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Bradley D, Garand C, Belda H, Gagnon-Arsenault I, Treeck M, Elowe S, Landry CR. The substrate quality of CK2 target sites has a determinant role on their function and evolution. Cell Syst 2024; 15:544-562.e8. [PMID: 38861992 DOI: 10.1016/j.cels.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 02/29/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
Most biological processes are regulated by signaling modules that bind to short linear motifs. For protein kinases, substrates may have full or only partial matches to the kinase recognition motif, a property known as "substrate quality." However, it is not clear whether differences in substrate quality represent neutral variation or if they have functional consequences. We examine this question for the kinase CK2, which has many fundamental functions. We show that optimal CK2 sites are phosphorylated at maximal stoichiometries and found in many conditions, whereas minimal substrates are more weakly phosphorylated and have regulatory functions. Optimal CK2 sites tend to be more conserved, and substrate quality is often tuned by selection. For intermediate sites, increases or decreases in substrate quality may be deleterious, as we demonstrate for a CK2 substrate at the kinetochore. The results together suggest a strong role for substrate quality in phosphosite function and evolution. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- David Bradley
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
| | - Chantal Garand
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Axe de Reproduction, Santé de la mère et de l'enfant, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Hugo Belda
- Signalling in Host-Pathogen Interaction Laboratory, The Francis Crick Institute, London NW11AT, UK
| | - Isabelle Gagnon-Arsenault
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Moritz Treeck
- Signalling in Host-Pathogen Interaction Laboratory, The Francis Crick Institute, London NW11AT, UK; Cell Biology of Host-Pathogen Interaction Laboratory, The Gulbenkian Institute of Science, Oeiras 2780-156, Portugal
| | - Sabine Elowe
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Axe de Reproduction, Santé de la mère et de l'enfant, CHU de Québec, Université Laval, Québec City, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université Laval, Québec City, QC, Canada; Centre de Recherche sur le Cancer, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
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2
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Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nat Commun 2024; 15:3909. [PMID: 38724493 PMCID: PMC11082183 DOI: 10.1038/s41467-024-47957-3] [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: 03/18/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. Leveraging progress in proteomic technologies and network-based methodologies, we introduce Virtual Enrichment-based Signaling Protein-activity Analysis (VESPA)-an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations-and use it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogating tumor-specific enzyme/substrate interactions accurately infers kinase and phosphatase activity, based on their substrate phosphorylation state, effectively accounting for signal crosstalk and sparse phosphoproteome coverage. The analysis elucidates time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring, experimentally confirmed by CRISPR knock-out assays, suggesting broad applicability to cancer and other diseases.
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Affiliation(s)
- George Rosenberger
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Mikko Turunen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jing He
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Prem S Subramaniam
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sergey Pampou
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron T Griffin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Karan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Patrick Kerwin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Diana Murray
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
- Chan Zuckerberg Biohub New York, New York, NY, USA.
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3
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Shi Y, Wu C, Shi J, Gao T, Ma H, Li L, Zhao Y. Protein phosphorylation and kinases: Potential therapeutic targets in necroptosis. Eur J Pharmacol 2024; 970:176508. [PMID: 38493913 DOI: 10.1016/j.ejphar.2024.176508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Necroptosis is a pivotal contributor to the pathogenesis of various human diseases, including those affecting the nervous system, cardiovascular system, pulmonary system, and kidneys. Extensive investigations have elucidated the mechanisms and physiological ramifications of necroptosis. Among these, protein phosphorylation emerges as a paramount regulatory process, facilitating the activation or inhibition of specific proteins through the addition of phosphate groups to their corresponding amino acid residues. Currently, the targeting of kinases has gained recognition as a firmly established and efficacious therapeutic approach for diverse diseases, notably cancer. In this comprehensive review, we elucidate the intricate role of phosphorylation in governing key molecular players in the necroptotic pathway. Moreover, we provide an in-depth analysis of recent advancements in the development of kinase inhibitors aimed at modulating necroptosis. Lastly, we deliberate on the prospects and challenges associated with the utilization of kinase inhibitors to modulate necroptotic processes.
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Affiliation(s)
- Yihui Shi
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chengkun Wu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Jiayi Shi
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Taotao Gao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huabin Ma
- Central Laboratory, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
| | - Long Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
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4
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Stewart R, Sharma S, Wu T, Okuda S, Xie G, Zhou XZ, Shilton B, Lu KP. The role of the master cancer regulator Pin1 in the development and treatment of cancer. Front Cell Dev Biol 2024; 12:1343938. [PMID: 38745861 PMCID: PMC11091292 DOI: 10.3389/fcell.2024.1343938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/28/2024] [Indexed: 05/16/2024] Open
Abstract
This review examines the complex role of Pin1 in the development and treatment of cancer. Pin1 is the only peptidyl-prolyl isomerase (PPIase) that can recognize and isomerize phosphorylated Ser/Thr-Pro peptide bonds. Pin1 catalyzes a structural change in phosphorylated Ser/Thr-Pro motifs that can modulate protein function and thereby impact cell cycle regulation and tumorigenesis. The molecular mechanisms by which Pin1 contributes to oncogenesis are reviewed, including Pin1 overexpression and its correlation with poor cancer prognosis, and the contribution of Pin1 to aggressive tumor phenotypes involved in therapeutic resistance is discussed, with an emphasis on cancer stem cells, the epithelial-to-mesenchymal transition (EMT), and immunosuppression. The therapeutic potential of Pin1 inhibition in cancer is discussed, along with the promise and the difficulties in identifying potent, drug-like, small-molecule Pin1 inhibitors. The available evidence supports the efficacy of targeting Pin1 as a novel cancer therapeutic by analyzing the role of Pin1 in a complex network of cancer-driving pathways and illustrating the potential of synergistic drug combinations with Pin1 inhibitors for treating aggressive and drug-resistant tumors.
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Affiliation(s)
- Robert Stewart
- Department of Biochemistry, Western University, London, ON, Canada
| | - Shaunik Sharma
- Department of Biochemistry, Western University, London, ON, Canada
| | - Timothy Wu
- Department of Biochemistry, Western University, London, ON, Canada
| | - Sho Okuda
- Department of Biochemistry, Western University, London, ON, Canada
| | - George Xie
- Department of Biochemistry, Western University, London, ON, Canada
| | - Xiao Zhen Zhou
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Brian Shilton
- Department of Biochemistry, Western University, London, ON, Canada
| | - Kun Ping Lu
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Oncology, Western University, London, ON, Canada
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5
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Wiltshire E, de Moura MC, Piñeyro D, Joshi RS. Cellular and clinical impact of protein phosphatase enzyme epigenetic silencing in multiple cancer tissues. Hum Genomics 2024; 18:24. [PMID: 38475971 DOI: 10.1186/s40246-024-00592-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Protein Phosphatase Enzymes (PPE) and protein kinases simultaneously control phosphorylation mechanisms that tightly regulate intracellular signalling pathways and stimulate cellular responses. In human malignancies, PPE and protein kinases are frequently mutated resulting in uncontrolled kinase activity and PPE suppression, leading to cell proliferation, migration and resistance to anti-cancer therapies. Cancer associated DNA hypermethylation at PPE promoters gives rise to transcriptional silencing (epimutations) and is a hallmark of cancer. Despite recent advances in sequencing technologies, data availability and computational capabilities, only a fraction of PPE have been reported as transcriptionally inactive as a consequence of epimutations. METHODS In this study, we examined promoter-associated DNA methylation profiles in Protein Phosphatase Enzymes and their Interacting Proteins (PPEIP) in a cohort of 705 cancer patients in five tissues (Large intestine, Oesophagus, Lung, Pancreas and Stomach) in three cell models (primary tumours, cancer cell lines and 3D embedded cancer cell cultures). As a subset of PPEIP are known tumour suppressor genes, we analysed the impact of PPEIP promoter hypermethylation marks on gene expression, cellular networks and in a clinical setting. RESULTS Here, we report epimutations in PPEIP are a frequent occurrence in the cancer genome and manifest independent of transcriptional activity. We observed that different tumours have varying susceptibility to epimutations and identify specific cellular signalling networks that are primarily affected by epimutations. Additionally, RNA-seq analysis showed the negative impact of epimutations on most (not all) Protein Tyrosine Phosphatase transcription. Finally, we detected novel clinical biomarkers that inform on patient mortality and anti-cancer treatment sensitivity. CONCLUSIONS We propose that DNA hypermethylation marks at PPEIP frequently contribute to the pathogenesis of malignancies and within the precision medicine space, hold promise as biomarkers to inform on clinical features such as patient survival and therapeutic response.
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Affiliation(s)
- Edward Wiltshire
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Ricky S Joshi
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK.
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6
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Deng Q, Zhang J, Liu J, Liu Y, Dai Z, Zou X, Li Z. Identifying Protein Phosphorylation Site-Disease Associations Based on Multi-Similarity Fusion and Negative Sample Selection by Convolutional Neural Network. Interdiscip Sci 2024:10.1007/s12539-024-00615-0. [PMID: 38457108 DOI: 10.1007/s12539-024-00615-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 03/09/2024]
Abstract
As one of the most important post-translational modifications (PTMs), protein phosphorylation plays a key role in a variety of biological processes. Many studies have shown that protein phosphorylation is associated with various human diseases. Therefore, identifying protein phosphorylation site-disease associations can help to elucidate the pathogenesis of disease and discover new drug targets. Networks of sequence similarity and Gaussian interaction profile kernel similarity were constructed for phosphorylation sites, as well as networks of disease semantic similarity, disease symptom similarity and Gaussian interaction profile kernel similarity were constructed for diseases. To effectively combine different phosphorylation sites and disease similarity information, random walk with restart algorithm was used to obtain the topology information of the network. Then, the diffusion component analysis method was utilized to obtain the comprehensive phosphorylation site similarity and disease similarity. Meanwhile, the reliable negative samples were screened based on the Euclidean distance method. Finally, a convolutional neural network (CNN) model was constructed to identify potential associations between phosphorylation sites and diseases. Based on tenfold cross-validation, the evaluation indicators were obtained including accuracy of 93.48%, specificity of 96.82%, sensitivity of 90.15%, precision of 96.62%, Matthew's correlation coefficient of 0.8719, area under the receiver operating characteristic curve of 0.9786 and area under the precision-recall curve of 0.9836. Additionally, most of the top 20 predicted disease-related phosphorylation sites (19/20 for Alzheimer's disease; 20/16 for neuroblastoma) were verified by literatures and databases. These results show that the proposed method has an outstanding prediction performance and a high practical value.
