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de Luna Vitorino FN, Levy MJ, Mansano Wailemann RA, Lopes M, Silva ML, Sardiu ME, Garcia BA, Machado Motta MC, Oliveira CC, Armelin HA, Florens LA, Washburn MP, Pinheiro Chagas da Cunha J. The antiproliferative effect of FGF2 in K-Ras-driven tumor cells involves modulation of rRNA and the nucleolus. J Cell Sci 2023; 136:jcs260989. [PMID: 37921359 PMCID: PMC11166202 DOI: 10.1242/jcs.260989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023] Open
Abstract
The nucleolus is sensitive to stress and can orchestrate a chain of cellular events in response to stress signals. Despite being a growth factor, FGF2 has antiproliferative and tumor-suppressive functions in some cellular contexts. In this work, we investigated how the antiproliferative effect of FGF2 modulates chromatin-, nucleolus- and rDNA-associated proteins. The chromatin and nucleolar proteome indicated that FGF2 stimulation modulates proteins related to transcription, rRNA expression and chromatin-remodeling proteins. The global transcriptional rate and nucleolus area increased along with nucleolar disorganization upon 24 h of FGF2 stimulation. FGF2 stimulation induced immature rRNA accumulation by increasing rRNA transcription. The rDNA-associated protein analysis reinforced that FGF2 stimulus interferes with transcription and rRNA processing. RNA Pol I inhibition partially reversed the growth arrest induced by FGF2, indicating that changes in rRNA expression might be crucial for triggering the antiproliferative effect. Taken together, we demonstrate that the antiproliferative FGF2 stimulus triggers significant transcriptional changes and modulates the main cell transcription site, the nucleolus.
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Affiliation(s)
- Francisca N. de Luna Vitorino
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | | | - Rosangela A. Mansano Wailemann
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
| | - Mariana Lopes
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
| | - Mariana Loterio Silva
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
| | | | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Maria Cristina Machado Motta
- Laboratório de Ultraestrutura Celular Hertha Meyer, Centro de Pesquisa em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ 21491-590, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ 21941-902, Brazil
| | - Carla Columbano Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Hugo Aguirre Armelin
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
| | | | | | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular – Center of Toxins, Immune-Response and Cell Signalling – CeTICS, Instituto Butantan, São Paulo, SP 055503-900, Brazil
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Zhang L, Xu L. Fgf2 and Ptpn11 play a role in cerebral injury caused by sevoflurane anesthesia. Medicine (Baltimore) 2023; 102:e36108. [PMID: 37960778 PMCID: PMC10637467 DOI: 10.1097/md.0000000000036108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Sevoflurane is a new inhaled anesthetic, which has better physical properties than the existing inhalational anesthetics, rapid induction, less tissue uptake, and faster recovery. Sevoflurane can directly dilators cerebral blood vessels and increase cerebral blood flow, but it also reduces cerebral oxygen metabolism rate, thereby reducing cerebral blood flow. However, the role of Fgf2 and Ptpn11 in cerebral injury caused by sevoflurane anesthesia remains unclear. The sevoflurane anesthesia brain tissue datasets GSE139220 and GSE141242 were downloaded from gene expression omnibus (GEO). Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. Construction and analysis of protein-protein interaction (PPI) Network. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG), comparative toxicogenomics database (CTD) were performed. A heat map of gene expression was drawn. TargetScan was used to screen miRNAs regulating DEGs. 500 DEGs were identified. According to GO, in Biological Process analysis, they were mainly enriched in response to hypoxia, blood vessel development, inner ear development, neural tube closure, and aging. In Cellular Component (CC), they were mainly enriched in plasma membrane, integral component of membrane, and basal lamina. In Molecular Function (MF), they were mainly associated with protein binding, Wnt-activated receptor activity, and organic anion transmembrane transporter activity. In the KEGG analysis, they were mainly enriched in proteoglycans in cancer, pathways in cancer, transcriptional misregulation in cancer, basal cell carcinoma, thyroid hormone signaling pathway. In the Metascape enrichment analysis, the GO enrichment items revealed upregulated regulation of vascular endothelial cell proliferation, platelet-derived growth factor receptor signaling pathway, inner ear development, and response to hypoxia. A total of 20 modules were generated. Gene Expression Heatmap showed that the core genes (Fgf2, Pdgfra, Ptpn11, Slc2a1) were highly expressed in sevoflurane anesthesia brain tissue samples. CTD Analysis showed that the 4 core genes (Fgf2, Pdgfra, Ptpn11, Slc2a1) were associated with neurodegenerative diseases, brain injuries, memory disorders, cognitive disorders, neurotoxicity, drug-induced abnormalities, neurological disorders, developmental disorders, and intellectual disabilities. Fgf2 and Ptpn11 are highly expressed in brain tissue after sevoflurane anesthesia, higher the expression level of Fgf2 and Ptpn11, worse the prognosis.
