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Taghehchian N, Samsami Y, Maharati A, Zangouei AS, Boroumand-Noughabi S, Moghbeli M. Molecular biology of microRNA-342 during tumor progression and invasion. Pathol Res Pract 2023; 248:154672. [PMID: 37413875 DOI: 10.1016/j.prp.2023.154672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
Cancer is considered as one of the main causes of human deaths and health challenges in the world. Various factors are involved in the high death rate of cancer patients, including late diagnosis and drug resistance that result in treatment failure and tumor recurrence. Invasive diagnostic methods are one of the main reasons of late tumor detection in cancer patients. Therefore, it is necessary to investigate the molecular tumor biology to introduce efficient non-invasive markers. MicroRNAs (miRNAs) are involved in regulation of the cellular mechanisms such as cell proliferation, apoptosis, and migration. MiRNAs deregulations have been also frequently shown in different tumor types. Here, we discussed the molecular mechanisms of miR-342 during tumor growth. MiR-342 mainly functions as a tumor suppressor by the regulation of transcription factors and signaling pathways such as WNT, PI3K/AKT, NF-kB, and MAPK. Therefore, miR-342 mimics can be used as a reliable therapeutic strategy to inhibit the tumor cells growth. The present review can also pave the way to introduce the miR-342 as a non-invasive diagnostic/prognostic marker in cancer patients.
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Affiliation(s)
- Negin Taghehchian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yalda Samsami
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Sadra Zangouei
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Boroumand-Noughabi
- Department of Hematology and Blood Bank, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Tang L, Gao Y, Li T. Pan-cancer analysis identifies the immunological and prognostic role of PAK4. Life Sci 2023; 312:121263. [PMID: 36470541 DOI: 10.1016/j.lfs.2022.121263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/21/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022]
Abstract
AIMS P21-activated kinase 4 (PAK4) belongs to the wider family of Serine/Threonine p21-activated kinases (PAKs) and functions as a hub for signaling pathways in cancer progression. Numerous studies have indicated the significance of PAK4 for tumorigenesis, but no systematic pan-cancer analysis has been performed. MAIN METHODS The current study aimed to investigate the prognostic and immunological functions of PAK4 through bioinformatic analysis of datasets from The Cancer Genome Atlas, UALCAN, GEPIA2, cBioPortal, TIMER2, and Human Protein Atlas. PAK4 expression was correlated with prognosis, DNA methylation, tumor mutational burden, microsatellite instability, and immune cell infiltration. KEY FINDINGS PAK4 was highly expressed in various cancers but showed decreased expression in colon adenocarcinoma, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, and thyroid carcinoma. PAK4 was found to have a positive or negative correlation with prognosis of different cancers. PAK4 expression was related to tumor mutational burden in 11 tumor types, and associated with microsatellite instability in 10 tumor types and was correlated with immune infiltration and immune checkpoint genes. SIGNIFICANCE PAK4 could be considered as a prognostic and immunotherapeutic marker for some types of malignant tumor.
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Affiliation(s)
- Lina Tang
- Advanced Medical Research Center of Zhengzhou University, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China.
| | - Yunling Gao
- Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the PRC and Key Laboratory of Medical Cell Biology, Ministry of Education of the PRC, China Medical University, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Tingting Li
- Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the PRC and Key Laboratory of Medical Cell Biology, Ministry of Education of the PRC, China Medical University, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
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3
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Láscarez-Lagunas LI, Nadarajan S, Martinez-Garcia M, Quinn JN, Todisco E, Thakkar T, Berson E, Eaford D, Crawley O, Montoya A, Faull P, Ferrandiz N, Barroso C, Labella S, Koury E, Smolikove S, Zetka M, Martinez-Perez E, Colaiácovo MP. ATM/ATR kinases link the synaptonemal complex and DNA double-strand break repair pathway choice. Curr Biol 2022; 32:4719-4726.e4. [PMID: 36137547 PMCID: PMC9643613 DOI: 10.1016/j.cub.2022.08.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/22/2022] [Accepted: 08/31/2022] [Indexed: 11/21/2022]
Abstract
DNA double-strand breaks (DSBs) are deleterious lesions, which must be repaired precisely to maintain genomic stability. During meiosis, programmed DSBs are repaired via homologous recombination (HR) while repair using the nonhomologous end joining (NHEJ) pathway is inhibited, thereby ensuring crossover formation and accurate chromosome segregation.1,2 How DSB repair pathway choice is implemented during meiosis is unknown. In C. elegans, meiotic DSB repair takes place in the context of the fully formed, highly dynamic zipper-like structure present between homologous chromosomes called the synaptonemal complex (SC).3,4,5,6,7,8,9 The SC consists of a pair of lateral elements bridged by a central region composed of the SYP proteins in C. elegans. How the structural components of the SC are regulated to maintain the architectural integrity of the assembled SC around DSB repair sites remained unclear. Here, we show that SYP-4, a central region component of the SC, is phosphorylated at Serine 447 in a manner dependent on DSBs and the ATM/ATR DNA damage response kinases. We show that this SYP-4 phosphorylation is critical for preserving the SC structure following exogenous (γ-IR-induced) DSB formation and for promoting normal DSB repair progression and crossover patterning following SPO-11-dependent and exogenous DSBs. We propose a model in which ATM/ATR-dependent phosphorylation of SYP-4 at the S447 site plays important roles both in maintaining the architectural integrity of the SC following DSB formation and in warding off repair via the NHEJ repair pathway, thereby preventing aneuploidy.
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Affiliation(s)
- Laura I Láscarez-Lagunas
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Saravanapriah Nadarajan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Marina Martinez-Garcia
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Julianna N Quinn
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Elena Todisco
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Tanuj Thakkar
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Elizaveta Berson
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Don Eaford
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA
| | - Oliver Crawley
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Alex Montoya
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Peter Faull
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Nuria Ferrandiz
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Consuelo Barroso
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Sara Labella
- McGill University, Biology Department, Stewart Biology Building, Room W5/24 1205 Dr. Penfield Avenue, Montreal, QC H3A1B1, Canada
| | - Emily Koury
- Department of Biology, The University of Iowa, Biology Building, Room 308, 129 E. Jefferson, Iowa City, IA 52242-1324, USA
| | - Sarit Smolikove
- Department of Biology, The University of Iowa, Biology Building, Room 308, 129 E. Jefferson, Iowa City, IA 52242-1324, USA
| | - Monique Zetka
- McGill University, Biology Department, Stewart Biology Building, Room W5/24 1205 Dr. Penfield Avenue, Montreal, QC H3A1B1, Canada
| | - Enrique Martinez-Perez
- MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Monica P Colaiácovo
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Room 334, Boston, MA 02115, USA.
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4
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Vu NT, Kim M, Stephenson DJ, MacKnight HP, Chalfant CE. Ceramide Kinase Inhibition Drives Ferroptosis and Sensitivity to Cisplatin in Mutant KRAS Lung Cancer by Dysregulating VDAC-Mediated Mitochondria Function. Mol Cancer Res 2022; 20:1429-1442. [PMID: 35560154 PMCID: PMC9444881 DOI: 10.1158/1541-7786.mcr-22-0085] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/15/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
Abstract
Ceramide kinase (CERK) is the mammalian lipid kinase from which the bioactive sphingolipid, ceramide-1-phosphate (C1P), is derived. CERK has been implicated in several promalignant phenotypes with little known as to mechanistic underpinnings. In this study, the mechanism of how CERK inhibition decreases cell survival in mutant (Mut) KRAS non-small cell lung cancer (NSCLC), a major lung cancer subtype, was revealed. Specifically, NSCLC cells possessing a KRAS mutation were more responsive to inhibition, downregulation, and genetic ablation of CERK compared with those with wild-type (WT) KRAS regarding a reduction in cell survival. Inhibition of CERK induced ferroptosis in Mut KRAS NSCLC cells, which required elevating VDAC-regulated mitochondria membrane potential (MMP) and the generation of cellular reactive oxygen species (ROS). Importantly, through modulation of VDAC, CERK inhibition synergized with the first-line NSCLC treatment, cisplatin, in reducing cell survival and in vivo tumor growth. Further mechanistic studies indicated that CERK inhibition affected MMP and cell survival by limiting AKT activation and translocation to mitochondria, and thus, blocking VDAC phosphorylation and tubulin recruitment. IMPLICATIONS Our findings depict how CERK inhibition may serve as a new key point in combination therapeutic strategy for NSCLC, specifically precision therapeutics targeting NSCLC possessing a KRAS mutation.