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Affiliation(s)
- Qian Deng
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jing Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jie Liu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yuqi Liu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Zong Dai
- School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Zhanchao Li
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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7
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Corda PO, Bollen M, Ribeiro D, Fardilha M. Emerging roles of the Protein Phosphatase 1 (PP1) in the context of viral infections. Cell Commun Signal 2024; 22:65. [PMID: 38267954 PMCID: PMC10807198 DOI: 10.1186/s12964-023-01468-8] [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: 10/16/2023] [Accepted: 12/30/2023] [Indexed: 01/26/2024] Open
Abstract
Protein Phosphatase 1 (PP1) is a major serine/threonine phosphatase in eukaryotes, participating in several cellular processes and metabolic pathways. Due to their low substrate specificity, PP1's catalytic subunits do not exist as free entities but instead bind to Regulatory Interactors of Protein Phosphatase One (RIPPO), which regulate PP1's substrate specificity and subcellular localization. Most RIPPOs bind to PP1 through combinations of short linear motifs (4-12 residues), forming highly specific PP1 holoenzymes. These PP1-binding motifs may, hence, represent attractive targets for the development of specific drugs that interfere with a subset of PP1 holoenzymes. Several viruses exploit the host cell protein (de)phosphorylation machinery to ensure efficient virus particle formation and propagation. While the role of many host cell kinases in viral life cycles has been extensively studied, the targeting of phosphatases by viral proteins has been studied in less detail. Here, we compile and review what is known concerning the role of PP1 in the context of viral infections and discuss how it may constitute a putative host-based target for the development of novel antiviral strategies.
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Affiliation(s)
- Pedro O Corda
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mathieu Bollen
- Department of Cellular and Molecular Medicine, Laboratory of Biosignaling & Therapeutics, Katholieke Universiteit Leuven, Louvain, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
| | - Margarida Fardilha
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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8
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Kommer DC, Stamatiou K, Vagnarelli P. Cell Cycle-Specific Protein Phosphatase 1 (PP1) Substrates Identification Using Genetically Modified Cell Lines. Methods Mol Biol 2024; 2740:37-61. [PMID: 38393468 DOI: 10.1007/978-1-0716-3557-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The identification of protein phosphatase 1 (PP1) holoenzyme substrates has proven to be a challenging task. PP1 can form different holoenzyme complexes with a variety of regulatory subunits, and many of those are cell cycle regulated. Although several methods have been used to identify PP1 substrates, their cell cycle specificity is still an unmet need. Here, we present a new strategy to investigate PP1 substrates throughout the cell cycle using clustered regularly interspersed short palindromic repeats (CRISPR)-Cas9 genome editing and generate cell lines with endogenously tagged PP1 regulatory subunit (regulatory interactor of protein phosphatase one, RIPPO). RIPPOs are tagged with the auxin-inducible degron (AID) or ascorbate peroxidase 2 (APEX2) modules, and PP1 substrate identification is conducted by SILAC proteomic-based approaches. Proteins in close proximity to RIPPOs are first identified through mass spectrometry (MS) analyses using the APEX2 system; then a list of differentially phosphorylated proteins upon RIPPOs rapid degradation (achieved via the AID system) is compiled via SILAC phospho-mass spectrometry. The "in silico" overlap between the two proteomes will be enriched for PP1 putative substrates. Several methods including fluorescence resonance energy transfer (FRET), proximity ligation assays (PLA), and in vitro assays can be used as substrate validations approaches.
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Affiliation(s)
- Dorothee C Kommer
- College of Health, Medicine and Life Science, Brunel University London, London, UK
| | | | - Paola Vagnarelli
- College of Health, Medicine and Life Science, Brunel University London, London, UK.
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9
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McClatchy DB, Powell SB, Yates JR. In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571320. [PMID: 38168169 PMCID: PMC10759996 DOI: 10.1101/2023.12.12.571320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Genetic analyses of Schizophrenia (SCZ) patients have identified thousands of risk factors. In silico protein-protein interaction (PPI) network analysis has provided strong evidence that disrupted PPI networks underlie SCZ pathogenesis. In this study, we performed in vivo PPI analysis of several SCZ risk factors in the rodent brain. Using endogenous antibody immunoprecipitations coupled to mass spectrometry (MS) analysis, we constructed a SCZ network comprising 1612 unique PPI with a 5% FDR. Over 90% of the PPI were novel, reflecting the lack of previous PPI MS studies in brain tissue. Our SCZ PPI network was enriched with known SCZ risk factors, which supports the hypothesis that an accumulation of disturbances in selected PPI networks underlies SCZ. We used Stable Isotope Labeling in Mammals (SILAM) to quantitate phencyclidine (PCP) perturbations in the SCZ network and found that PCP weakened most PPI but also led to some enhanced or new PPI. These findings demonstrate that quantitating PPI in perturbed biological states can reveal alterations to network biology.
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10
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Wilcockson SG, Guglielmi L, Araguas Rodriguez P, Amoyel M, Hill CS. An improved Erk biosensor detects oscillatory Erk dynamics driven by mitotic erasure during early development. Dev Cell 2023; 58:2802-2818.e5. [PMID: 37714159 PMCID: PMC7615346 DOI: 10.1016/j.devcel.2023.08.021] [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: 11/01/2022] [Revised: 06/02/2023] [Accepted: 08/15/2023] [Indexed: 09/17/2023]
Abstract
Extracellular signal-regulated kinase (Erk) signaling dynamics elicit distinct cellular responses in a variety of contexts. The early zebrafish embryo is an ideal model to explore the role of Erk signaling dynamics in vivo, as a gradient of activated diphosphorylated Erk (P-Erk) is induced by fibroblast growth factor (Fgf) signaling at the blastula margin. Here, we describe an improved Erk-specific biosensor, which we term modified Erk kinase translocation reporter (modErk-KTR). We demonstrate the utility of this biosensor in vitro and in developing zebrafish and Drosophila embryos. Moreover, we show that Fgf/Erk signaling is dynamic and coupled to tissue growth during both early zebrafish and Drosophila development. Erk activity is rapidly extinguished just prior to mitosis, which we refer to as mitotic erasure, inducing periods of inactivity, thus providing a source of heterogeneity in an asynchronously dividing tissue. Our modified reporter and transgenic lines represent an important resource for interrogating the role of Erk signaling dynamics in vivo.
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Affiliation(s)
- Scott G Wilcockson
- Developmental Signalling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Pablo Araguas Rodriguez
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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11
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Peng Y, Liu Y, Zheng R, Ye Y, Fu Y, Yin L, Gao Y, Fu Y, Qi X, Deng T, Zhang S, Li X. PLK1 maintains DNA methylation and cell viability by regulating phosphorylation-dependent UHRF1 protein stability. Cell Death Discov 2023; 9:367. [PMID: 37788997 PMCID: PMC10547799 DOI: 10.1038/s41420-023-01667-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023] Open
Abstract
PLK1 is a key serine/threonine kinase as well as a master mitotic regulator, but it has never been reported that PLK1 regulates DNA methylation. In the present study, we for the first time found that PLK1 inhibition disrupted global DNA methylation and elevated the expression level of tumor suppressor genes. Mechanistically, we found that PLK1 interacts UHRF1 protein to induce its phosphorylation at serine 265. Phosphorylation is required for the maintenance of UHRF1 protein stability by recruiting a deubiquitinase USP7. Conversely, PLK1 inhibition decreases UHRF1 protein interaction with USP7 and activates the ubiquitin-proteasome pathway, thereby accelerating UHRF1 protein degradation. UHRF1 degradation decreases the recruitment of DNMT1 to chromatin, and decreases the level of genome-wide DNA methylation, thereby elevating the expression of tumor suppressor genes and decreasing cell viability. We here presented the first report on the novel role of PLK1 in DNA methylation maintenance through UHRF1-DNMT1 pathway, and revealed a novel anticancer mechanism of PLK1 inhibitors.
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Affiliation(s)
- Yuchong Peng
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Youhong Liu
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Rirong Zheng
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Yubing Ye
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Yongming Fu
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Linglong Yin
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Yingxue Gao
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yuxin Fu
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xuli Qi
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Tanggang Deng
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Songwei Zhang
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiong Li
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China.
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China.
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China.
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China.
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12
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Zhang K, Sun L, Kang Y. Regulation of phosphoglycerate kinase 1 and its critical role in cancer. Cell Commun Signal 2023; 21:240. [PMID: 37723547 PMCID: PMC10506215 DOI: 10.1186/s12964-023-01256-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/01/2023] [Indexed: 09/20/2023] Open
Abstract
Cells that undergo normal differentiation mainly rely on mitochondrial oxidative phosphorylation to provide energy, but most tumour cells rely on aerobic glycolysis. This phenomenon is called the "Warburg effect". Phosphoglycerate kinase 1 (PGK1) is a key enzyme in aerobic glycolysis. PGK1 is involved in glucose metabolism as well as a variety of biological activities, including angiogenesis, EMT, mediated autophagy initiation, mitochondrial metabolism, DNA replication and repair, and other processes related to tumorigenesis and development. Recently, an increasing number of studies have proven that PGK1 plays an important role in cancer. In this manuscript, we discussed the effects of the structure, function, molecular mechanisms underlying PGK1 regulation on the initiation and progression of cancer. Additionally, PGK1 is associated with chemotherapy resistance and prognosis in tumour patients. This review presents an overview of the different roles played by PGK1 during tumorigenesis, which will help in the design of experimental studies involving PGK1 and enhance the potential for the use of PGK1 as a therapeutic target in cancer. Video Abstract.
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Affiliation(s)
- Kexin Zhang
- Department of Emergency and Oral Medicine, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 North Nanjing Street, Heping Area, Shenyang, 110002, People's Republic of China
| | - Lixue Sun
- Department of Emergency and Oral Medicine, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 North Nanjing Street, Heping Area, Shenyang, 110002, People's Republic of China
| | - Yuanyuan Kang
- Department of Emergency and Oral Medicine, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 North Nanjing Street, Heping Area, Shenyang, 110002, People's Republic of China.