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Affiliation(s)
- Lin Zhang
- Department of Anesthesiology, The Third Affiliated Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Lingyan Xu
- Department of Disease Control and Prevention, The Third Affiliated Hospital of Beijing University of Chinese Medicine, Beijing, China
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Zeng H, Wang L, Li J, Luo S, Han Q, Su F, Wei J, Wei X, Wu J, Li B, Huang J, Tang P, Cao C, Zhou Y, Yang Q. Single-cell RNA-sequencing reveals distinct immune cell subsets and signaling pathways in IgA nephropathy. Cell Biosci 2021; 11:203. [PMID: 34895340 PMCID: PMC8665497 DOI: 10.1186/s13578-021-00706-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/31/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND IgA nephropathy (IgAN) is the most common primary glomerulonephritis globally. Increasing evidence suggests the importance of host immunity in the development of IgAN, but its dynamics during the early stage of IgAN are still largely unclear. RESULTS Here we successfully resolved the early transcriptomic changes in immune cells of IgAN by conducting single-cell RNA-sequencing (scRNA-seq) with peripheral blood mononuclear cells. The differentially expressed genes (DEGs) between control and IgAN were predominantly enriched in NK cell-mediated cytotoxicity and cell killing pathways. Interestingly, we discovered that the number and cytotoxicity of NK cells are significantly reduced in IgAN patients, where both the number and marker genes of NK cells were negatively associated with the clinical parameters, including the levels of urine protein creatinine ratio (UPCR), serum galactose-deficient IgA1 and IgA. A distinctive B cell subset, which had suppressed NFκB signaling was predominantly in IgAN and positively associated with disease progression. Moreover, the DEGs of B cells were enriched in different viral infection pathways. Classical monocytes also significantly changed in IgAN and a monocyte subset expressing interferon-induced genes was positively associated with the clinical severity of IgAN. Finally, we identified vast dynamics in intercellular communications in IgAN. CONCLUSIONS We dissected the immune landscape of IgAN at the single-cell resolution, which provides new insights in developing novel biomarkers and immunotherapy against glomerulonephritis.
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Affiliation(s)
- Honghui Zeng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Le Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jiajia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Siweier Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Qianqian Han
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Fang Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jing Wei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Xiaona Wei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jianping Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Bin Li
- Clinical Trials Unit, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jingang Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Patrick Tang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chunwei Cao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
| | - Yiming Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
| | - Qiongqiong Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
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Lund PJ, Lopes M, Sidoli S, Coradin M, Vitorino FNDL, da Cunha JPC, Garcia BA. FGF-2 induces a failure of cell cycle progression in cells harboring amplified K-Ras, revealing new insights into oncogene-induced senescence. Mol Omics 2021; 17:725-739. [PMID: 34636387 PMCID: PMC8511509 DOI: 10.1039/d1mo00019e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paradoxically, oncogenes that drive cell cycle progression may also trigger pathways leading to senescence, thereby inhibiting the growth of tumorigenic cells. Knowledge of how these pathways operate, and how tumor cells may evade these pathways, is important for understanding tumorigenesis. The Y1 cell line, which harbors an amplification of the proto-oncogene Ras, rapidly senesces in response to the mitogen fibroblast growth factor-2 (FGF-2). To gain a more complete picture of how FGF-2 promotes senescence, we employed a multi-omics approach to analyze histone modifications, mRNA and protein expression, and protein phosphorylation in Y1 cells treated with FGF-2. Compared to control cells treated with serum alone, FGF-2 caused a delayed accumulation of acetylation on histone H4 and higher levels of H3K27me3. Sequencing analysis revealed decreased expression of cell cycle-related genes with concomitant loss of H3K27ac. At the same time, FGF-2 promoted the expression of p21, various cytokines, and MAPK-related genes. Nuclear envelope proteins, particularly lamin B1, displayed increased phosphorylation in response to FGF-2. Proteome analysis suggested alterations in cellular metabolism, as evident by modulated expression of enzymes involved in purine biosynthesis, tRNA aminoacylation, and the TCA cycle. We propose that Y1 cells senesce due to an inability to progress through the cell cycle, which may stem from DNA damage or TGFb signaling. Altogether, the phenotype of Y1 cells is consistent with rapidly established oncogene-induced senescence, demonstrating the synergy between growth factors and oncogenes in driving senescence and bringing additional insight into this tumor suppressor mechanism.
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Affiliation(s)
- Peder J Lund
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Mariana Lopes
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Mariel Coradin
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Francisca Nathália de Luna Vitorino
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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