumor types. Activation of cell-cell adhesion and oxidation-reduction process stimulate CCRCC growth and epithelial cell differentiation and transferrin transport was involved in CHRCC growth, We also found that oxidative phosphorylation is activated in CHRCC and inhibited in CCRCC. More importantly, we found and confirmed that upregulation of glycogen phosphorylase liver type in CCRCC and glycogen phosphorylase brain type in CHRCC mediated differential glycogenolysis in the two tumor types, which could serve as potential therapeutic targets. CONCLUSION We found different expression of glycogen phosphorylases in CCRCC and CHRCC by quantitative proteomics, which provides potential therapeutic targets in the future.
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Affiliation(s)
- Yang Lu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Guangda Luo
- Department of Urology, Chinese PLA General Hospital, Fuxing Road 28, Beijing, 100853 China
- Chinese PLA No. 69241, Urumqi, China
| | - Songbiao Zhu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Wang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - ZhouHuan Dong
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Shiyu Wang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Di Wu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Jun Dong
- Department of Urology, Chinese PLA General Hospital, Fuxing Road 28, Beijing, 100853 China
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Wu D, Pepowski B, Takahashi S, Kron SJ. A cmap-enabled gene expression signature-matching approach identifies small-molecule inducers of accelerated cell senescence. BMC Genomics 2019; 20:290. [PMID: 30987592 PMCID: PMC6466706 DOI: 10.1186/s12864-019-5653-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 03/27/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Diverse stresses including genotoxic therapy can induce proliferating cancer cells to undergo cellular senescence and take on the characteristic phenotypes of replicative cellular aging. This accelerated or therapy-induced senescence has been alternatively proposed to contribute to therapeutic efficacy or resistance. Toward better understanding this cell state, we sought to define the core transcriptome of accelerated senescence in cancer cells. RESULTS We examined senescence induced by ionizing irradiation or ectopic overexpression of the stoichiometric cyclin-dependent kinase (CDK) inhibitor p21CIP/WAF1/SDI1 in the human breast cancer cell line MCF7. While radiation produces a strong DNA damage response, ectopic expression of p21 arrests cell cycle progression independently of DNA damage. Both conditions promoted senescence within 5 days. Microarray analysis revealed 378 up- and 391 down-regulated genes that were shared between the two conditions, representing a candidate signature. Systems analysis of the shared differentially expressed genes (DEGs) revealed strong signals for cell cycle control and DNA damage response pathways and predicted multiple upstream regulators previously linked to senescence. Querying the shared DEGs against the Connectivity Map (cmap) database of transcriptional responses to small molecules yielded 20 compounds that induce a similar gene expression pattern in MCF7 cells. Of 16 agents evaluated, six induced senescence on their own. Of these, the selective estrogen receptor degrader fulvestrant and the histone acetyltransferase inhibitor vorinostat did so without causing chromosomal damage. CONCLUSIONS Using a systems biology approach with experimental validation, we have defined a core gene expression signature for therapy-induced senescence.
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Affiliation(s)
- Ding Wu
- Department of Molecular Genetics and Cell Biology and Ludwig Center for Metastasis Research, The University of Chicago, 929 East 57th Street, GCIS W522A, Chicago, IL 60637 USA
| | - Brett Pepowski
- Department of Molecular Genetics and Cell Biology and Ludwig Center for Metastasis Research, The University of Chicago, 929 East 57th Street, GCIS W522A, Chicago, IL 60637 USA
| | - Satoe Takahashi
- Department of Otolaryngology - Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Stephen J. Kron
- Department of Molecular Genetics and Cell Biology and Ludwig Center for Metastasis Research, The University of Chicago, 929 East 57th Street, GCIS W522A, Chicago, IL 60637 USA
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Zhan S, Li J, Wang T, Ge W. Quantitative Proteomics Analysis of Sporadic Medullary Thyroid Cancer Reveals FN1 as a Potential Novel Candidate Prognostic Biomarker. Oncologist 2018; 23:1415-1425. [PMID: 29739896 DOI: 10.1634/theoncologist.2017-0399] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/23/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Sporadic medullary thyroid cancer (MTC) is a rare neuroendocrine tumor. Currently, although the diagnosis of sporadic MTC is relatively simple, the need to discover novel candidate prognostic biomarkers for sporadic MTC and investigate the underlying mechanism involved in this rare disease is urgent. MATERIALS AND METHODS We employed tandem mass tag-based liquid chromatography-mass spectrometry to identify and analyze differentially expressed proteins (DEPs) in sporadic MTC. Western blotting was used to validate the DEPs. Immunohistochemistry was performed to investigate FN1 and RPS6KA3 in an independent set of sporadic MTC tissues. Immunohistochemical data were analyzed by different statistical methods. RESULTS Three hundred eighty-eight DEPs were identified in mass spectrometry, mainly involved in the extracellular matrix, cytoskeletal remodeling, or oxidoreductase activity. Among them, THBS1, MMP9, FN1, RPS6KA3, SYT1, and carcinoembryonic antigen were successfully validated by Western blot. In addition, FN1 and RPS6KA3, enriched in extracellular matrix (ECM) remodeling and the mitogen-activated protein kinase (MAPK) signaling pathway, respectively, were investigated in an independent set of sporadic MTC tissues. Receiver-operator characteristic curve analysis showed that FN1 and RPS6KA3 can be used for discriminating sporadic MTC tumorous tissues from paired normal thyroid tissues, and the clinical biomarker calcitonin was positively correlated with FN1 and RPS6KA3 in tumorous tissues. Furthermore, the immunohistochemical scores of FN1 in tumorous tissue showed an inverse relationship with tumor classification, lymph node classification, and American Joint Committee on Cancer stage. Through univariate and multivariate analysis for progression-free survival, we also found that low FN1 expression in tumorous tissues was an independent worse prognostic factor for progression-free survival. CONCLUSION We identified that the pathophysiology of sporadic MTC involve numerous pathways, including the synaptic vesicle pathway, the MAPK signaling pathway, and the ECM remodeling pathway. Furthermore, our study also identified FN1 as novel prognostic biomarkers related to the pathophysiologic changes in sporadic MTC. IMPLICATIONS FOR PRACTICE Proteomic dissection and prognostic biomarkers are scarce in sporadic medullary thyroid cancer (MTC). This article reports the use of proteomics technology to comprehensively investigate the molecular mechanisms of sporadic MTC, which resulted in the identification of FN1 as a novel candidate prognostic biomarker.
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Affiliation(s)
- Shaohua Zhan
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, National Key Laboratory of Medical Molecular Biology & Department of Immunology, Beijing, People's Republic of China
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Tianxiao Wang
- Key Laboratory of Carcinogenesis and Translational Research, Department of Head and Neck Surgery, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Wei Ge
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, National Key Laboratory of Medical Molecular Biology & Department of Immunology, Beijing, People's Republic of China
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