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13
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Lan L, Cao H, Zhao L, Cui W, Wang B. PTPN12 down-regulated by miR-146b-3p gene affects the malignant progression of laryngeal squamous cell carcinoma. Open Med (Wars) 2023; 18:20230727. [PMID: 37333450 PMCID: PMC10276617 DOI: 10.1515/med-2023-0727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 03/31/2023] [Accepted: 05/07/2023] [Indexed: 06/20/2023] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a common malignancy among men in the anatomical position of head and neck. Hoarseness, pharyngalgia, and dyspnea are common symptoms. LSCC is a complex polygenic carcinoma that is caused by many factors involving polygenic alteration, environmental pollution, tobacco, and human papillomavirus. Classical protein tyrosine phosphatase nonreceptor type 12 (PTPN12) has been extensively studied to decipher its mechanism as a tumor suppressor gene in various human carcinomas; however, there is no comprehensive elucidation of the PTPN12 expression and its regulatory mechanisms in LSCC. As such, we expect to provide new insights for finding new biomarkers and effective therapeutic targets in LSCC. Immunohistochemical staining, western blot (WB), and quantitative real-time RT-PCR (qRT-PCR) were used for the messenger RNA (mRNA) and protein expression analyses of PTPN12, respectively. 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, clone formation, transwell migration, and transwell invasion assays were used to assess the proliferation, migration, and invasion ability of LSCC cells. Online prediction and design software tools (http://www.targetscan.org/ and http://www.microRNA.org) were used to predict associated miRNA. Studying the targeted regulatory relationship between miR-146b-3p and PTPN12 was based on dual luciferase reporter gene analysis. qRT-PCR was used to assess miR-146b-3p expression in LSCC. miR-146b-3p inhibitor and mimic were transfected, followed by qRT-PCR and WB assays to detect the expression of PTPN12. The gain and loss functional experiments were used to investigate the effects of miR-146b-3p transfection on the proliferation, migration, and invasion of tumor cells. Online bioinformatics prediction software (https://cn.string-db.org/ and https://www.genecards.org/) was used to determine potential downstream target genes of PTPN12. qRT-PCR and WB analyses were used to assess the mRNA and protein expression levels of target genes. Our study showed significantly decreased mRNA and protein expression levels of PTPN12 in LSCC compared with the adjacent normal tissues. The lower PTPN12 mRNA expression was correlated with pathological differentiation, and lower PTPN12 protein expression was correlated with the TNM stage in LSCC tissues. The subsequent in vitro functional analyses showed the inhibitory effect of PTPN12 over-expression on the proliferation, migration, and invasiveness abilities of LSCC cell line. Using online prediction and design software, miR-146b-3p was searched to target PTPN12. The miR-146b-3p was expressed at a high level in LSCC tissues and cell lines. Luciferase reporter assay exhibited that miR-146b-3p inhibited the luciferase activity of PTPN12 markedly. The functional analyses showed the tumor-promoting role of miR-146b-3p on the proliferation, migration, and invasiveness abilities of LSCC cell. Furthermore, co-transfection of cells with miR-146b-3p and PTPN12 significantly restored the inhibitory effect of PTPN12 on LSCC cell growth, migration, and invasiveness. This phenomenon unveiled that miR-146b-3p regulated the proliferation, migration, and invasion of LSCC cells by targeting PTPN12. EGFR and ERBB2 were selected as the downstream-regulation target genes. Up-regulation of PTPN12 significantly suppressed EGFR expression. Accordingly, the miR-146b-3p mimic significantly up-regulated the EGFR expression. However, up-regulation of PTPN12 and miR-146b-3p mimic suppressed ERBB2 protein expression but induced its gene expression. Down-regulation of PTPN12 is associated with up-regulation of miR-146b-3p in LSCC. Moreover, PTPN12 serves as a tumor suppressor gene through regulating the proliferation, migration, and invasion of LSCC cells. miR-146b-3p/PTPN12 axis is expected to be a novel therapeutic target in LSCC.
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Affiliation(s)
- Lili Lan
- Otolaryngology Head and Neck Surgery Department, The Second Hospital of Hebei Medical University, Shijiazhuang050005, Hebei, China
- Otolaryngology Head and Neck Surgery Department, The Fourth Hospital of Hebei Medical University, Shijiazhuang050011, Hebei, China
| | - Huan Cao
- Otolaryngology Head and Neck Surgery Department, The Second Hospital of Hebei Medical University, Shijiazhuang050005, Hebei, China
| | - Lei Zhao
- Otolaryngology Head and Neck Surgery Department, The Second Hospital of Hebei Medical University, Shijiazhuang050005, Hebei, China
| | - Weina Cui
- Otolaryngology Head and Neck Surgery Department, The Second Hospital of Hebei Medical University, Shijiazhuang050005, Hebei, China
| | - Baoshan Wang
- Otolaryngology Head and Neck Surgery Department, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang050005, Hebei, China
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Hegde M, Girisa S, Kunnumakkara AB. A compilation of bioinformatic approaches to identify novel downstream targets for the detection and prophylaxis of cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:75-113. [PMID: 36858743 DOI: 10.1016/bs.apcsb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The paradigm of cancer genomics has been radically changed by the development in next-generation sequencing (NGS) technologies making it possible to envisage individualized treatment based on tumor and stromal cells genome in a clinical setting within a short timeframe. The abundance of data has led to new avenues for studying coordinated alterations that impair biological processes, which in turn has increased the demand for bioinformatic tools for pathway analysis. While most of this work has been concentrated on optimizing certain algorithms to obtain quicker and more accurate results. Large volumes of these existing algorithm-based data are difficult for the biologists and clinicians to access, download and reanalyze them. In the present study, we have listed the bioinformatics algorithms and user-friendly graphical user interface (GUI) tools that enable code-independent analysis of big data without compromising the quality and time. We have also described the advantages and drawbacks of each of these platforms. Additionally, we emphasize the importance of creating new, more user-friendly solutions to provide better access to open data and talk about relevant problems like data sharing and patient privacy.
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Affiliation(s)
- Mangala Hegde
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Sosmitha Girisa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India.
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Nojima Y, Aoki M, Re S, Hirano H, Abe Y, Narumi R, Muraoka S, Shoji H, Honda K, Tomonaga T, Mizuguchi K, Boku N, Adachi J. Integration of pharmacoproteomic and computational approaches reveals the cellular signal transduction pathways affected by apatinib in gastric cancer cell lines. Comput Struct Biotechnol J 2023; 21:2172-2187. [PMID: 37013003 PMCID: PMC10066531 DOI: 10.1016/j.csbj.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Apatinib is known to be a highly selective vascular endothelial growth factor receptor 2 (VEGFR2) inhibitor with anti-angiogenic and anti-tumor properties. In a phase III study, the objective response rate to apatinib was low. It remains unclear why the effectivity of apatinib varies among patients and what type of patients are candidates for the treatment. In this study, we investigated the anti-tumor efficacy of apatinib against 13 gastric cancer cell lines and found that it differed depending on the cell line. Using integrated wet and dry approaches, we showed that apatinib was a multi-kinase inhibitor of c-Kit, RAF1, VEGFR1, VEGFR2, and VEGFR3, predominantly inhibiting c-Kit. Notably, KATO-III, which was the most apatinib-sensitive among the gastric cancer cell lines investigated, was the only cell line expressing c-Kit, RAF1, VEGFR1, and VEGFR3 but not VEGFR2. Furthermore, we identified SNW1 as a molecule affected by apatinib that plays an important role in cell survival. Finally, we identified the molecular network related to SNW1 that was affected by treatment with apatinib. These results suggest that the mechanism of action of apatinib in KATO-III cells is independent of VEGFR2 and that the differential efficacy of apatinib was due to differences in expression patterns of receptor tyrosine kinases. Furthermore, our results suggest that the differential efficacy of apatinib in gastric cell lines may be attributed to SNW1 phosphorylation levels at a steady state. These findings contribute to a deeper understanding of the mechanism of action of apatinib in gastric cancer cells.
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Affiliation(s)
- Yosui Nojima
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Center for Mathematical Modeling and Data Science, Osaka University, Osaka 560–8531, Japan
| | - Masahiko Aoki
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Department of Early Clinical Development, Graduate School of Medicine, Kyoto University Hospital, Kyoto 606–8507, Japan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
| | - Hidekazu Hirano
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya 464–8681, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Satoshi Muraoka
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Hirokazu Shoji
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
| | - Kazufumi Honda
- Department of Biomarkers for Early Detection of Cancer, National Cancer Center Research Institute, Tokyo 104–0045, Japan
- Department of Bioregulation, Graduate School of Medicine, Nippon Medical School, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Proteobiologics Co., Ltd., Osaka 567–0085, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Institute for Protein Research, Osaka University, Osaka 565–0871, Japan
| | - Narikazu Boku
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, Tokyo 108–8639, Japan
- Correspondence to: Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, 4–6-1 Minato-ku, Shiroganedai, Tokyo 108–8639, Japan.
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Correspondence to: Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, 7–6-8 Saito-asagi, Ibaraki, Osaka 567–0085, Japan.
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Khan MA, Tania M. Cordycepin and kinase inhibition in cancer. Drug Discov Today 2023; 28:103481. [PMID: 36584876 DOI: 10.1016/j.drudis.2022.103481] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Cordycepin, a nucleoside from Cordyceps mushrooms, has many beneficial properties for health, including anticancer activities. In cancer cells, cordycepin targets various signaling molecules. Here, we review the possible anticancer mechanisms of cordycepin involving the targeting of kinases. Abnormal kinase expression is involved in cancer development and progression through different molecular mechanisms, including phosphorylation, amplification, genetic mutations, and epigenetic regulation. Research suggests that kinases, such as the c-Jun N-terminal kinase (JNK), mitogen-activated protein kinase (MAPK), AMP kinase (AMPK), phosphoinositide 3-kinase (PI3K)/Akt, extracellular signal-regulated kinase (ERK), mammalian target of rapamycin (mTOR), glycogen synthase kinase (GSK)-3β, and focal adhesion kinase (FAK) pathways, can be targeted by cordycepin and disrupting their activity. Given that kinase inhibitors can have crucial roles in cancer treatment, targeting kinases might be one of the molecular mechanisms involved in the anticancer potential of cordycepin.
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Affiliation(s)
- Md Asaduzzaman Khan
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China; Nature Study Society of Bangladesh, Dhaka, Bangladesh.
| | - Mousumi Tania
- Nature Study Society of Bangladesh, Dhaka, Bangladesh; Division of Molecular Cancer Biology, The Red-Green Research Center, Dhaka, Bangladesh.
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Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528736. [PMID: 36824919 PMCID: PMC9949144 DOI: 10.1101/2023.02.15.528736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. By leveraging progress in proteomic technologies and network-based methodologies, over the past decade, we developed VESPA-an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations-and used it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogation of tumor-specific enzyme/substrate interactions accurately inferred kinase and phosphatase activity, based on their inferred substrate phosphorylation state, effectively accounting for signal cross-talk and sparse phosphoproteome coverage. The analysis elucidated time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring that was experimentally confirmed by CRISPRko assays, suggesting broad applicability to cancer and other diseases.
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Affiliation(s)
- George Rosenberger
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Mikko Turunen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jing He
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Present address: Regeneron Genetics Center, Tarrytown, NY, USA
| | - Prem S Subramaniam
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sergey Pampou
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron T Griffin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Karan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Patrick Kerwin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Diana Murray
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
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Sharma A, Rahman G, Gorelik J, Bhargava A. Voltage-Gated T-Type Calcium Channel Modulation by Kinases and Phosphatases: The Old Ones, the New Ones, and the Missing Ones. Cells 2023; 12:461. [PMID: 36766802 PMCID: PMC9913649 DOI: 10.3390/cells12030461] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/14/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Calcium (Ca2+) can regulate a wide variety of cellular fates, such as proliferation, apoptosis, and autophagy. More importantly, changes in the intracellular Ca2+ level can modulate signaling pathways that control a broad range of physiological as well as pathological cellular events, including those important to cellular excitability, cell cycle, gene-transcription, contraction, cancer progression, etc. Not only intracellular Ca2+ level but the distribution of Ca2+ in the intracellular compartments is also a highly regulated process. For this Ca2+ homeostasis, numerous Ca2+ chelating, storage, and transport mechanisms are required. There are also specialized proteins that are responsible for buffering and transport of Ca2+. T-type Ca2+ channels (TTCCs) are one of those specialized proteins which play a key role in the signal transduction of many excitable and non-excitable cell types. TTCCs are low-voltage activated channels that belong to the family of voltage-gated Ca2+ channels. Over decades, multiple kinases and phosphatases have been shown to modulate the activity of TTCCs, thus playing an indirect role in maintaining cellular physiology. In this review, we provide information on the kinase and phosphatase modulation of TTCC isoforms Cav3.1, Cav3.2, and Cav3.3, which are mostly described for roles unrelated to cellular excitability. We also describe possible potential modulations that are yet to be explored. For example, both mitogen-activated protein kinase and citron kinase show affinity for different TTCC isoforms; however, the effect of such interaction on TTCC current/kinetics has not been studied yet.