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Affiliation(s)
- Ngoc T. Vu
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA,Institute of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, Vietnam
| | - Minjung Kim
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Daniel J. Stephenson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA,Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA, 22903
| | - H. Patrick MacKnight
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA,Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA, 22903
| | - Charles E. Chalfant
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA,Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA, 22903,Department of Cell Biology, University of Virginia, Charlottesville, VA, 22903,Program in Cancer Biology, University of Virginia Cancer Center, Charlottesville, VA, 22903,Research Service, Richmond Veterans Administration Medical Center, Richmond VA, 23298,To whom correspondence should be addressed: Charles E. Chalfant, Professor, Department of Medicine, Division of Hematology & Oncology, P.O. Box 801398, University of Virginia, Charlottesville, VA, 22903, or
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5
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Chen J, Yang S, Li P, Wu A, Nepovimova E, Long M, Wu W, Kuca K. MicroRNA regulates the toxicological mechanism of four mycotoxins in vivo and in vitro. J Anim Sci Biotechnol 2022; 13:37. [PMID: 35197116 PMCID: PMC8867758 DOI: 10.1186/s40104-021-00653-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/21/2021] [Indexed: 11/30/2022] Open
Abstract
Mycotoxins can cause body poisoning and induce carcinogenesis, often with a high mortality rate. Therefore, it is of great significance to seek new targets that indicate mycotoxin activity and to diagnose and intervene in mycotoxin-induced diseases in their early stages. MicroRNAs (miRNAs) are physiological regulators whose dysregulation is closely related to the development of diseases. They are thus important markers for the occurrence and development of diseases. In this review, consideration is given to the toxicological mechanisms associated with four major mycotoxins (ochratoxin A, aflatoxin B1, deoxynivalenol, and zearalenone). The roles that miRNAs play in these mechanisms and the interactions between them and their target genes are explained, and summarize the important role of histone modifications in their toxicity. As a result, the ways that miRNAs are regulated in the pathogenicity signaling pathways are revealed which highlights the roles played by miRNAs in preventing and controlling the harmful effects of the mycotoxins. It is hoped that this review will provide a theoretical basis for the prevention and control of the damage caused by these mycotoxins.
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Affiliation(s)
- Jia Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shuhua Yang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Peng Li
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Aibo Wu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 50003, Czech Republic
| | - Miao Long
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Wenda Wu
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 50003, Czech Republic. .,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 50003, Czech Republic. .,Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, 50003, Czech Republic.
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6
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Baskaran Y, Tay FPL, Ng EYW, Swa CLF, Wee S, Gunaratne J, Manser E. Proximity proteomics identifies PAK4 as a component of Afadin-Nectin junctions. Nat Commun 2021; 12:5315. [PMID: 34493720 PMCID: PMC8423818 DOI: 10.1038/s41467-021-25011-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Human PAK4 is an ubiquitously expressed p21-activated kinase which acts downstream of Cdc42. Since PAK4 is enriched in cell-cell junctions, we probed the local protein environment around the kinase with a view to understanding its location and substrates. We report that U2OS cells expressing PAK4-BirA-GFP identify a subset of 27 PAK4-proximal proteins that are primarily cell-cell junction components. Afadin/AF6 showed the highest relative biotin labelling and links to the nectin family of homophilic junctional proteins. Reciprocally >50% of the PAK4-proximal proteins were identified by Afadin BioID. Co-precipitation experiments failed to identify junctional proteins, emphasizing the advantage of the BioID method. Mechanistically PAK4 depended on Afadin for its junctional localization, which is similar to the situation in Drosophila. A highly ranked PAK4-proximal protein LZTS2 was immuno-localized with Afadin at cell-cell junctions. Though PAK4 and Cdc42 are junctional, BioID analysis did not yield conventional cadherins, indicating their spatial segregation. To identify cellular PAK4 substrates we then assessed rapid changes (12') in phospho-proteome after treatment with two PAK inhibitors. Among the PAK4-proximal junctional proteins seventeen PAK4 sites were identified. We anticipate mammalian group II PAKs are selective for the Afadin/nectin sub-compartment, with a demonstrably distinct localization from tight and cadherin junctions.
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Affiliation(s)
- Yohendran Baskaran
- sGSK Group, Institute of Molecular & Cell Biology, A*STAR, Singapore, Singapore
| | - Felicia Pei-Ling Tay
- FB Laboratory, Institute of Molecular & Cell Biology, A*STAR, Singapore, Singapore
| | - Elsa Yuen Wai Ng
- sGSK Group, Institute of Molecular & Cell Biology, A*STAR, Singapore, Singapore
| | - Claire Lee Foon Swa
- Quantitative Proteomics Group, Institute of Molecular & Cell Biology, Singapore, Singapore
| | - Sheena Wee
- Quantitative Proteomics Group, Institute of Molecular & Cell Biology, Singapore, Singapore
| | - Jayantha Gunaratne
- Quantitative Proteomics Group, Institute of Molecular & Cell Biology, Singapore, Singapore
| | - Edward Manser
- sGSK Group, Institute of Molecular & Cell Biology, A*STAR, Singapore, Singapore.
- Department of Pharmacology, National University of Singapore, Singapore, Singapore.
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7
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Naїja A, Merhi M, Inchakalody V, Fernandes Q, Mestiri S, Prabhu KS, Uddin S, Dermime S. The role of PAK4 in the immune system and its potential implication in cancer immunotherapy. Cell Immunol 2021; 367:104408. [PMID: 34246086 DOI: 10.1016/j.cellimm.2021.104408] [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: 05/23/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 01/06/2023]
Abstract
The p21 activated kinases (PAKs) are known to play a role in the regulation of cell morphology and functions. Among the various members of PAKs family, only the PAK4 protein has been shown to be overexpressed in cancer cells and its upregulation was associated with tumor development. Indeed, several studies have shown that PAK4 overexpression is implicated in carcinogenesis by different mechanisms including promotion of cell proliferation, invasion and migration, protection of cells from apoptosis, stimulation of the tumor-specific anchorage-independent cell growth and regulation of the cytoskeletal organisation and adhesion. Moreover, high PAK4 protein levels have been observed in several solid tumors and have been shown able to enhance cancer cell resistance to many treatments especially chemotherapy. Interestingly, it has been recently demonstrated that PAK4 downregulation can inhibit the PD-1/PD-L1 immune regulatory pathway. Taken together, these findings not only implicate PAK4 in oncogenic transformation and in prediction of tumor response to treatment but also suggest its role as an attractive target for immunotherapy. In the current review we will summarize the different mechanisms of PAK4 implication in tumor development, describe its role as a regulator of the immune response and as a potential novel target for cancer immunotherapy.
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Affiliation(s)
- Azza Naїja
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Inchakalody
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Queenie Fernandes
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; College of Medicine, Qatar University, Doha, Qatar
| | - Sarra Mestiri
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic health system, Hamad medical Corporation, Doha, Qatar
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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8
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Ou J, Liu H, Nirala NK, Stukalov A, Acharya U, Green MR, Zhu LJ. dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data. PLoS One 2020; 15:e0242030. [PMID: 33156866 PMCID: PMC7647101 DOI: 10.1371/journal.pone.0242030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/23/2020] [Indexed: 11/18/2022] Open
Abstract
Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. To fill this gap, we developed an R/Bioconductor package dagLogo, which has several advantages over existing tools. First, dagLogo allows various formats for input sets and provides comprehensive options to build optimal background models. It implements different reduced AA alphabets to group AAs of similar properties. Furthermore, dagLogo provides statistical and visual solutions for differential AA (or AA group) usage analysis of both large and small data sets. Case studies showed that dagLogo can better identify and visualize conserved protein sequence patterns from different types of inputs and can potentially reveal the biological patterns that could be missed by other logo generators.