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Affiliation(s)
- Ankush Sharma
- Department of Biotechnology, Indian Institute of Technology Hyderabad (IITH), Kandi 502284, Telangana, India
| | - Ghazala Rahman
- Department of Biotechnology, Indian Institute of Technology Hyderabad (IITH), Kandi 502284, Telangana, India
| | - Julia Gorelik
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Anamika Bhargava
- Department of Biotechnology, Indian Institute of Technology Hyderabad (IITH), Kandi 502284, Telangana, India
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Liu Y, Zhang J, Du Z, Huang J, Cheng Y, Yi W, Li T, Yang J, Chen C. Comprehensive analysis of PTPN family expression and prognosis in acute myeloid leukemia. Front Genet 2023; 13:1087938. [PMID: 36699453 PMCID: PMC9868563 DOI: 10.3389/fgene.2022.1087938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Background: Tyrosyl phosphorylation is carried out by a group of enzymes known as non-receptor protein tyrosine phosphatases (PTPNs). In the current investigation, it is hoped to shed light on the relationships between the expression patterns of PTPN family members and the prognosis of acute myeloid leukemia (AML). Methods: PTPN expression was examined using GEPIA and GEO databases. To investigate the connection between PTPN expression and survival in AML patients, we downloaded data from the Broad TCGA Firehose and Clinical Proteomic Tumor Analysis (CPTAC) of the Cancer Genome Atlas (TCGA). We used quantitative real-time PCR (qRT-PCR) to confirm that essential genes were performed in clinical samples and cell lines. We then used western blot to verify that the genes expressed in the above databases were positive in normal tissues, AML patient samples, and AML cell lines. Next, we investigated associations between genome-wide expression profiles and PTPN6 expression using the GEO datasets. We investigated the interactive exploration of multidimensional cancer genomics using the cBioPortal datasets. Using the DAVID database, a study of gene ontology enrichment was performed. The protein-protein interaction (PPI) network was created using the STRING portal, and the gene-gene interaction network was performed using GeneMANIA. Results: Data from GEO and GEPIA revealed that most PTPN family members were linked to AML. Patients with leukemia have elevated levels of several PTPN members. All of the AML patients' poor overall survival (OS, p < .05) was significantly linked with higher expression of PTPN1, PTPN6, and PTPN7. Additionally, clinical samples showed that the expression of PTPN 6, PTPN 7, PTPN 13, and PTPN 14 was higher than normal in AML patients (p = .0116, p = .0034, p = .0092, and p = .0057, respectively) and AML cell lines (p = .0004, p = .0035, p = .0357, and p = .0177, respectively). Western blotting results showed that the expression of PTPN6 in AML samples and AML cell lines was significantly higher than that in normal control samples. Conclusion: Differentially expressed PTPN family members were found in AML. The prognosis of patients and PTPN gene expression were shown to be correlated. PTPN6 is one of these members and may be used as an AML diagnostic and prognostic marker.
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Affiliation(s)
- Yong Liu
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Jing Zhang
- Department of Breast and Thyroid Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Zefan Du
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Junbin Huang
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Yucai Cheng
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Wenfang Yi
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Tianwen Li
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Jing Yang
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Chun Chen
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China,*Correspondence: Chun Chen,
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20
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Ulengin-Talkish I, Cyert MS. A cellular atlas of calcineurin signaling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119366. [PMID: 36191737 PMCID: PMC9948804 DOI: 10.1016/j.bbamcr.2022.119366] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Intracellular Ca2+ signals are temporally controlled and spatially restricted. Signaling occurs adjacent to sites of Ca2+ entry and/or release, where Ca2+-dependent effectors and their substrates co-localize to form signaling microdomains. Here we review signaling by calcineurin, the Ca2+/calmodulin regulated protein phosphatase and target of immunosuppressant drugs, Cyclosporin A and FK506. Although well known for its activation of the adaptive immune response via NFAT dephosphorylation, systematic mapping of human calcineurin substrates and regulators reveals unexpected roles for this versatile phosphatase throughout the cell. We discuss calcineurin function, with an emphasis on where signaling occurs and mechanisms that target calcineurin and its substrates to signaling microdomains, especially binding of cognate short linear peptide motifs (SLiMs). Calcineurin is ubiquitously expressed and regulates events at the plasma membrane, other intracellular membranes, mitochondria, the nuclear pore complex and centrosomes/cilia. Based on our expanding knowledge of localized CN actions, we describe a cellular atlas of Ca2+/calcineurin signaling.
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Affiliation(s)
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA 94035, United States.
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21
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Bersching K, Michna T, Tenzer S, Jacob S. Data-Independent Acquisition (DIA) Is Superior for High Precision Phospho-Peptide Quantification in Magnaporthe oryzae. J Fungi (Basel) 2022; 9:jof9010063. [PMID: 36675884 PMCID: PMC9863866 DOI: 10.3390/jof9010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
The dynamic interplay of signaling networks in most major cellular processes is characterized by the orchestration of reversible protein phosphorylation. Consequently, analytic methods such as quantitative phospho-peptidomics have been pushed forward from a highly specialized edge-technique to a powerful and versatile platform for comprehensively analyzing the phosphorylation profile of living organisms. Despite enormous progress in instrumentation and bioinformatics, a high number of missing values caused by the experimental procedure remains a major problem, due to either a random phospho-peptide enrichment selectivity or borderline signal intensities, which both cause the exclusion for fragmentation using the commonly applied data dependent acquisition (DDA) mode. Consequently, an incomplete dataset reduces confidence in the subsequent statistical bioinformatic processing. Here, we successfully applied data independent acquisition (DIA) by using the filamentous fungus Magnaporthe oryzae as a model organism, and could prove that while maintaining data quality (such as phosphosite and peptide sequence confidence), the data completeness increases dramatically. Since the method presented here reduces the LC-MS/MS analysis from 3 h to 1 h and increases the number of phosphosites identified up to 10-fold in contrast to published studies in Magnaporthe oryzae, we provide a refined methodology and a sophisticated resource for investigation of signaling processes in filamentous fungi.
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Affiliation(s)
- Katharina Bersching
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55131 Mainz, Germany
| | - Thomas Michna
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Helmholtz-Institute for Translational Oncology Mainz (HI-TRON), 55131 Mainz, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Jacob
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55131 Mainz, Germany
- Correspondence:
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22
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Chojnacki JE, Scheinost L, Wang Y, Köhn M. Membrane targeting with palmitoylated lysine added to PP1-disrupting peptide induces PP1-independent signaling. J Pept Sci 2022; 29:e3469. [PMID: 36525306 DOI: 10.1002/psc.3469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/27/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Protein phosphatase-1 (PP1) is a ubiquitous enzyme involved in multiple processes inside cells. PP1-disrupting peptides (PDPs) are chemical tools that selectively bind to PP1 and release its activity. To restrict the activity of PDPs to a cellular compartment, we developed PDP-Mem, a cell membrane-targeting PDP. The membrane localization was achieved through the introduction of a palmitoylated lysine. PDP-Mem was shown to activate PP1α in vitro and to localize to the membrane of HeLa Kyoto and U2OS cells. However, in cells, the combination of the polybasic sequence for cell penetration and the membrane targeting palmitoylated lysine activates the MAPK signaling pathway and induces cytoplasmic calcium release independently of PP1 activation. Therefore, when targeting peptides to cellular membranes, undesired effects induced by the targeting sequence and lipid modification need to be considered.
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Affiliation(s)
- Jeremy E Chojnacki
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Laura Scheinost
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Yansong Wang
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maja Köhn
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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23
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Zhao P, Malik S. The phosphorylation to acetylation/methylation cascade in transcriptional regulation: how kinases regulate transcriptional activities of DNA/histone-modifying enzymes. Cell Biosci 2022; 12:83. [PMID: 35659740 PMCID: PMC9164400 DOI: 10.1186/s13578-022-00821-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022] Open
Abstract
Transcription factors directly regulate gene expression by recognizing and binding to specific DNA sequences, involving the dynamic alterations of chromatin structure and the formation of a complex with different kinds of cofactors, like DNA/histone modifying-enzymes, chromatin remodeling factors, and cell cycle factors. Despite the significance of transcription factors, it remains unclear to determine how these cofactors are regulated to cooperate with transcription factors, especially DNA/histone modifying-enzymes. It has been known that DNA/histone modifying-enzymes are regulated by post-translational modifications. And the most common and important modification is phosphorylation. Even though various DNA/histone modifying-enzymes have been classified and partly explained how phosphorylated sites of these enzymes function characteristically in recent studies. It still needs to find out the relationship between phosphorylation of these enzymes and the diseases-associated transcriptional regulation. Here this review describes how phosphorylation affects the transcription activity of these enzymes and other functions, including protein stability, subcellular localization, binding to chromatin, and interaction with other proteins.
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24
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Tang S, Xue Y, Dengqi X, Shao L. Design, development and evaluation of a prodrug-type TrkA-selective inhibitor with antinociceptive effects in vivo. Eur J Med Chem 2022; 245:114901. [DOI: 10.1016/j.ejmech.2022.114901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
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25
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Waudby CA, Alvarez-Teijeiro S, Josue Ruiz E, Suppinger S, Pinotsis N, Brown PR, Behrens A, Christodoulou J, Mylona A. An intrinsic temporal order of c-JUN N-terminal phosphorylation regulates its activity by orchestrating co-factor recruitment. Nat Commun 2022; 13:6133. [PMID: 36253406 PMCID: PMC9576782 DOI: 10.1038/s41467-022-33866-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Protein phosphorylation is a major regulatory mechanism of cellular signalling. The c-JUN proto-oncoprotein is phosphorylated at four residues within its transactivation domain (TAD) by the JNK family kinases, but the functional significance of c-JUN multisite phosphorylation has remained elusive. Here we show that c-JUN phosphorylation by JNK exhibits defined temporal kinetics, with serine63 and serine73 being phosphorylated more rapidly than threonine91 and threonine93. We identify the positioning of the phosphorylation sites relative to the kinase docking motif, and their primary sequence, as the main factors controlling phosphorylation kinetics. Functional analysis reveals three c-JUN phosphorylation states: unphosphorylated c-JUN recruits the MBD3 repressor, serine63/73 doubly-phosphorylated c-JUN binds to the TCF4 co-activator, whereas the fully phosphorylated form disfavours TCF4 binding attenuating JNK signalling. Thus, c-JUN phosphorylation encodes multiple functional states that drive a complex signalling response from a single JNK input.
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Affiliation(s)
- Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London, UK
- School of Pharmacy, University College London, London, UK
| | - Saul Alvarez-Teijeiro
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - E Josue Ruiz
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK
| | - Simon Suppinger
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Paul R Brown
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College, London, UK
| | - Axel Behrens
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
- CR-UK Convergence Science Centre, Imperial College, London, SW7 2BU, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London, London, UK.
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.
| | - Anastasia Mylona
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK.
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26
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Kokot T, Köhn M. Emerging insights into serine/threonine-specific phosphoprotein phosphatase function and selectivity. J Cell Sci 2022; 135:277104. [DOI: 10.1242/jcs.259618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
ABSTRACT
Protein phosphorylation on serine and threonine residues is a widely distributed post-translational modification on proteins that acts to regulate their function. Phosphoprotein phosphatases (PPPs) contribute significantly to a plethora of cellular functions through the accurate dephosphorylation of phosphorylated residues. Most PPPs accomplish their purpose through the formation of complex holoenzymes composed of a catalytic subunit with various regulatory subunits. PPP holoenzymes then bind and dephosphorylate substrates in a highly specific manner. Despite the high prevalence of PPPs and their important role for cellular function, their mechanisms of action in the cell are still not well understood. Nevertheless, substantial experimental advancements in (phospho-)proteomics, structural and computational biology have contributed significantly to a better understanding of PPP biology in recent years. This Review focuses on recent approaches and provides an overview of substantial new insights into the complex mechanism of PPP holoenzyme regulation and substrate selectivity.
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Affiliation(s)
- Thomas Kokot
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg 1 , Freiburg 79104 , Germany
- University of Freiburg, 2 Faculty of Biology , Freiburg 79104 , Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg 1 , Freiburg 79104 , Germany
- University of Freiburg, 2 Faculty of Biology , Freiburg 79104 , Germany
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27
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Wang F, Wang X, Liu L, Deng S, Ji W, Liu Y, Wang X, Wang R, Zhao X, Gao E. Comprehensive analysis of PTPN gene family revealing PTPN7 as a novel biomarker for immuno-hot tumors in breast cancer. Front Genet 2022; 13:981603. [PMID: 36226189 PMCID: PMC9548886 DOI: 10.3389/fgene.2022.981603] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/26/2022] [Indexed: 11/23/2022] Open
Abstract
Background: The non-receptor protein tyrosine phosphatase (PTPN) gene family has been considered to be involved in the oncogenesis and development of multiple cancers. However, its prognostic utility and immunological relevance in breast cancer (BrCa) have not been clarified. Methods: A transcriptional level interpretation of the expressions and prognostic values was analyzed using the data from The Cancer Genome Atlas (TCGA) cohort. In addition, GO and DAVID pinpoint the functional enrichment of PTPNs. Moreover, the immune correlations of PTPN7 in BrCa and pan-cancer were further investigated based on the TCGA cohort and were testified using the in-house and the Gene Expression Omnibus (GEO) cohorts. Results: For systematic analysis of the PTPN family, we found that the expression levels of PTPN1, PTPN6, PTPN7, PTPN18, PTPN20, and PTPN22 was promoted in tumor tissues while comparing with paraneoplastic tissues during our study. We further investigated their functions and protein-protein interactions (PPI), and these results strongly suggested that PTPN family was associated with protein dephosphorylation. Next, we performed an immunological relevance analysis and found that PTPN7 was correlated with immune infiltration, suggesting a stronger association of PTPN7 with immuno-hot tumors in BrCa. In addition, results from the in-house cohort confirmed the positive correlation between PTPN7 and PD-L1. The pan-cancer analysis revealed that PTPN7 was related to PD-L1 and CTLA-4 expression in almost all cancer types. Finally, the predictive value of PTPN7 for immunotherapy was significant in two independent GEO cohorts. Conclusion: In conclusion, this is the first extensive research on the correlation between PTPN family expression and immune characterization in BrCa. As results, PTPN7 expression is associated with immuno-hot tumors and could be a promising predictive biomarker for immunotherapy in not only BrCa but multiple cancers.
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Affiliation(s)
- Fengxu Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xuehai Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Lei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Siyuan Deng
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Wenqian Ji
- College of International Studies, Southwest University, Chongqing, China
| | - Yang Liu
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xiangdong Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Rui Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xinyuan Zhao
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
- *Correspondence: Xinyuan Zhao, ; Erli Gao,
| | - Erli Gao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Xinyuan Zhao, ; Erli Gao,
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28
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Genome-Wide Identification and Analysis of the Growth-Regulating Factor Family in Zanthoxylum armatum DC and Functional Analysis of ZaGRF6 in Leaf Size and Longevity Regulation. Int J Mol Sci 2022; 23:ijms23169043. [PMID: 36012309 PMCID: PMC9409285 DOI: 10.3390/ijms23169043] [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: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that play an important role in plant growth and development. In this study, fifteen GRF gene members containing QLQ and WRC domains were identified in Zanthoxylum armatum. Phylogenetic and collinearity analysis showed that ZaGRFs were closely related to CsGRFs and AtGRFs, and distantly related to OsGRFs. There are a large number of cis-acting elements related to hormone response and stress induction in the GRF gene promoter region of Z. armatum. Tissue-specific expression analysis showed that except for ZaGRF7, all the ZaGRFs were highly expressed in young parts with active growth and development, including terminal buds, seeds, and young flowers, suggesting their key roles in Z. armatum growth and development. Eight ZaGRFs were selected to investigate the transcriptional response to auxin, gibberellin and drought treatments. A total of six ZaGRFs in the NAA treatment, four ZaGRFs in the GA3 treatment, and six ZaGRFs in the PEG treatment were induced and significantly up-regulated. Overexpression of ZaGRF6 increased branching and chlorophyll content and delayed senescence of transgenic Nicotiana benthamiana. ZaGRF6 increased the expression of CRF2 and suppressed the expression of ARR4 and CKX1, indicating that ZaGRF6 is involved in cytokinin metabolism and signal transduction. These research results lay a foundation for further analysis of the GRF gene function of Z. armatum and provide candidate genes for growth, development, and stress resistance breeding of Z. armatum.
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29
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Yin C, Sun Z, Ji C, Li F, Wu H. Toxicological effects of tris(1,3-dichloro-2-propyl) phosphate in oyster Crassostrea gigas using proteomic and phosphoproteomic analyses. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128824. [PMID: 35427976 DOI: 10.1016/j.jhazmat.2022.128824] [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: 01/28/2022] [Revised: 03/18/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
As a typical organophosphorus pollutant, tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) has been widely detected in aquatic environment. Previous studies showed that protein phosphorylation might be a vital way of TDCIPP to exert multiple toxic effects. However, there is a lack of high-throughput investigations on how TDCIPP affected protein phosphorylation. In this study, the toxicological effects of TDCIPP were explored by proteomic and phosphoproteomic analyses together with traditional means in oysters Crassostrea gigas treated with 0.5, 5 and 50 μg/L TDCIPP for 28 days. Integration of omic analyses revealed that TDCIPP dysregulated transcription, energy metabolism, and apoptosis and cell proliferation by either directly phosphorylating pivotal proteins or phosphorylating their upstream signaling pathways. The U-shaped response of acetylcholinesterase activities suggested the neurotoxicity of TDCIPP in a hormesis manner. What's more, the increase in caspase-9 activity as well as the expression or phosphorylation alterations in eukaryotic translation initiation factor 4E, cell division control protein 42 and transforming growth factor-β1-induced protein indicated the disruption of homeostasis between apoptosis and cell proliferation, which was consistent with the observation of shedding of digestive cells. Overall, combination of proteomic and phosphoproteomic analyses showed the capability of identifying molecular events, which provided new insights into the toxicological mechanisms of TDCIPP.
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Affiliation(s)
- Chengcheng Yin
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zuodeng Sun
- Shandong Fisheries Development and Resource Conservation Center, Ji'nan 250013, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao 266071, PR China.
| | - Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao 266071, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao 266071, PR China.
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30
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Fontanillo M, Trebacz M, Reinkemeier CD, Avilés Huerta D, Uhrig U, Sehr P, Köhn M. Short peptide pharmacophores developed from protein phosphatase-1 disrupting peptides (PDPs). Bioorg Med Chem 2022; 65:116785. [PMID: 35525109 PMCID: PMC7613447 DOI: 10.1016/j.bmc.2022.116785] [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: 03/30/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/28/2022]
Abstract
PP1 is a major phosphoserine/threonine-specific phosphatase that is involved in diseases such as heart insufficiency and diabetes. PP1-disrupting peptides (PDPs) are selective modulators of PP1 activity that release its catalytic subunit, which then dephosphorylates nearby substrates. Recently, PDPs enabled the creation of phosphatase-recruiting chimeras, which are bifunctional molecules that guide PP1 to a kinase to dephosphorylate and inactivate it. However, PDPs are 23mer peptides, which is not optimal for their use in therapy due to potential stability and immunogenicity issues. Therefore, we present here the sequence optimization of the 23mer PDP to a 5mer peptide, involving several attempts considering structure-based virtual screening, high throughput screening and peptide sequence optimization. We provide here a strong pharmacophore as lead structure to enable PP1 targeting in therapy or its use in phosphatase-recruiting chimeras in the future.
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Affiliation(s)
| | - Malgorzata Trebacz
- Centres for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | | | | | - Ulrike Uhrig
- Chemical Biology Core Facility, EMBL, Heidelberg, Germany
| | - Peter Sehr
- Chemical Biology Core Facility, EMBL, Heidelberg, Germany
| | - Maja Köhn
- Genome Biology Unit, EMBL, Heidelberg, Germany; Centres for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany.