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Affiliation(s)
- Jianhong Ou
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Regeneration NEXT, Duke University School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Haibo Liu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Niraj K. Nirala
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Alexey Stukalov
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Usha Acharya
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michael R. Green
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lihua Julie Zhu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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9
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Tian Y, Zhang MY, Li N, Wang JJ, Ge W, Tan SJ, Shen W, Li L. Zearalenone exposure triggered porcine granulosa cells apoptosis via microRNAs-mediated focal adhesion pathway. Toxicol Lett 2020; 330:80-89. [PMID: 32439583 DOI: 10.1016/j.toxlet.2020.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 01/08/2023]
Abstract
Zearalenone (ZEA), a metabolite of Fusarium, which is commonly found in moldy feed crops, is a well-known exogenous endocrine disruptor and has serious negative effects on animal reproduction. In order to understand the toxic effects of ZEA exposure on porcine granulosa cells (pGCs), which were exposed to 10 μM and 30 μM ZEA for 48 h in vitro, several methods were used for analysis. Flow cytometry and TUNEL analysis showed that the apoptosis of pGCs significantly increased in a dose-dependent manner after ZEA exposure compared with that of the control group. Whole transcriptome RNA-seq analysis was performed to reveal the mRNAs and miRNAs expression changes of pGCs after ZEA exposure and it was found that the expression of apoptosis-related genes was altered after ZEA exposure, and miRNAs were also significantly different among the experimental groups. In particular, ZEA exposure affected the expression of miRNAs associated with apoptosis-related pathways, such as miR-744, miR-1343 and miR-331-3p, as well as focal adhesion pathways related genes, Pak4 and Elk1, which were also involved in the apoptosis-related pathways. Moreover, the regulation networks between apoptosis-related mRNA and miRNAs were confirmed with the results of RT-qPCR and immunofluorescence. In conclusion, our results here demonstrated that ZEA exposure impaired pGCs growth and apoptosis via miRNAs-mediated focal adhesion pathway.
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Affiliation(s)
- Yu Tian
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ming-Yu Zhang
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Na Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jun-Jie Wang
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wei Ge
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shao-Jing Tan
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wei Shen
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lan Li
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
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10
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Hirst NL, Nebel JC, Lawton SP, Walker AJ. Deep phosphoproteome analysis of Schistosoma mansoni leads development of a kinomic array that highlights sex-biased differences in adult worm protein phosphorylation. PLoS Negl Trop Dis 2020; 14:e0008115. [PMID: 32203512 PMCID: PMC7089424 DOI: 10.1371/journal.pntd.0008115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Although helminth parasites cause enormous suffering worldwide we know little of how protein phosphorylation, one of the most important post-translational modifications used for molecular signalling, regulates their homeostasis and function. This is particularly the case for schistosomes. Herein, we report a deep phosphoproteome exploration of adult Schistosoma mansoni, providing one of the richest phosphoprotein resources for any parasite so far, and employ the data to build the first parasite-specific kinomic array. Complementary phosphopeptide enrichment strategies were used to detect 15,844 unique phosphopeptides mapping to 3,176 proteins. The phosphoproteins were predicted to be involved in a wide range of biological processes and phosphoprotein interactome analysis revealed 55 highly interconnected clusters including those enriched with ribosome, proteasome, phagosome, spliceosome, glycolysis, and signalling proteins. 93 distinct phosphorylation motifs were identified, with 67 providing a ‘footprint’ of protein kinase activity; CaMKII, PKA and CK1/2 were highly represented supporting their central importance to schistosome function. Within the kinome, 808 phosphorylation sites were matched to 136 protein kinases, and 68 sites within 37 activation loops were discovered. Analysis of putative protein kinase-phosphoprotein interactions revealed canonical networks but also novel interactions between signalling partners. Kinomic array analysis of male and female adult worm extracts revealed high phosphorylation of transformation:transcription domain associated protein by both sexes, and CDK and AMPK peptides by females. Moreover, eight peptides including protein phosphatase 2C gamma, Akt, Rho2 GTPase, SmTK4, and the insulin receptor were more highly phosphorylated by female extracts, highlighting their possible importance to female worm function. We envision that these findings, tools and methodology will help drive new research into the functional biology of schistosomes and other helminth parasites, and support efforts to develop new therapeutics for their control. Schistosomes are formidable parasites that cause the debilitating and life-threatening disease human schistosomiasis. We need to better understand the cellular biology of these parasites to develop novel strategies for their control. Within cells, a process called protein phosphorylation controls many aspects of molecular communication or ‘signalling’ and is central to cellular function and homeostasis. Here, using complementary strategies, we have performed the first in-depth characterisation and functional annotation of protein phosphorylation events in schistosomes, providing one of the richest phosphoprotein resources for any parasite to date. Using this knowledge, we have developed a novel tool to simultaneously evaluate signalling processes in these worms and highlight sex-biased differences in adult worm protein phosphorylation. Several proteins were found to be more greatly phosphorylated by female worm extracts, suggesting their possible importance to female worm function. This work will help drive new research into the fundamental biology of schistosomes, as well as related parasites, and will support efforts to develop new drug or vaccine-based therapeutics for their control.
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Affiliation(s)
- Natasha L. Hirst
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Jean-Christophe Nebel
- School of Computer Science and Mathematics, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Scott P. Lawton
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Anthony J. Walker
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
- * E-mail:
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11
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Wang H, Gao Z, Song P, Hu B, Wang J, Cheng M. Molecular dynamics simulation and QM/MM calculation reveal the selectivity mechanism of type I 1/2 kinase inhibitors: the effect of intramolecular H-bonds and conformational restriction for improved selectivity. Phys Chem Chem Phys 2019; 21:24147-24164. [PMID: 31657381 DOI: 10.1039/c9cp04353e] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding the selectivity mechanisms of inhibitors towards highly similar proteins is extremely important work on the way to a new drug. Here, we aim to reveal the selectivity mechanisms of type I 1/2 kinase inhibitors towards p21-activated kinase (PAK4) and mitogen-activated protein kinase kinase kinase 14 (MAP3K14, NIK). PAK4, belonging to the serine/threonine protein kinases, is involved in cell signaling pathways and controls cellular functions and has received attention as an attractive drug target. The high sequence identity between PAK4 and NIK makes it challenging to design selective PAK4 inhibitors. In this work, computational methods including protein comparison, molecular docking, QM/MM, molecular dynamics simulations, and density functional theory (DFT) calculation were employed to explore the binding mechanisms of selective inhibitors against NIK and PAK4. The simulation results revealed the crucial factors accounting for selective inhibition of PAK4 over NIK, including different protein-ligand interactions, the positions and conformations of key residues, and the ligands flexibilities. This study will shed light on understanding the selectivity mechanisms of PAK4 and NIK inhibitors.
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Affiliation(s)
- Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
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12
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Erickson KE, Rukhlenko OS, Posner RG, Hlavacek WS, Kholodenko BN. New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling. Semin Cancer Biol 2019; 54:162-173. [PMID: 29518522 PMCID: PMC6123307 DOI: 10.1016/j.semcancer.2018.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 01/04/2023]
Abstract
RAS is the most frequently mutated gene across human cancers, but developing inhibitors of mutant RAS has proven to be challenging. Given the difficulties of targeting RAS directly, drugs that impact the other components of pathways where mutant RAS operates may potentially be effective. However, the system-level features, including different localizations of RAS isoforms, competition between downstream effectors, and interlocking feedback and feed-forward loops, must be understood to fully grasp the opportunities and limitations of inhibiting specific targets. Mathematical modeling can help us discern the system-level impacts of these features in normal and cancer cells. New technologies enable the acquisition of experimental data that will facilitate development of realistic models of oncogenic RAS behavior. In light of the wealth of empirical data accumulated over decades of study and the advancement of experimental methods for gathering new data, modelers now have the opportunity to advance progress toward realization of targeted treatment for mutant RAS-driven cancers.
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Affiliation(s)
- Keesha E Erickson
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Richard G Posner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - William S Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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13
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Liu Y, Jiao D, Tian Z. MicroRNA‑663 inhibits the proliferation and invasion of clear cell renal cell carcinoma cells by directly targeting PAK4. Mol Med Rep 2018; 19:711-718. [PMID: 30431118 DOI: 10.3892/mmr.2018.9652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/16/2018] [Indexed: 11/06/2022] Open
Abstract
Accumulating evidence has demonstrated that microRNAs (miRNAs) are key gene regulators and are abnormally expressed in clear cell renal cell carcinoma (ccRCC). The dysregulation of miRNAs has been implicated in the initiation and progression of ccRCC. Therefore, identification of ccRCC‑associated miRNAs may facilitate the determination of promising therapeutic targets for anti‑cancer treatment. In the present study, miRNA‑663 (miR‑663) expression was downregulated in ccRCC tissues and cell lines. Functional experiments suggested that restoration of miR‑663 expression inhibited the proliferation and invasion of ccRCC cells. In addition, p21 activated kinase 4 (PAK4) was validated as a direct target of miR‑663 in ccRCC cells. PAK4 was upregulated in ccRCC tissues, and the expression level of PAK4 was inversely correlated with the miR‑663 expression level. PAK4 restoration partially attenuated the suppressive roles of miR‑663 overexpression on the proliferation and invasion of ccRCC cells. The present results provide novel insight into the mechanism underlying the occurrence and development of ccRCC, suggesting that the miR‑663/PAK4 axis may be a novel therapeutic target for treatment of patients with ccRCC.
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Affiliation(s)
- Yingying Liu
- Department of Nephrology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Dan Jiao
- Department of Ultrasound, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhen Tian
- Department of Cardiology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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14
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Govek EE, Wu Z, Acehan D, Molina H, Rivera K, Zhu X, Fang Y, Tessier-Lavigne M, Hatten ME. Cdc42 Regulates Neuronal Polarity during Cerebellar Axon Formation and Glial-Guided Migration. iScience 2018; 1:35-48. [PMID: 29888765 PMCID: PMC5993048 DOI: 10.1016/j.isci.2018.01.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
CNS cortical histogenesis depends on polarity signaling pathways that regulate cell adhesion and motility. Here we report that conditional deletion of the Rho GTPase Cdc42 in cerebellar granule cell precursors (GCPs) results in abnormalities in cerebellar foliation revealed by iDISCO clearing methodology, a loss of columnar organization of proliferating GCPs in the external germinal layer (EGL), disordered parallel fiber organization in the molecular layer (ML), and a failure to extend a leading process and form a neuron-glial junction during migration along Bergmann glia (BG). Notably, GCPs lacking Cdc42 had a multi-polar morphology and slowed migration rate. In addition, secondary defects occurred in BG development and organization, especially in the lateral cerebellar hemispheres. By phosphoproteomic analysis, affected Cdc42 targets included regulators of the cytoskeleton, cell adhesion and polarity. Thus, Cdc42 signaling pathways are critical regulators of GCP polarity and the formation of neuron-glial junctions during cerebellar development. Conditional deletion of Cdc42 in GCPs perturbs cerebellar cortical histogenesis Loss of Cdc42 in GCPs disrupts GCP neuron-glial junctions Cdc42 deficiency causes a loss of GCP polarity and slows their migration Phosphoproteomics reveals changes in cytoskeletal, adhesion, and polarity proteins
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Affiliation(s)
- Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA
| | - Zhuhao Wu
- Laboratory of Brain Development and Repair, The Rockefeller University, New York, NY 10065, USA
| | - Devrim Acehan
- The Rockefeller University Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Henrik Molina
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Keith Rivera
- Mass Spectrometry Shared Resource, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaodong Zhu
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA
| | - Yin Fang
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA
| | - Marc Tessier-Lavigne
- Laboratory of Brain Development and Repair, The Rockefeller University, New York, NY 10065, USA.,Stanford University, Palo Alto, CA 94305-2061, USA
| | - Mary Elizabeth Hatten
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA
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15
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Mao K, Lei D, Zhang H, You C. MicroRNA-485 inhibits malignant biological behaviour of glioblastoma cells by directly targeting PAK4. Int J Oncol 2017; 51:1521-1532. [DOI: 10.3892/ijo.2017.4122] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/04/2017] [Indexed: 11/06/2022] Open
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16
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Zhao M, Spiess M, Johansson HJ, Olofsson H, Hu J, Lehtiö J, Strömblad S. Identification of the PAK4 interactome reveals PAK4 phosphorylation of N-WASP and promotion of Arp2/3-dependent actin polymerization. Oncotarget 2017; 8:77061-77074. [PMID: 29100370 PMCID: PMC5652764 DOI: 10.18632/oncotarget.20352] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022] Open
Abstract
p21-activated kinase 4 (PAK4) regulates cell proliferation, apoptosis, cell motility and F-actin remodeling, but the PAK4 interactome has not been systematically analyzed. Here, we comprehensively characterized the human PAK4 interactome by iTRAQ quantitative mass spectrometry of PAK4-immunoprecipitations. Consistent with its multiple reported functions, the PAK4 interactome was enriched in diverse protein networks, including the 14-3-3, proteasome, replication fork, CCT and Arp2/3 complexes. Because PAK4 co-immunoprecipitated most subunits of the Arp2/3 complex, we hypothesized that PAK4 may play a role in Arp2/3 dependent actin regulation. Indeed, we found that PAK4 interacts with and phosphorylates the nucleation promoting factor N-WASP at Ser484/Ser485 and promotes Arp2/3-dependent actin polymerization in vitro. Also, PAK4 ablation in vivo reduced N-WASP Ser484/Ser485 phosphorylation and altered the cellular balance between G- and F-actin as well as the actin organization. By presenting the PAK4 interactome, we here provide a powerful resource for further investigations and as proof of principle, we also indicate a novel mechanism by which PAK4 regulates actin cytoskeleton remodeling.
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Affiliation(s)
- Miao Zhao
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Spiess
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Henrik J Johansson
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Helene Olofsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Jianjiang Hu
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Janne Lehtiö
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Staffan Strömblad
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
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17
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Lu X, Wang H, Su Z, Cai L, Li W. MicroRNA-342 inhibits the progression of glioma by directly targeting PAK4. Oncol Rep 2017; 38:1240-1250. [PMID: 28677773 DOI: 10.3892/or.2017.5783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/20/2017] [Indexed: 11/06/2022] Open
Abstract
Glioma is an extremely aggressive and lethal type of brain tumour that originates from glial cells. MicroRNA (miRNA) dysregulation has been implicated in the occurrence and progression of many human cancers, including glioma. Thus, some specific miRNAs are potential therapeutic targets for glioma diagnosis, therapy and prognosis. MicroRNA-342 (miR‑342) has been reported to be abnormally expressed in various types of cancer. However, the precise roles of miR‑342 in glioma remain unknown. The present study showed that miR‑342 is relatively downregulated in glioma tissues and cell lines compared with that in adjacent normal tissues and normal human astrocytes. We observed that low miR‑342 expression levels are correlated with advanced WHO grades and low KPS scores of glioma patients. In addition, the results of the functional assays demonstrated that miR‑342 overexpression inhibits the proliferation and invasion of glioma cells and induces apoptosis. Further investigation revealed that P21 activated kinases 4 (PAK4) is a direct target of miR‑342 in glioma. PAK4 was significantly upregulated in glioma tissues and inversely correlated with miR‑342 expression. Moreover, PAK4 knockdown can mimic the effects of miR‑342 on glioma cell proliferation, invasion and apoptosis. Notably, restoration of expression of PAK4 reversed the suppressive effects induced by the miR‑342 in the glioma cells. The upregulation of miR‑342 inactivated the AKT and ERK pathways in glioma. These findings may contribute to the understanding of the molecular mechanism underlying the carcinogenesis and progression of glioma, and to provide novel therapeutic target for the treatment of glioma patients.
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Affiliation(s)
- Xianghe Lu
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Haowen Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhipeng Su
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Lin Cai
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Wenfeng Li
- Department of Radiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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18
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Dogan T, Gnad F, Chan J, Phu L, Young A, Chen MJ, Doll S, Stokes MP, Belvin M, Friedman LS, Kirkpatrick DS, Hoeflich KP, Hatzivassiliou G. Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling pathways to the cell cycle. J Biol Chem 2017; 292:14311-14324. [PMID: 28655764 PMCID: PMC5582827 DOI: 10.1074/jbc.m117.792754] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Indexed: 11/23/2022] Open
Abstract
The interconnected PI3K and MAPK signaling pathways are commonly perturbed in cancer. Dual inhibition of these pathways by the small-molecule PI3K inhibitor pictilisib (GDC-0941) and the MEK inhibitor cobimetinib (GDC-0973) suppresses cell proliferation and induces cell death better than either single agent in several preclinical models. Using mass spectrometry-based phosphoproteomics, we have identified the RING finger E3 ubiquitin ligase RNF157 as a target at the intersection of PI3K and MAPK signaling. We demonstrate that RNF157 phosphorylation downstream of the PI3K and MAPK pathways influences the ubiquitination and stability of RNF157 during the cell cycle in an anaphase-promoting complex/cyclosome–CDH1-dependent manner. Deletion of these phosphorylation-targeted residues on RNF157 disrupts binding to CDH1 and protects RNF157 from ubiquitination and degradation. Expression of the cyclin-dependent kinase 2 (CDK2), itself a downstream target of PI3K/MAPK signaling, leads to increased phosphorylation of RNF157 on the same residues modulated by PI3K and MAPK signaling. Inhibition of PI3K and MEK in combination or of CDK2 by their respective small-molecule inhibitors reduces RNF157 phosphorylation at these residues and attenuates RNF157 interaction with CDH1 and its subsequent degradation. Knockdown of endogenous RNF157 in melanoma cells leads to late S phase and G2/M arrest and induces apoptosis, the latter further potentiated by concurrent PI3K/MEK inhibition, consistent with a role for RNF157 in the cell cycle. We propose that RNF157 serves as a novel node integrating oncogenic signaling pathways with the cell cycle machinery and promoting optimal cell cycle progression in transformed cells.