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31
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Guo X, Mao X, Tian D, Liao Y, Su B, Ye C, Shi D, Liu TF, Ling Y, Hao Y. Cryptococcus neoformans Infection Induces IL-17 Production by Promoting STAT3 Phosphorylation in CD4 + T Cells. Front Immunol 2022; 13:872286. [PMID: 35720334 PMCID: PMC9197778 DOI: 10.3389/fimmu.2022.872286] [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: 02/09/2022] [Accepted: 04/14/2022] [Indexed: 12/02/2022] Open
Abstract
Cryptococcus neoformans infection in the central nervous system is a severe infectious disease with poor outcomes and high mortality. It has been estimated that there are 220,000 new cases each year. Over 90% of C. neoformans meningitis cases were diagnosed in AIDS patients with CD4+ T cell count <100 cells/μl; however, the mechanism of cryptococcal meningitis in patients with normal immune functions remains unclear. IL-17 is a pro-inflammatory cytokine and plays an important role in anti-fungal immunity. Here we report that significantly high levels of IL-17 were predominantly detected in the cerebrospinal fluid of patients with either AIDS- or non-AIDS-associated C. neoformans meningitis but not in patients with tuberculous meningitis or non-neurosyphilis. Antifungal therapy minimized the IL-17 level in the cerebrospinal fluid. An in vitro mechanistic study showed that C. neoformans stimulation of healthy peripheral blood mononuclear cells prompted IL-17 production, and CD4+ T cells were the predominant IL-17-producing cells. IL-17 production by C. neoformans stimulation was STAT3 signaling dependent. Inhibition of STAT3 phosphorylation attenuated the C. neoformans-mediated IL-17 expression. Our data highlighted the significance of CD4+ T cells in antifungal immunity and suggested IL-17 as a diagnostic biomarker of C. neoformans infection and STAT3 as a checkpoint for antifungal targeted therapies.
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Affiliation(s)
- Xiaoman Guo
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinru Mao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Di Tian
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yixin Liao
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Bintao Su
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Laboratory Medicine, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaoliang Ye
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongling Shi
- Department of Infectious Disease, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Tie Fu Liu
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yun Ling
- Department of Infectious Disease, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yi Hao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Hidden Multivalency in Phosphatase Recruitment by a Disordered AKAP Scaffold. J Mol Biol 2022; 434:167682. [PMID: 35697294 DOI: 10.1016/j.jmb.2022.167682] [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: 05/08/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022]
Abstract
Disordered scaffold proteins provide multivalent landing pads that, via a series of embedded Short Linear Motifs (SLiMs), bring together the components of a complex to orchestrate precise spatial and temporal regulation of cellular processes. One such protein is AKAP5 (previously AKAP79), which contains SLiMs that anchor PKA and Calcineurin, and recruit substrate (the TRPV1 receptor). Calcineurin is anchored to AKAP5 by a well-characterised PxIxIT SLiM. Here we show, using a combination of biochemical and biophysical approaches, that the Calcineurin PxIxIT-binding groove also recognises several hitherto unknown lower-affinity SLiMs in addition to the PxIxIT motif. We demonstrate that the assembly is in reality a complex system with conserved SLiMs spanning a wide affinity range. The capture is analogous to that seen for many DNA-binding proteins that have a weak non-specific affinity for DNA outside the canonical binding site, but different in that it involves (i) two proteins, and (ii) hydrophobic rather than electrostatic interactions. It is also compatible with the requirement for both stable anchoring of the enzyme and responsive downstream signalling. We conclude that the AKAP5 C-terminus is enriched in lower-affinity/mini-SLiMs that, together with the canonical SLiM, maintain a structurally disordered but tightly regulated signalosome.
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Differential mRNA Expression Profiling Reveals the Role of MiR-375 in Inflammation of Bovine Mammary Epithelial Cells. Animals (Basel) 2022; 12:ani12111431. [PMID: 35681895 PMCID: PMC9179474 DOI: 10.3390/ani12111431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Bovine mammary epithelial cells (bMECs) are often used as cell models for mammary gland research. They are the most important cells for mammary gland function and the first line of defense for pathogen identification. MicroRNAs (miRNAs) are important regulatory factors involved in many physiological and pathological processes. Here, we examined a transcriptome profile of bovine mammary epithelial cell lines transfected with miR-375 inhibitor or negative control (NC) inhibitor, and further reveal the potential role of miR-375 in bMECs by differentially expressed mRNA analysis. We found that miR-375 potentially promotes inflammation in the mammary gland through the MAPK signaling pathway. Abstract MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate post-transcriptional gene expression and several biological processes. Bovine mammary epithelial cells (bMECs) mediate critical immune responses in the mammary gland and the occurrence of mastitis. Current research focuses on miRNA regulation of bMECs, but the miR-375 regulatory mechanism in bMECs is unclear. This study explored the role of miR-375 by profiling the transcriptome of miR-375-silenced bMECs using RNA-seq and identifying differentially expressed mRNAs (DIE-mRNAs). There were 63 DIE-mRNAs, including 48 down-regulated and 15 up-regulated mRNAs between miR-375-silenced bMECs and the controls. The Kyoto encyclopedia of genes and genomes (KEGG) and Gene Ontology (GO) functional analysis showed that the DIE-mRNAs enriched nuclear receptor subfamily 4 group A member 1 (NR4A1) and protein tyrosine phosphatase non-receptor type 5 (PTPN5) anti-inflammatory genes of the mitogen-activated protein kinase (MAPK) signaling pathway. However, they showed an opposite trend to the expression of miR-375 silencing, suggesting that miR-375 promotes bMEC inflammation through the MAPK signaling pathway. The findings of this study provide a new reference for understanding the regulation of bMEC inflammation and cow mastitis.
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Kuang W, Wang X, Ding J, Li J, Ji M, Chen W, Wang L, Yang P. PTPN2, A Key Predictor of Prognosis for Pancreatic Adenocarcinoma, Significantly Regulates Cell Cycles, Apoptosis, and Metastasis. Front Immunol 2022; 13:805311. [PMID: 35154122 PMCID: PMC8829144 DOI: 10.3389/fimmu.2022.805311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
Objective This study conducted a comprehensive analysis of the members of the PTPN family and emphasized the key role of PTPN2 as a potential therapeutic target and diagnostic biomarker in improving the survival rate of PAAD. Method Oncomine was used to analyze the pan-cancer expression of the PTPN gene family. The Cancer Genome Atlas (TCGA) data as well as Genotype-Tissue Expression (GTEx) data were downloaded to analyze the expression and prognosis of PTPNs. The diagnosis of PTPNs was evaluated by the experimental ROC curve. The protein-protein interaction (PPI) network was constructed by combining STRING and Cytoscape. The genes of 50 proteins most closely related to PTPN2 were screened and analyzed by GO and KEGG enrichment. The differentially expressed genes of PTPN2 were found by RNA sequencing, and GSEA enrichment analysis was carried out to find the downstream pathways and targets, which were verified by online tools and experiments. Finally, the relationship between PTPN2 and immune cell infiltration in PAAD, and the relationship with immune score and immune checkpoint were studied. Result The expression patterns and the prognostic value of multiple PTPNs in PAAD have been reported through bioinformatic analyzes. Among these members, PTPN2 is the most important prognostic signature that regulates the progression of PAAD by activating JAK-STAT signaling pathway. Comparison of two PAAD cell lines with normal pancreatic epithelial cell lines revealed that PTPN2 expression was up-regulated as a key regulator of PAAD, which was associated with poor prognosis. Knockdown of PTPN2 caused a profound decrease in PAAD cell growth, migration, invasion, and induced PAAD cell cycle and apoptosis. In addition, we conducted a series of enrichment analyses to investigate the PTPN2-binding proteins and the PTPN2 expression-correlated genes. We suggest that STAT1 and EGFR are the key factors to regulate PTPN2, which are involved in the progression of PAAD. Meanwhile, the silencing of PTPN2 induced the repression of STAT1 and EGFR expression. Conclusion These findings provide a comprehensive analysis of the PTPN family members, and for PAAD, they also demonstrate that PTPN2 is a diagnostic biomarker and a therapeutic target.
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Affiliation(s)
- Wenbin Kuang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiao Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jiayu Ding
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jiaxing Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Minghui Ji
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Weijiao Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Liping Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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35
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Gao R, Li X, Gao H, Zhao K, Liu X, Liu J, Wang Q, Zhu Y, Chen H, Xiang S, Zhan Y, Yin R, Yu M, Ning H, Yang X, Li C. Protein phosphatase 2A catalytic subunit β suppresses PMA/ionomycin-induced T-cell activation by negatively regulating PI3K/Akt signaling. FEBS J 2022; 289:4518-4535. [PMID: 35068054 DOI: 10.1111/febs.16370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/16/2021] [Accepted: 01/20/2022] [Indexed: 01/07/2023]
Abstract
The precise regulation of the T-cell activation process is critical for overall immune homeostasis. Although protein phosphatase 2A (PP2A) is required for T-cell development and function, the role of PPP2CB, which is the catalytic subunit β isoform of PP2A, remains unknown. In the present study, using a T cell-specific knockout mouse of PPP2CB (PPP2CBfl/fl Lck-Cre+ ), we demonstrated that PPP2CB was dispensable for T-cell development in the thymus and peripheral lymphoid organs. Furthermore, PPP2CB deletion did not affect T-cell receptor (TCR)-induced T-cell activation or cytokine-induced T-cell responses; however, it specifically enhanced phorbol myristate acetate (PMA) plus ionomycin-induced T-cell activation with increased cellular proliferation, elevated CD69 and CD25 expression, and enhanced cytokine production (inteferon-γ, interleukin-2 and tumor necrosis factor). Mechanistic analyses suggested that the PPP2CB deletion enhanced activation of the phosphoinositide 3-kinase/Akt signaling pathway and Ca2+ flux following stimulation with PMA plus ionomycin. Moreover, the specific PI3K inhibitor rescued the augmented cell activation in PPP2CB-deficient T cells. Using mass spectrometry-based phospho-peptide analysis, we identified potential substrates of PPP2CB during PMA plus ionomycin-induced T-cell activation. Collectively, our study provides evidence of the specific role of PPP2CB in controlling PMA plus ionomycin-induced T-cell activation.
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Affiliation(s)
- Rui Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Xin Li
- Department of Hematopoietic Stem Cell Transplantation, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Huiying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Ke Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Xian Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Jinfang Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Qi Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yaxin Zhu
- School of Life Sciences, Hebei University, Baoding, China
| | - Hui Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Shensi Xiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Yiqun Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Ronghua Yin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Miao Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Hongmei Ning
- Department of Hematopoietic Stem Cell Transplantation, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaoming Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
| | - Changyan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, China
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36
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Kliche J, Ivarsson Y. Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. Biochem J 2022; 479:1-22. [PMID: 34989786 PMCID: PMC8786283 DOI: 10.1042/bcj20200714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the interactions. In addition, motif-based interactions are involved in targeting serine/threonine kinases and phosphatases to their substrate and contribute to the specificity of the enzymatic actions regulating which sites are phosphorylated. Here, we review how SLiM-based interactions assist in determining the specificity of serine/threonine kinases and phosphatases, and how phosphorylation, in turn, affects motif-based interactions. We provide examples of SLiM-based interactions that are turned on/off, or are tuned by serine/threonine phosphorylation and exemplify how this affects SLiM-based protein complex formation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
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37
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Phosphorylation of TRIP13 at Y56 induces radiation resistance but sensitizes head and neck cancer to cetuximab. Mol Ther 2022; 30:468-484. [PMID: 34111559 PMCID: PMC8753291 DOI: 10.1016/j.ymthe.2021.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 01/07/2023] Open
Abstract
Radiation therapy, a mainstay of treatment for head and neck cancer, is not always curative due to the development of treatment resistance; additionally, multi-institutional trials have questioned the efficacy of concurrent radiation with cetuximab, the epidermal growth factor receptor (EGFR) inhibitor. We unraveled a mechanism for radiation resistance; that is, radiation induces EGFR, which phosphorylates TRIP13 (thyroid hormone receptor interactor 13) on tyrosine 56. Phosphorylated (phospho-)TRIP13 promotes non-homologous end joining (NHEJ) repair to induce radiation resistance. NHEJ is the main repair pathway for radiation-induced DNA damage. Tumors expressing high TRIP13 do not respond to radiation but are sensitive to cetuximab or cetuximab combined with radiation. Suppression of phosphorylation of TRIP13 at Y56 abrogates these effects. These findings show that EGFR-mediated phosphorylation of TRIP13 at Y56 is a vital mechanism of radiation resistance. Notably, TRIP13-pY56 could be used to predict the response to radiation or cetuximab and could be explored as an actionable target.