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Affiliation(s)
- Taner Dogan
- From the Departments of Translational Oncology
| | | | | | - Lilian Phu
- Microchemistry Proteomics and Lipidomics, and
| | - Amy Young
- From the Departments of Translational Oncology
| | | | - Sophia Doll
- Microchemistry Proteomics and Lipidomics, and
| | | | - Marcia Belvin
- From the Departments of Translational Oncology.,Cancer Immunology, Genentech, Inc., South San Francisco, California 94080 and
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19
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Hao C, Huang W, Li X, Guo J, Chen M, Yan Z, Wang K, Jiang X, Song S, Wang J, Zhao D, Li F, Cheng M. Development of 2, 4-diaminoquinazoline derivatives as potent PAK4 inhibitors by the core refinement strategy. Eur J Med Chem 2017; 131:1-13. [DOI: 10.1016/j.ejmech.2017.02.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 11/25/2022]
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20
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Guo X, Huang X, Chen MJ. Reversible phosphorylation of the 26S proteasome. Protein Cell 2017; 8:255-272. [PMID: 28258412 PMCID: PMC5359188 DOI: 10.1007/s13238-017-0382-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/26/2017] [Indexed: 01/09/2023] Open
Abstract
The 26S proteasome at the center of the ubiquitin-proteasome system (UPS) is essential for virtually all cellular processes of eukaryotes. A common misconception about the proteasome is that, once made, it remains as a static and uniform complex with spontaneous and constitutive activity for protein degradation. Recent discoveries have provided compelling evidence to support the exact opposite insomuch as the 26S proteasome undergoes dynamic and reversible phosphorylation under a variety of physiopathological conditions. In this review, we summarize the history and current understanding of proteasome phosphorylation, and advocate the idea of targeting proteasome kinases/phosphatases as a new strategy for clinical interventions of several human diseases.
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Affiliation(s)
- Xing Guo
- The Life Sciences Institute of Zhejiang University, Hangzhou, 310058, China.
| | - Xiuliang Huang
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mark J Chen
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, 94080, USA
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21
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King H, Thillai K, Whale A, Arumugam P, Eldaly H, Kocher HM, Wells CM. PAK4 interacts with p85 alpha: implications for pancreatic cancer cell migration. Sci Rep 2017; 7:42575. [PMID: 28205613 PMCID: PMC5312077 DOI: 10.1038/srep42575] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 01/12/2017] [Indexed: 01/23/2023] Open
Abstract
It has been reported that p21-activated kinase 4 (PAK4) is amplified in pancreatic cancer tissue. PAK4 is a member of the PAK family of serine/threonine kinases, which act as effectors for several small GTPases, and has been specifically identified to function downstream of HGF-mediated c-Met activation in a PI3K dependent manner. However, the functionality of PAK4 in pancreatic cancer and the contribution made by HGF signalling to pancreatic cancer cell motility remain to be elucidated. We now find that elevated PAK4 expression is coincident with increased expression levels of c-Met and the p85α subunit of PI3K. Furthermore, we demonstrate that pancreatic cancer cells have a specific motility response to HGF both in 2D and 3D physiomimetic organotypic assays; which can be suppressed by inhibition of PI3K. Significantly, we report a specific interaction between PAK4 and p85α and find that PAK4 deficient cells exhibit a reduction in Akt phosphorylation downstream of HGF signalling. These results implicate a novel role for PAK4 within the PI3K pathway via interaction with p85α. Thus, PAK4 could be an essential player in PDAC progression representing an interesting therapeutic opportunity.
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Affiliation(s)
- Helen King
- Division of Cancer Studies, King's College London, UK
| | | | - Andrew Whale
- Division of Cancer Studies, King's College London, UK
| | - Prabhu Arumugam
- Barts Cancer Institute, a CRUK centre of Excellance, Queen Mary University of London, UK
| | - Hesham Eldaly
- Dept of Haematopathology Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge, UK
| | - Hemant M Kocher
- Barts Cancer Institute, a CRUK centre of Excellance, Queen Mary University of London, UK
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22
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Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M. Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network. Proteomics 2016; 16:1992-7. [DOI: 10.1002/pmic.201600118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/08/2016] [Accepted: 06/07/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Florian Gnad
- Department of Bioinformatics and Computational Biology; Genentech Inc; South San Francisco CA USA
| | - Jeffrey Wallin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Kyle Edgar
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Sophia Doll
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - David Arnott
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - Liliane Robillard
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | | | - Ulka Vijapurkar
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | - Lori S. Friedman
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Marcia Belvin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
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23
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Study on the expression of PAK4 and P54 protein in breast cancer. World J Surg Oncol 2016; 14:160. [PMID: 27297086 PMCID: PMC4906770 DOI: 10.1186/s12957-016-0913-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/09/2016] [Indexed: 01/28/2023] Open
Abstract
Background Previous evidence have demonstrated that p21-activated kinase PAK4 was correlated with breast cancer. The aim of this paper is to study the expression and interaction of p21-activated kinase (pAK)-4 and P54 protein in breast cancer. Methods A total of 80 patients were enrolled in our study (breast fibroma n = 20, breast noninvasive cancer n = 20, early breast invasive cancer n = 20, and advanced breast invasive cancer). The expression of PAK4 was detected by immunohistochemical S-P method, and the relationship between them and the different pathological characteristics were compared. The subcellular localization of P54 and PAK4 in vitro was observed by immunofluorescence assay. Results The expression of both PAK4 and P54 in breast cancer was much higher than that in breast fibroma. Meanwhile, we found that both PAK4 and P54 increased gradually as breast cancer progressed (advanced invasive > early invasive > noninvasive). The positive staining of P54 were mainly located in the cytoplasm, especially around the nucleus. There was no significant stained region in the cell matrix. The P54 localization in the cytoplasm was verified by confocal experiment, and the PAK4 was co-localized. Conclusions PAK4 and P54 proteins may be used as molecular markers for diagnosis and treatment of breast cancer.
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24
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Gu H, Ren JM, Jia X, Levy T, Rikova K, Yang V, Lee KA, Stokes MP, Silva JC. Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion. Mol Cell Proteomics 2015; 15:692-702. [PMID: 26635363 DOI: 10.1074/mcp.o115.052266] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 12/24/2022] Open
Abstract
A robust method was developed and optimized for enrichment and quantitative analysis of posttranslational modifications (PTMs) in serum/plasma samples by combining immunoaffinity purification and LC-MS/MS without depletion of abundant proteins. The method was used to survey serum samples of patients with acute myeloid leukemia (AML), breast cancer (BC), and nonsmall cell lung cancer (NSCLC). Peptides were identified from serum samples containing phosphorylation, acetylation, lysine methylation, and arginine methylation. Of the PTMs identified, lysine acetylation (AcK) and arginine mono-methylation (Rme) were more prevalent than other PTMs. Label-free quantitative analysis of AcK and Rme peptides was performed for sera from AML, BC, and NSCLC patients. Several AcK and Rme sites showed distinct abundance distribution patterns across the three cancer types. The identification and quantification of posttranslationally modified peptides in serum samples reported here can be used for patient profiling and biomarker discovery research.
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Affiliation(s)
- Hongbo Gu
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Jian Min Ren
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Xiaoying Jia
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Tyler Levy
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Klarisa Rikova
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Vicky Yang
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Kimberly A Lee
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Matthew P Stokes
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Jeffrey C Silva
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
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25
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Vlasschaert C, Xia X, Coulombe J, Gray DA. Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11. BMC Evol Biol 2015; 15:230. [PMID: 26503449 PMCID: PMC4624187 DOI: 10.1186/s12862-015-0511-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/17/2015] [Indexed: 12/19/2022] Open
Abstract
Background USP4, USP15 and USP11 are paralogous deubiquitinating enzymes as evidenced by structural organization and sequence similarity. Based on known interactions and substrates it would appear that they have partially redundant roles in pathways vital to cell proliferation, development and innate immunity, and elevated expression of all three has been reported in various human malignancies. The nature and order of duplication events that gave rise to these extant genes has not been determined, nor has their functional redundancy been established experimentally at the organismal level. Methods We have employed phylogenetic and syntenic reconstruction methods to determine the chronology of the duplication events that generated the three paralogs and have performed genetic crosses to evaluate redundancy in mice. Results Our analyses indicate that USP4 and USP15 arose from whole genome duplication prior to the emergence of jawed vertebrates. Despite having lower sequence identity USP11 was generated later in vertebrate evolution by small-scale duplication of the USP4-encoding region. While USP11 was subsequently lost in many vertebrate species, all available genomes retain a functional copy of either USP4 or USP15, and through genetic crosses of mice with inactivating mutations we have confirmed that viability is contingent on a functional copy of USP4 or USP15. Loss of ubiquitin-exchange regulation, constitutive skipping of the seventh exon and neural-specific expression patterns are derived states of USP11. Post-translational modification sites differ between USP4, USP15 and USP11 throughout evolution. Conclusions In isolation sequence alignments can generate erroneous USP gene phylogenies. Through a combination of methodologies the gene duplication events that gave rise to USP4, USP15, and USP11 have been established. Although it operates in the same molecular pathways as the other USPs, the rapid divergence of the more recently generated USP11 enzyme precludes its functional interchangeability with USP4 and USP15. Given their multiplicity of substrates the emergence (and in some cases subsequent loss) of these USP paralogs would be expected to alter the dynamics of the networks in which they are embedded. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0511-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caitlyn Vlasschaert
- Department of Biology, University of Ottawa, Ottawa, Canada. .,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada. .,The Ottawa Hospital Research Institute, Ottawa, Canada.
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, Canada. .,Ottawa Institute of Systems Biology, Ottawa, Canada.
| | | | - Douglas A Gray
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada. .,The Ottawa Hospital Research Institute, Ottawa, Canada. .,Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.
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26
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A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling. Proc Natl Acad Sci U S A 2015; 112:E5679-88. [PMID: 26438848 DOI: 10.1073/pnas.1517932112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) govern cellular homeostasis by inducing signaling. H2O2 modulates the activity of phosphatases and many other signaling molecules through oxidation of critical cysteine residues, which led to the notion that initiation of ROS signaling is broad and nonspecific, and thus fundamentally distinct from other signaling pathways. Here, we report that H2O2 signaling bears hallmarks of a regular signal transduction cascade. It is controlled by hierarchical signaling events resulting in a focused response as the results place the mitochondrial respiratory chain upstream of tyrosine-protein kinase Lyn, Lyn upstream of tyrosine-protein kinase SYK (Syk), and Syk upstream of numerous targets involved in signaling, transcription, translation, metabolism, and cell cycle regulation. The active mediators of H2O2 signaling colocalize as H2O2 induces mitochondria-associated Lyn and Syk phosphorylation, and a pool of Lyn and Syk reside in the mitochondrial intermembrane space. Finally, the same intermediaries control the signaling response in tissues and species responsive to H2O2 as the respiratory chain, Lyn, and Syk were similarly required for H2O2 signaling in mouse B cells, fibroblasts, and chicken DT40 B cells. Consistent with a broad role, the Syk pathway is coexpressed across tissues, is of early metazoan origin, and displays evidence of evolutionary constraint in the human. These results suggest that H2O2 signaling is under control of a signal transduction pathway that links the respiratory chain to the mitochondrial intermembrane space-localized, ubiquitous, and ancient Syk pathway in hematopoietic and nonhematopoietic cells.
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27
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Kauko O, Laajala TD, Jumppanen M, Hintsanen P, Suni V, Haapaniemi P, Corthals G, Aittokallio T, Westermarck J, Imanishi SY. Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling. Sci Rep 2015; 5:13099. [PMID: 26278961 PMCID: PMC4642524 DOI: 10.1038/srep13099] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/06/2015] [Indexed: 11/11/2022] Open
Abstract
Hyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set, and synergistic relationship between CIP2A and KRAS depletion in colony growth assays.
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Affiliation(s)
- Otto Kauko
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Department of Pathology, University of Turku, FI-20520 Turku, Finland [3] Turku Doctoral Program of Biomedical Sciences (TuBS), Turku, Finland
| | - Teemu Daniel Laajala
- 1] Department of Mathematics and Statistics, University of Turku, FI-20014 Turku, Finland [2] Drug Research Doctoral Programme (DRDP), Turku, Finland
| | - Mikael Jumppanen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
| | - Petteri Hintsanen
- Institute for Molecular Medicine Finland, Tukholmankatu 8, FI-00290 Helsinki, Finland
| | - Veronika Suni
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Turku Centre for Computer Science, FI-20520 Turku, Finland
| | - Pekka Haapaniemi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
| | - Garry Corthals
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Tukholmankatu 8, FI-00290 Helsinki, Finland
| | - Jukka Westermarck
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Department of Pathology, University of Turku, FI-20520 Turku, Finland
| | - Susumu Y Imanishi
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
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28
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Complementary PTM Profiling of Drug Response in Human Gastric Carcinoma by Immunoaffinity and IMAC Methods with Total Proteome Analysis. Proteomes 2015; 3:160-183. [PMID: 28248267 PMCID: PMC5217380 DOI: 10.3390/proteomes3030160] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 01/14/2023] Open
Abstract
Gaining insight into normal cellular signaling and disease biology is a critical goal of proteomic analyses. The ability to perform these studies successfully to extract the maximum value and discovery of biologically relevant candidate biomarkers is therefore of primary importance. Many successful studies in the past have focused on total proteome analysis (changes at the protein level) combined with phosphorylation analysis by metal affinity enrichment (changes at the PTM level). Here, we use the gastric carcinoma cell line MKN-45 treated with the c-Met inhibitor SU11274 and PKC inhibitor staurosporine to investigate the most efficient and most comprehensive strategies for both total protein and PTM analysis. Under the conditions used, total protein analysis yielded few changes in response to either compound, while analysis of phosphorylation identified thousands of sites that changed differentially between the two treatments. Both metal affinity and antibody-based enrichments were used to assess phosphopeptide changes, and the data generated by the two methods was largely complementary (non-overlapping). Label-free quantitation of peptide peak abundances was used to accurately determine fold-changes between control and treated samples. Protein interaction network analysis allowed the data to be placed in a biologically relevant context, and follow-up validation of selected findings confirmed the accuracy of the proteomic data. Together, this study provides a framework for start-to-finish proteomic analysis of any experimental system under investigation to maximize the value of the proteomic study and yield the best chance for uncovering actionable target candidates.
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29
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Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng ACY, Doench JG, Root DE, Clish CB, Xavier RJ. Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst. Nat Commun 2015; 6:7838. [PMID: 26194095 PMCID: PMC4518307 DOI: 10.1038/ncomms8838] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/17/2015] [Indexed: 01/06/2023] Open
Abstract
The phagocyte oxidative burst, mediated by Nox2 NADPH oxidase-derived reactive oxygen species, confers host defense against a broad spectrum of bacterial and fungal pathogens. Loss-of-function mutations that impair function of the Nox2 complex result in a life-threatening immunodeficiency, and genetic variants of Nox2 subunits have been implicated in pathogenesis of inflammatory bowel disease (IBD). Thus, alterations in the oxidative burst can profoundly impact host defense, yet little is known about regulatory mechanisms that fine-tune this response. Here we report the discovery of regulatory nodes controlling oxidative burst by functional screening of genes within loci linked to human inflammatory disease. Implementing a multi-omics approach, we define transcriptional, metabolic and ubiquitin-cycling nodes controlled by Rbpj, Pfkl and Rnf145, respectively. Furthermore, we implicate Rnf145 in proteostasis of the Nox2 complex by endoplasmic reticulum-associated degradation. Consequently, ablation of Rnf145 in murine macrophages enhances bacterial clearance, and rescues the oxidative burst defects associated with Ncf4 haploinsufficiency.