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38
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Regulation of Viral Restriction by Post-Translational Modifications. Viruses 2021; 13:v13112197. [PMID: 34835003 PMCID: PMC8618861 DOI: 10.3390/v13112197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022] Open
Abstract
Intrinsic immunity is orchestrated by a wide range of host cellular proteins called restriction factors. They have the capacity to interfere with viral replication, and most of them are tightly regulated by interferons (IFNs). In addition, their regulation through post-translational modifications (PTMs) constitutes a major mechanism to shape their action positively or negatively. Following viral infection, restriction factor modification can be decisive. Palmitoylation of IFITM3, SUMOylation of MxA, SAMHD1 and TRIM5α or glycosylation of BST2 are some of those PTMs required for their antiviral activity. Nonetheless, for their benefit and by manipulating the PTMs machinery, viruses have evolved sophisticated mechanisms to counteract restriction factors. Indeed, many viral proteins evade restriction activity by inducing their ubiquitination and subsequent degradation. Studies on PTMs and their substrates are essential for the understanding of the antiviral defense mechanisms and provide a global vision of all possible regulations of the immune response at a given time and under specific infection conditions. Our aim was to provide an overview of current knowledge regarding the role of PTMs on restriction factors with an emphasis on their impact on viral replication.
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Guo X, He H, Yu J, Shi S. PKSPS: a novel method for predicting kinase of specific phosphorylation sites based on maximum weighted bipartite matching algorithm and phosphorylation sequence enrichment analysis. Brief Bioinform 2021; 23:6398688. [PMID: 34661630 DOI: 10.1093/bib/bbab436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 11/14/2022] Open
Abstract
With the development of biotechnology, a large number of phosphorylation sites have been experimentally confirmed and collected, but only a few of them have kinase annotations. Since experimental methods to detect kinases at specific phosphorylation sites are expensive and accidental, some computational methods have been proposed to predict the kinase of these sites, but most methods only consider single sequence information or single functional network information. In this study, a new method Predicting Kinase of Specific Phosphorylation Sites (PKSPS) is developed to predict kinases of specific phosphorylation sites in human proteins by combining PKSPS-Net with PKSPS-Seq, which considers protein-protein interaction (PPI) network information and sequence information. For PKSPS-Net, kinase-kinase and substrate-substrate similarity are quantified based on the topological similarity of proteins in the PPI network, and maximum weighted bipartite matching algorithm is proposed to predict kinase-substrate relationship. In PKSPS-Seq, phosphorylation sequence enrichment analysis is used to analyze the similarity of local sequences around phosphorylation sites and predict the kinase of specific phosphorylation sites (KSP). PKSPS has been proved to be more effective than the PKSPS-Net or PKSPS-Seq on different sets of kinases. Further comparison results show that the PKSPS method performs better than existing methods. Finally, the case study demonstrates the effectiveness of the PKSPS in predicting kinases of specific phosphorylation sites. The open source code and data of the PKSPS can be obtained from https://github.com/guoxinyunncu/PKSPS.
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Affiliation(s)
- Xinyun Guo
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang 330031, China
| | - Huan He
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang 330031, China
| | - Jialin Yu
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang 330031, China
| | - Shaoping Shi
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang 330031, China
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40
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Schwarz JJ, Grundmann L, Kokot T, Kläsener K, Fotteler S, Medgyesi D, Köhn M, Reth M, Warscheid B. Quantitative proteomics identifies PTP1B as modulator of B cell antigen receptor signaling. Life Sci Alliance 2021; 4:4/11/e202101084. [PMID: 34526379 PMCID: PMC8473724 DOI: 10.26508/lsa.202101084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022] Open
Abstract
This study analyses the function of the protein tyrosine phosphatase 1B identifying its binding partners and dephosphorylation targets for modulating B cell antigen receptor signaling. B cell antigen receptor (BCR) signaling is initiated by protein kinases and limited by counteracting phosphatases that currently are less well studied in their regulation of BCR signaling. Here, we used the B cell line Ramos to identify and quantify human B cell signaling components. Specifically, a protein tyrosine phosphatase profiling revealed a high expression of the protein tyrosine phosphatase 1B (PTP1B) in Ramos and human naïve B cells. The loss of PTP1B leads to increased B cell activation. Through substrate trapping in combination with quantitative mass spectrometry, we identified 22 putative substrates or interactors of PTP1B. We validated Igα, CD22, PLCγ1/2, CBL, BCAP, and APLP2 as specific substrates of PTP1B in Ramos B cells. The tyrosine kinase BTK and the two adaptor proteins GRB2 and VAV1 were identified as direct binding partners and potential substrates of PTP1B. We showed that PTP1B dephosphorylates the inhibitory receptor protein CD22 at phosphotyrosine 807. We conclude that PTP1B negatively modulates BCR signaling by dephosphorylating distinct phosphotyrosines in B cell-specific receptor proteins and various downstream signaling components.
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Affiliation(s)
- Jennifer J Schwarz
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Lorenz Grundmann
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Thomas Kokot
- Integrative Signalling Research, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Kathrin Kläsener
- Department for Molecular Immunology, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Sandra Fotteler
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - David Medgyesi
- Department for Molecular Immunology, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maja Köhn
- Integrative Signalling Research, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Michael Reth
- Department for Molecular Immunology, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany .,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
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Zhou MH, Chen SR, Wang L, Huang Y, Deng M, Zhang J, Zhang J, Chen H, Yan J, Pan HL. Protein Kinase C-Mediated Phosphorylation and α2δ-1 Interdependently Regulate NMDA Receptor Trafficking and Activity. J Neurosci 2021; 41:6415-6429. [PMID: 34252035 PMCID: PMC8318084 DOI: 10.1523/jneurosci.0757-21.2021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 11/21/2022] Open
Abstract
N-methyl-d-aspartate receptors (NMDARs) are important for synaptic plasticity associated with many physiological functions and neurologic disorders. Protein kinase C (PKC) activation increases the phosphorylation and activity of NMDARs, and α2δ-1 is a critical NMDAR-interacting protein and controls synaptic trafficking of NMDARs. In this study, we determined the relative roles of PKC and α2δ-1 in the control of NMDAR activity. We found that α2δ-1 coexpression significantly increased NMDAR activity in HEK293 cells transfected with GluN1/GluN2A or GluN1/GluN2B. PKC activation with phorbol 12-myristate 13-acetate (PMA) increased receptor activity only in cells coexpressing GluN1/GluN2A and α2δ-1. Remarkably, PKC inhibition with Gӧ6983 abolished α2δ-1-coexpression-induced potentiation of NMDAR activity in cells transfected with GluN1/GluN2A or GluN1/GluN2B. Treatment with PMA increased the α2δ-1-GluN1 interaction and promoted α2δ-1 and GluN1 cell surface trafficking. PMA also significantly increased NMDAR activity of spinal dorsal horn neurons and the amount of α2δ-1-bound GluN1 protein complexes in spinal cord synaptosomes in wild-type mice, but not in α2δ-1 knockout mice. Furthermore, inhibiting α2δ-1 with pregabalin or disrupting the α2δ-1-NMDAR interaction with the α2δ-1 C-terminus peptide abolished the potentiating effect of PMA on NMDAR activity. Additionally, using quantitative phosphoproteomics and mutagenesis analyses, we identified S929 on GluN2A and S1413 (S1415 in humans) on GluN2B as the phosphorylation sites responsible for NMDAR potentiation by PKC and α2δ-1. Together, our findings demonstrate the interdependence of α2δ-1 and PKC phosphorylation in regulating NMDAR trafficking and activity. The phosphorylation-dependent, dynamic α2δ-1-NMDAR interaction constitutes an important molecular mechanism of synaptic plasticity.SIGNIFICANCE STATEMENT A major challenge in studies of protein phosphorylation is to define the functional significance of each phosphorylation event and determine how various signaling pathways are coordinated in response to neuronal activity to shape synaptic plasticity. PKC phosphorylates transporters, ion channels, and G-protein-coupled receptors in signal transduction. In this study, we showed that α2δ-1 is indispensable for PKC-activation-induced surface and synaptic trafficking of NMDARs, whereas the α2δ-1-NMDAR interaction is controlled by PKC-induced phosphorylation. Our findings reveal that α2δ-1 mainly functions as a phospho-binding protein in the control of NMDAR trafficking and activity. This information provides new mechanistic insight into the reciprocal roles of PKC-mediated phosphorylation and α2δ-1 in regulating NMDARs and in the therapeutic actions of gabapentinoids.
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Affiliation(s)
- Meng-Hua Zhou
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Shao-Rui Chen
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Li Wang
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Yuying Huang
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Meichun Deng
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Jixiang Zhang
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Jiyuan Zhang
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Hong Chen
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Jiusheng Yan
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Hui-Lin Pan
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
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42
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Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. Methods Mol Biol 2021. [PMID: 34270057 DOI: 10.1007/978-1-0716-1625-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Most proteins undergo some form of modification after translation, and phosphorylation is one of the most relevant and ubiquitous post-translational modifications. The succession of protein phosphorylation and dephosphorylation catalyzed by protein kinase and phosphatase, respectively, constitutes a key mechanism of molecular information flow in cellular systems. The protein interactions of kinases, phosphatases, and their regulatory subunits and substrates are the main part of phosphorylation networks. To elucidate the landscape of phosphorylation events has been a central goal pursued by both experimental and computational approaches. Substrate specificity (e.g., sequence, structure) or the phosphoproteome has been utilized in an array of different statistical learning methods to infer phosphorylation networks. In this chapter, different computational phosphorylation network inference-related methods and resources are summarized and discussed.
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Stecher C, Marinkov S, Mayr-Harting L, Katic A, Kastner MT, Rieder-Rommer FJJ, Lin X, Nekhai S, Steininger C. Protein Phosphatase 1 Regulates Human Cytomegalovirus Protein Translation by Restraining AMPK Signaling. Front Microbiol 2021; 12:698603. [PMID: 34335531 PMCID: PMC8320725 DOI: 10.3389/fmicb.2021.698603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/31/2021] [Indexed: 11/22/2022] Open
Abstract
Human cytomegalovirus (HCMV) carries the human protein phosphatase 1 (PP1) and other human proteins important for protein translation in its tegument layer for a rapid supply upon infection. However, the biological relevance behind PP1 incorporation and its role during infection is unclear. Additionally, PP1 is a difficult molecular target due to its promiscuity and similarities between the catalytic domain of multiple phosphatases. In this study, we circumvented these shortcomings by using 1E7-03, a small molecule protein–protein interaction inhibitor, as a molecular tool of noncatalytic PP1 inhibition. 1E7-03 treatment of human fibroblasts severely impaired HCMV replication and viral protein translation. More specifically, PP1 inhibition led to the deregulation of metabolic signaling pathways starting at very early time points post-infection. This effect was at least partly mediated by the prevention of AMP-activated protein kinase dephosphorylation, leading to elongation factor 2 hyperphosphorylation and reduced translation rates. These findings reveal an important mechanism of PP1 for lytic HCMV infection.
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Affiliation(s)
- Carmen Stecher
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Sanja Marinkov
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Lucia Mayr-Harting
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Ana Katic
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marie-Theres Kastner
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Franz J J Rieder-Rommer
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Xionghao Lin
- Center for Sickle Cell Disease, Howard University, Washington, DC, United States
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, Washington, DC, United States
| | - Christoph Steininger
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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Zhang Q, Fan Z, Zhang L, You Q, Wang L. Strategies for Targeting Serine/Threonine Protein Phosphatases with Small Molecules in Cancer. J Med Chem 2021; 64:8916-8938. [PMID: 34156850 DOI: 10.1021/acs.jmedchem.1c00631] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Among numerous posttranslational regulation patterns, phosphorylation is reversibly controlled by the balance of kinases and phosphatases. The major form of cellular signaling involves the reversible phosphorylation of proteins on tyrosine, serine, or threonine residues. However, altered phosphorylation levels are found in diverse diseases, including cancer, making kinases and phosphatases ideal drug targets. In contrast to the success of prosperous kinase inhibitors, design of small molecules targeting phosphatase is struggling due to past bias and difficulty. This is especially true for serine/threonine phosphatases, one of the largest phosphatase families. From this perspective, we aim to provide insights into serine/threonine phosphatases and the small molecules targeting these proteins for drug development, especially in cancer. Through highlighting the modulation strategies, we aim to provide basic principles for the design of small molecules and future perspectives for the application of drugs targeting serine/threonine phosphatases.
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Affiliation(s)
- Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhongjiao Fan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lianshan Zhang
- Shanghai Hengrui Pharmaceutical Co., Ltd., Shanghai 200245, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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Evolutionary crossroads of cell signaling: PP1 and PP2A substrate sites in intrinsically disordered regions. Biochem Soc Trans 2021; 49:1065-1074. [PMID: 34100859 PMCID: PMC8286827 DOI: 10.1042/bst20200175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023]
Abstract
Phosphorylation of the hydroxyl group of the amino acids serine and threonine is among the most prevalent post-translational modifications in mammalian cells. Phospho-serine (pSer) and -threonine (pThr) represent a central cornerstone in the cell's toolbox for adaptation to signal input. The true power for the fast modulation of the regulatory pSer/pThr sites arises from the timely attachment, binding and removal of the phosphate. The phosphorylation of serine and threonine by kinases and the binding of pSer/pThr by phosphorylation-dependent scaffold proteins is largely determined by the sequence motif surrounding the phosphorylation site (p-site). The removal of the phosphate is regulated by pSer/pThr-specific phosphatases with the two most prominent ones being PP1 and PP2A. For this family, recent advances brought forward a more complex mechanism for p-site selection. The interaction of regulatory proteins with the substrate protein constitutes a first layer for substrate recognition, but also interactions of the catalytic subunit with the amino acids in close proximity to pSer/pThr contribute to p-site selection. Here, we review the current pieces of evidence for this multi-layered, complex mechanism and hypothesize that, depending on the degree of higher structure surrounding the substrate site, recognition is more strongly influenced by regulatory subunits away from the active site for structured substrate regions, whereas the motif context is of strong relevance with p-sites in disordered regions. The latter makes these amino acid sequences crossroads for signaling and motif strength between kinases, pSer/pThr-binding proteins and phosphatases.
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Licheva M, Raman B, Kraft C, Reggiori F. Phosphoregulation of the autophagy machinery by kinases and phosphatases. Autophagy 2021; 18:104-123. [PMID: 33970777 PMCID: PMC8865292 DOI: 10.1080/15548627.2021.1909407] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells use post-translational modifications to diversify and dynamically coordinate the function and properties of protein networks within various cellular processes. For example, the process of autophagy strongly depends on the balanced action of kinases and phosphatases. Highly conserved from the budding yeast Saccharomyces cerevisiae to humans, autophagy is a tightly regulated self-degradation process that is crucial for survival, stress adaptation, maintenance of cellular and organismal homeostasis, and cell differentiation and development. Many studies have emphasized the importance of kinases and phosphatases in the regulation of autophagy and identified many of the core autophagy proteins as their direct targets. In this review, we summarize the current knowledge on kinases and phosphatases acting on the core autophagy machinery and discuss the relevance of phosphoregulation for the overall process of autophagy.
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Affiliation(s)
- Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Babu Raman
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, AV Groningen, The Netherlands
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, AV Groningen, The Netherlands
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47
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Gao Y, Ha YS, Kwon TG, Cho YC, Lee S, Lee JN. Characterization of Kinase Expression Related to Increased Migration of PC-3M Cells Using Global Comparative Phosphoproteome Analysis. Cancer Genomics Proteomics 2021; 17:543-553. [PMID: 32859632 DOI: 10.21873/cgp.20210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND/AIM Prostate cancer (PCa) is the second-most commonly occurring cancer among men, worldwide. Although the mechanisms associated with the progression of castration-resistant prostate cancer (CRPC) have been widely studied, the mechanism associated with more distant metastases from the bone remains unknown. This study aimed to characterize potential pathogenic kinases associated with highly metastatic PCa, that may regulate phosphorylation in extensively involved and diverse signaling pathways that are associated with the development of various cancers. MATERIALS AND METHODS A mass spectrometry (MS)-based comparative phosphoproteome strategy was utilized to identify differentially expressed kinases between the highly aggressive PCa cell-lines PC-3 and PC-3M. RESULTS Among 2,968 phosphorylation sites in PCa cells, 151 differently expressed phosphoproteins were identified. Seven motifs: -SP-, -SxxE-, -PxS-, -PxSP-, -SxxK-, -SPxK-, and -SxxxxxP- were found to be highly expressed in PC-3M cells. Based on these motifs, the kinases p21-activated kinase (PAK)2, Ste20-like kinase (SLK), mammalian Ste20-like kinase (MST)4, mitogen-activated kinase kinase (MAP2K)2, and A-Raf proto-oncogene serine/threonine kinase (ARAF) were up-regulated in PC-3M cells. CONCLUSION PAK2, SLK, MST4, MAP2K2, and ARAF are kinases that are potentially associated with the progression of increased migration in PC-3M cells and may represent molecule regulators or drug targets for highly metastatic PCa therapy.
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Affiliation(s)
- Yan Gao
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Yun-Sok Ha
- Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Tae Gyun Kwon
- Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Joint Institute for Regenerative Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Young-Chang Cho
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Sangkyu Lee
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jun Nyung Lee
- Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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Sieradzan AK, Korneev A, Begun A, Kachlishvili K, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2021; 17:3203-3220. [PMID: 33909430 DOI: 10.1021/acs.jctc.1c00155] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP218-62) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time dependence of formation of contacts between Cαs of selected pairs of residues. The key residues involved in the folding of the pT37pT46 4E-BP218-62 are elucidated by this analysis. The correlations between local and global motions are identified. Moreover, for a better understanding of the physics of the formation of the folded state, the experimental structure of the pT37pT46 4E-BP218-62 is analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is shown that without molecular dynamics simulations the kinks are able to identify not only the phosphorylated sites of protein, the key players in folding, but also the reasons for the weak stability of the pT37pT46 4E-BP218-62.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Anatolii Korneev
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Alexander Begun
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Khatuna Kachlishvili
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Alexander Molochkov
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Patrick Senet
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States.,Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Antti J Niemi
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia.,Laboratoire de Mathematiques et Physique Theorique, CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours, France.,Nordita, Stockholm University and Uppsala University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden.,School of Physics, Beijing Institute of Technology, Beijing 100081, P.R. China
| | - Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv 2021; 49:107757. [PMID: 33895332 DOI: 10.1016/j.biotechadv.2021.107757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Chinese hamster ovary (CHO) cells are one of the most commonly used host cell lines used for the production human therapeutic proteins. Much research over the past two decades has focussed on improving the growth, titre and cell specific productivity of CHO cells and in turn lowering the costs associated with production of recombinant proteins. CHO cell engineering has become of particular interest in recent years following the publication of the CHO cell genome and the availability of data relating to the proteome, transcriptome and metabolome of CHO cells. However, data relating to the cellular post-translational modification (PTMs) which can affect the functionality of CHO cellular proteins has only begun to be presented in recent years. PTMs are important to many cellular processes and can further alter proteins by increasing the complexity of proteins and their interactions. In this review, we describe the research presented from CHO cells to date related on three of the most important PTMs; glycosylation, phosphorylation and ubiquitination.
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Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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Role of protein S-Glutathionylation in cancer progression and development of resistance to anti-cancer drugs. Arch Biochem Biophys 2021; 704:108890. [PMID: 33894196 DOI: 10.1016/j.abb.2021.108890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]
Abstract
The survival, functioning and proliferation of mammalian cells are highly dependent on the cellular response and adaptation to changes in their redox environment. Cancer cells often live in an altered redox environment due to aberrant neo-vasculature, metabolic reprogramming and dysregulated proliferation. Thus, redox adaptations are critical for their survival. Glutathione plays an essential role in maintaining redox homeostasis inside the cells by binding to redox-sensitive cysteine residues in proteins by a process called S-glutathionylation. S-Glutathionylation not only protects the labile cysteine residues from oxidation, but also serves as a sensor of redox status, and acts as a signal for stimulation of downstream processes and adaptive responses to ensure redox equilibrium. The present review aims to provide an updated overview of the role of the unique redox adaptations during carcinogenesis and cancer progression, focusing on their dependence on S-glutathionylation of specific redox-sensitive proteins involved in a wide range of processes including signalling, transcription, structural maintenance, mitochondrial functions, apoptosis and protein recycling. We also provide insights into the role of S-glutathionylation in the development of resistance to chemotherapy. Finally, we provide a strong rationale for the development of redox targeting drugs for treatment of refractory/resistant cancers.
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