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Affiliation(s)
- Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Christine E Becker
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Aivi Doan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Gautam Goel
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Eduardo J Villablanca
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Amanda Mok
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Aylwin C Y Ng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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30
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Ong CC, Gierke S, Pitt C, Sagolla M, Cheng CK, Zhou W, Jubb AM, Strickland L, Schmidt M, Duron SG, Campbell DA, Zheng W, Dehdashti S, Shen M, Yang N, Behnke ML, Huang W, McKew JC, Chernoff J, Forrest WF, Haverty PM, Chin SF, Rakha EA, Green AR, Ellis IO, Caldas C, O'Brien T, Friedman LS, Koeppen H, Rudolph J, Hoeflich KP. Small molecule inhibition of group I p21-activated kinases in breast cancer induces apoptosis and potentiates the activity of microtubule stabilizing agents. Breast Cancer Res 2015; 17:59. [PMID: 25902869 PMCID: PMC4445529 DOI: 10.1186/s13058-015-0564-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 03/16/2015] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Breast cancer, the most common cause of cancer-related deaths worldwide among women, is a molecularly and clinically heterogeneous disease. Extensive genetic and epigenetic profiling of breast tumors has recently revealed novel putative driver genes, including p21-activated kinase (PAK)1. PAK1 is a serine/threonine kinase downstream of small GTP-binding proteins, Rac1 and Cdc42, and is an integral component of growth factor signaling networks and cellular functions fundamental to tumorigenesis. METHODS PAK1 dysregulation (copy number gain, mRNA and protein expression) was evaluated in two cohorts of breast cancer tissues (n=980 and 1,108). A novel small molecule inhibitor, FRAX1036, and RNA interference were used to examine PAK1 loss of function and combination with docetaxel in vitro. Mechanism of action for the therapeutic combination, both cellular and molecular, was assessed via time-lapse microscopy and immunoblotting. RESULTS We demonstrate that focal genomic amplification and overexpression of PAK1 are associated with poor clinical outcome in the luminal subtype of breast cancer (P=1.29×10(-4) and P=0.015, respectively). Given the role for PAK1 in regulating cytoskeletal organization, we hypothesized that combination of PAK1 inhibition with taxane treatment could be combined to further interfere with microtubule dynamics and cell survival. Consistent with this, administration of docetaxel with either a novel small molecule inhibitor of group I PAKs, FRAX1036, or PAK1 small interfering RNA oligonucleotides dramatically altered signaling to cytoskeletal-associated proteins, such as stathmin, and induced microtubule disorganization and cellular apoptosis. Live-cell imaging revealed that the duration of mitotic arrest mediated by docetaxel was significantly reduced in the presence of FRAX1036, and this was associated with increased kinetics of apoptosis. CONCLUSIONS Taken together, these findings further support PAK1 as a potential target in breast cancer and suggest combination with taxanes as a viable strategy to increase anti-tumor efficacy.
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Affiliation(s)
- Christy C Ong
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, USA.
| | - Sarah Gierke
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA.
| | - Cameron Pitt
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, USA.
- New address: University of California, San Francisco, CA, USA.
| | - Meredith Sagolla
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA.
| | - Christine K Cheng
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, USA.
| | - Wei Zhou
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, USA.
| | - Adrian M Jubb
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA.
| | - Laura Strickland
- Department of Diagnostics, Genentech, Inc., South San Francisco, CA, USA.
| | - Maike Schmidt
- Department of Diagnostics, Genentech, Inc., South San Francisco, CA, USA.
| | - Sergio G Duron
- Afraxis, La Jolla, CA, USA.
- New address: COI Pharmaceuticals, La Jolla, CA, USA.
| | - David A Campbell
- Afraxis, La Jolla, CA, USA.
- New address: COI Pharmaceuticals, La Jolla, CA, USA.
| | - Wei Zheng
- National Center for Advancing Translational Sciences, Bethesda, MD, USA.
| | - Seameen Dehdashti
- National Center for Advancing Translational Sciences, Bethesda, MD, USA.
- New address: Food and Drug Administration, Silver Spring, MD, USA.
| | - Min Shen
- National Center for Advancing Translational Sciences, Bethesda, MD, USA.
| | - Nora Yang
- National Center for Advancing Translational Sciences, Bethesda, MD, USA.
| | - Mark L Behnke
- National Center for Advancing Translational Sciences, Bethesda, MD, USA.
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, Bethesda, MD, USA.
| | - John C McKew
- National Center for Advancing Translational Sciences, Bethesda, MD, USA.
- New address: aTyr Pharma, San Diego, CA, USA.
| | | | - William F Forrest
- Department of Biostatistics, Genentech, Inc., South San Francisco, CA, USA.
| | - Peter M Haverty
- Department of Bioinformatics, Genentech, Inc., South San Francisco, CA, USA.
| | | | - Emad A Rakha
- Histopathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals, Nottingham, UK.
| | - Andrew R Green
- Histopathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals, Nottingham, UK.
| | - Ian O Ellis
- Histopathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospitals, Nottingham, UK.
| | - Carlos Caldas
- Cancer Research UK, University of Cambridge, Cambridge, UK.
| | - Thomas O'Brien
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, USA.
| | - Lori S Friedman
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, USA.
| | - Hartmut Koeppen
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA.
| | - Joachim Rudolph
- Discovery Chemistry, Genentech, Inc., South San Francisco, CA, USA.
| | - Klaus P Hoeflich
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, USA.
- New address: Blueprint Medicines, Cambridge, MA, UK.
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31
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Bouchut A, Chawla AR, Jeffers V, Hudmon A, Sullivan WJ. Proteome-wide lysine acetylation in cortical astrocytes and alterations that occur during infection with brain parasite Toxoplasma gondii. PLoS One 2015; 10:e0117966. [PMID: 25786129 PMCID: PMC4364782 DOI: 10.1371/journal.pone.0117966] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/20/2014] [Indexed: 01/22/2023] Open
Abstract
Lysine acetylation is a reversible post-translational modification (PTM) that has been detected on thousands of proteins in nearly all cellular compartments. The role of this widespread PTM has yet to be fully elucidated, but can impact protein localization, interactions, activity, and stability. Here we present the first proteome-wide survey of lysine acetylation in cortical astrocytes, a subtype of glia that is a component of the blood-brain barrier and a key regulator of neuronal function and plasticity. We identified 529 lysine acetylation sites across 304 proteins found in multiple cellular compartments that largely function in RNA processing/transcription, metabolism, chromatin biology, and translation. Two hundred and seventy-seven of the acetylated lysines we identified on 186 proteins have not been reported previously in any other cell type. We also mapped an acetylome of astrocytes infected with the brain parasite, Toxoplasma gondii. It has been shown that infection with T. gondii modulates host cell gene expression, including several lysine acetyltransferase (KAT) and deacetylase (KDAC) genes, suggesting that the host acetylome may also be altered during infection. In the T. gondii-infected astrocytes, we identified 34 proteins exhibiting a level of acetylation >2-fold and 24 with a level of acetylation <2-fold relative to uninfected astrocytes. Our study documents the first acetylome map for cortical astrocytes, uncovers novel lysine acetylation sites, and demonstrates that T. gondii infection produces an altered acetylome.
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Affiliation(s)
- Anne Bouchut
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Aarti R. Chawla
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Victoria Jeffers
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - Andy Hudmon
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
| | - William J. Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, United States of America
- * E-mail:
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32
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Silva-Sanchez C, Li H, Chen S. Recent advances and challenges in plant phosphoproteomics. Proteomics 2015; 15:1127-41. [PMID: 25429768 DOI: 10.1002/pmic.201400410] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/29/2014] [Accepted: 11/24/2014] [Indexed: 12/13/2022]
Abstract
Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.
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Affiliation(s)
- Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
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33
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Gu H, Stokes MP, Silva JC. Proteomic Analysis of Posttranslational Modifications in Neurobiology. ANALYSIS OF POST-TRANSLATIONAL MODIFICATIONS AND PROTEOLYSIS IN NEUROSCIENCE 2015. [DOI: 10.1007/7657_2015_99] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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34
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Rudolph J, Crawford JJ, Hoeflich KP, Wang W. Inhibitors of p21-activated kinases (PAKs). J Med Chem 2014; 58:111-29. [PMID: 25415869 DOI: 10.1021/jm501613q] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The p21-activated kinase (PAK) family of serine/threonine protein kinases plays important roles in cytoskeletal organization, cellular morphogenesis, and survival, and members of this family have been implicated in many diseases including cancer, infectious diseases, and neurological disorders. Owing to their large and flexible ATP binding cleft, PAKs, particularly group I PAKs (PAK1, -2, and -3), are difficult to drug; hence, few PAK inhibitors with satisfactory kinase selectivity and druglike properties have been reported to date. Examples are a recently discovered group II PAK (PAK4, -5, -6) selective inhibitor series based on a benzimidazole core, a group I PAK selective series based on a pyrido[2,3-d]pyrimidine-7-one core, and an allosteric dibenzodiazepine PAK1 inhibitor series. Only one compound, an aminopyrazole based pan-PAK inhibitor, entered clinical trials but did not progress beyond phase I trials. Clinical proof of concept for pan-group I, pan-group II, or PAK isoform selective inhibition has yet to be demonstrated.
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Affiliation(s)
- Joachim Rudolph
- Discovery Chemistry, and ‡Structural Biology, Genentech , 1 DNA Way, South San Francisco, California 94080, United States
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35
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Gerarduzzi C, He Q, Antoniou J, Di Battista JA. Quantitative phosphoproteomic analysis of signaling downstream of the prostaglandin e2/g-protein coupled receptor in human synovial fibroblasts: potential antifibrotic networks. J Proteome Res 2014; 13:5262-80. [PMID: 25223752 DOI: 10.1021/pr500495s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Prostaglandin E2 (PGE2) signaling mechanism within fibroblasts is of growing interest as it has been shown to prevent numerous fibrotic features of fibroblast activation with limited evidence of downstream pathways. To understand the mechanisms of fibroblasts producing tremendous amounts of PGE2 with autocrine effects, we apply a strategy of combining a wide-screening of PGE2-induced kinases with quantitative phosphoproteomics. Our large-scale proteomic approach identified a PKA signal transmitted through phosphorylation of its substrates harboring the R(R/X)X(S*/T*) motif. We documented 115 substrates, of which 72 had 89 sites with a 2.5-fold phosphorylation difference in PGE2-treated cells than in untreated cells, where approximately half of such sites were defined as being novel. They were compiled by networking software to focus on highlighted activities and to associate them with a functional readout of fibroblasts. The substrates were associated with a variety of cellular functions including cytoskeletal structures (migration/motility), regulators of G-protein coupled receptor function, protein kinases, and transcriptional/translational regulators. For the first time, we extended the PGE2 pathway into an elaborate network of interconnecting phosphoproteins, providing vital information to a once restricted signalosome. These data provide new insights into eicosanoid-initiated cell signaling with regards to the regulation of fibroblast activation and the identification of new targets for evidenced-based pharmacotherapy against fibrosis.
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Affiliation(s)
- Casimiro Gerarduzzi
- Department of Experimental Medicine, McGill University , 687 Pine Avenue West, Montreal, Quebec H3A 1A1, Canada
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Abstract
Constitutive activity of kinases is known to be crucial for a tumor to maintain its malignant phenotype, a phenomenon which is often referred to as oncogene addiction. The in-depth analysis of aberrant signaling pathways by the analysis of protein phosphorylation has become feasible through recent advances in proteomics technology. In this article we will review developments in the field of phosphoproteomics and its application in cancer research. The most widely used technologies for the generic enrichment of phosphopeptides are discussed as well as targeted approaches for the analysis of a specific subset of phosphopeptides. Validation experiments of phosphorylation sites using targeted mass spectrometry are also explained. Finally, we will highlight applications of phosphoproteomic technology in cancer research using cell lines and tissue.
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Affiliation(s)
- Benjamin Ruprecht
- Technische Universität München, Freising, Germany and Center for Integrated Protein Science Munich, Munich, Germany
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Staben ST, Feng JA, Lyle K, Belvin M, Boggs J, Burch JD, Chua CC, Cui H, DiPasquale AG, Friedman LS, Heise C, Koeppen H, Kotey A, Mintzer R, Oh A, Roberts DA, Rouge L, Rudolph J, Tam C, Wang W, Xiao Y, Young A, Zhang Y, Hoeflich KP. Back Pocket Flexibility Provides Group II p21-Activated Kinase (PAK) Selectivity for Type I 1/2 Kinase Inhibitors. J Med Chem 2014; 57:1033-45. [DOI: 10.1021/jm401768t] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | | | | | - Ching-ching Chua
- Medicinal
Chemistry, Evotec, Abingdon, Oxfordshire OX144SA, United Kingdom
| | - Haifeng Cui
- Pharmaron-Beijing, 6 Taihe Road, Beijing 100176, People’s Republic of China
| | - Antonio G. DiPasquale
- X-ray
Crystallography Facility, University of California, Berkeley, California 94720, United States
| | | | | | | | - Adrian Kotey
- Medicinal
Chemistry, Evotec, Abingdon, Oxfordshire OX144SA, United Kingdom
| | | | | | | | | | | | | | | | - Yisong Xiao
- Wuxi AppTec, 288 Fute Zhong
Road, Shanghai 200131, People’s Republic of China
| | | | - Yamin Zhang
- Pharmaron-Beijing, 6 Taihe Road, Beijing 100176, People’s Republic of China
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Mielcarek M, Seredenina T, Stokes MP, Osborne GF, Landles C, Inuabasi L, Franklin SA, Silva JC, Luthi-Carter R, Beaumont V, Bates GP. HDAC4 does not act as a protein deacetylase in the postnatal murine brain in vivo. PLoS One 2013; 8:e80849. [PMID: 24278330 PMCID: PMC3838388 DOI: 10.1371/journal.pone.0080849] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/09/2013] [Indexed: 11/24/2022] Open
Abstract
Reversible protein acetylation provides a central mechanism for controlling gene expression and cellular signaling events. It is governed by the antagonistic commitment of two enzymes families: the histone acetyltransferases (HATs) and the histone deacetylases (HDACs). HDAC4, like its class IIa counterparts, is a potent transcriptional repressor through interactions with tissue specific transcription factors via its N-terminal domain. Whilst the lysine deacetylase activity of the class IIa HDACs is much less potent than that of the class I enzymes, HDAC4 has been reported to influence protein deacetylation through its interaction with HDAC3. To investigate the influence of HDAC4 on protein acetylation we employed the immunoaffinity-based AcetylScan proteomic method. We identified many proteins known to be modified by acetylation, but found that the absence of HDAC4 had no effect on the acetylation profile of the murine neonate brain. This is consistent with the biochemical data suggesting that HDAC4 may not function as a lysine deacetylase, but these in vivo data do not support the previous report showing that the enzymatic activity of HDAC3 might be modified by its interaction with HDAC4. To complement this work, we used Affymetrix arrays to investigate the effect of HDAC4 knock-out on the transcriptional profile of the postnatal murine brain. There was no effect on global transcription, consistent with the absence of a differential histone acetylation profile. Validation of the array data by Taq-man qPCR indicated that only protamine 1 and Igfbp6 mRNA levels were increased by more than one-fold and only Calml4 was decreased. The lack of a major effect on the transcriptional profile is consistent with the cytoplasmic location of HDAC4 in the P3 murine brain.
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Affiliation(s)
- Michal Mielcarek
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Tamara Seredenina
- Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Matthew P. Stokes
- Cell Signaling Technology, Danvers, Massachusetts, United States of America
| | - Georgina F. Osborne
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Christian Landles
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Linda Inuabasi
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Sophie A. Franklin
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Jeffrey C. Silva
- Cell Signaling Technology, Danvers, Massachusetts, United States of America
| | - Ruth Luthi-Carter
- Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Vahri Beaumont
- CHDI Management Inc./CHDI Foundation Inc., Los Angeles, California, United States of America
| | - Gillian P. Bates
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- * E-mail:
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39
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Rudolph J, Crawford JJ, Hoeflich KP, Chernoff J. p21-Activated Kinase Inhibitors. ACTA ACUST UNITED AC 2013; 34 Pt. B:157-80. [DOI: 10.1016/b978-0-12-420146-0.00007-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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