1
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Li C, Boutet A, Pascariu CM, Nelson T, Courcelles M, Wu Z, Comtois-Marotte S, Emery G, Thibault P. SUMO Proteomics Analyses Identify Protein Inhibitor of Activated STAT-Mediated Regulatory Networks Involved in Cell Cycle and Cell Proliferation. J Proteome Res 2023; 22:812-825. [PMID: 36723483 PMCID: PMC9990128 DOI: 10.1021/acs.jproteome.2c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Protein inhibitor of activated STAT (PIAS) proteins are E3 SUMO ligases playing important roles in protein stability and signaling transduction pathways. PIAS proteins are overexpressed in the triple-negative breast cancer cell line MDA-MB-231, and PIAS knockout (KO) results in a reduction in cell proliferation and cell arrest in the S phase. However, the molecular mechanisms underlying PIAS functions in cell proliferation and cell cycle remain largely unknown. Here, we used quantitative SUMO proteomics to explore the regulatory role of PIAS SUMO E3 ligases upon CRISPR/Cas9 KO of individual PIAS. A total of 1422 sites were identified, and around 10% of SUMO sites were regulated following KO of one or more PIAS genes. We identified protein substrates that were either specific to individual PIAS ligase or regulated by several PIAS ligases. Ki-67 and TOP2A, which are involved in cell proliferation and epithelial-to-mesenchymal transition, are SUMOylated at several lysine residues by all PIAS ligases, suggesting a level of redundancy between these proteins. Confocal microscopy and biochemical experiments revealed that SUMOylation regulated TOP2A protein stability, while this modification is involved in the recruitment of Ki-67 nucleolar proteins containing the SUMO interacting motif. These results provide novel insights into both the redundant and specific regulatory mechanisms of cell proliferation and cell cycle mediated by PIAS SUMO E3 ligases.
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Affiliation(s)
- Chongyang Li
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Alison Boutet
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada.,Molecular Biology program, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Cristina Mirela Pascariu
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Trent Nelson
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada.,Molecular Biology program, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Zhaoguan Wu
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada.,Department of Chemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Simon Comtois-Marotte
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Gregory Emery
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada.,Department of Pathology and Cell Biology, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada.,Molecular Biology program, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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2
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Liu TT, Yang H, Zhuo FF, Yang Z, Zhao MM, Guo Q, Liu Y, Liu D, Zeng KW, Tu PF. Atypical E3 ligase ZFP91 promotes small-molecule-induced E2F2 transcription factor degradation for cancer therapy. EBioMedicine 2022; 86:104353. [PMID: 36375317 PMCID: PMC9667253 DOI: 10.1016/j.ebiom.2022.104353] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The E2F family of transcription factors play a crucial role in the development of various cancers. However, E2F members lack targetable binding pockets and are typically considered "undruggable". Unlike canonical small-molecule therapeutics, molecular glues mediate new E3 ligase-protein interactions to induce selective proteasomal degradation, which represents an attractive option to overcome these limitations. METHODS Human proteome microarray was utilized to identify a natural product-derived molecular glue for targeting E2F2 degradation. Co-IP analysis with stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomics was carried out to further explore the E3 ligase for E2F2 degradation. FINDINGS In this study, we identified a molecular glue bufalin, which significantly promoted E2F2 degradation. Unexpectedly, E2F2 underwent ubiquitination and proteasomal degradation via a previously undisclosed atypical E3 ligase, zinc finger protein 91 (ZFP91). In particular, we observed that bufalin markedly promoted E2F2-ZFP91 complex formation, thereby leading to E2F2 polyubiquitination via K48-linked ubiquitin chains for degradation. E2F2 degradation subsequently caused transcriptional suppression of multiple oncogenes including c-Myc, CCNE1, CCNE2, MCM5 and CDK1, and inhibited hepatocellular carcinoma growth in vitro and in vivo. INTERPRETATION Collectively, our findings open up a new direction for transcription factors degradation by targeting atypical E3 ligase ZFP91. Meanwhile, the chemical knockdown strategy with molecular glue may promote innovative transcription factor degrader development in cancer therapy. FUNDING This work was financially supported by the National Key Research and Development Project of China (2022YFC3501601), National Natural Sciences Foundation of China (81973505, 82174008, 82030114), and China Postdoctoral Science Foundation (2019M650396), the Fundamental Research Funds for the Central Universities.
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Affiliation(s)
- Ting-Ting Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Heng Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Fang-Fang Zhuo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhuo Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Mei-Mei Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qiang Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Dan Liu
- Proteomics Laboratory, Medical and Healthy Analytical Center, Peking University Health Science Center, Beijing 100191, China
| | - Ke-Wu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China,Corresponding author.
| | - Peng-Fei Tu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China,Corresponding author.
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3
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Solís-Fernández G, Montero-Calle A, Alonso-Navarro M, Fernandez-Torres MÁ, Lledó VE, Garranzo-Asensio M, Barderas R, Guzman-Aranguez A. Protein Microarrays for Ocular Diseases. Methods Mol Biol 2021; 2344:239-265. [PMID: 34115364 DOI: 10.1007/978-1-0716-1562-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The eye is a multifaceted organ organized in several compartments with particular properties that reflect their diverse functions. The prevalence of ocular diseases is increasing, mainly because of its relationship with aging and of generalized lifestyle changes. However, the pathogenic molecular mechanisms of many common eye pathologies remain poorly understood. Considering the unquestionable importance of proteins in cellular processes and disease progression, proteomic techniques, such as protein microarrays, represent a valuable approach to analyze pathophysiological protein changes in the ocular environment. This technology enables to perform multiplex high-throughput protein expression profiling with minimal sample volume requirements broadening our knowledge of ocular proteome network in eye diseases.In this review, we present a brief summary of the main types of protein microarrays (antibody microarrays, reverse-phase protein microarrays, and protein microarrays) and their application for protein change detection in chronic ocular diseases such as dry eye, age-related macular degeneration, diabetic retinopathy, and glaucoma. The validation of these specific protein changes in eye pathologies may lead to the identification of new biomarkers, depiction of ocular disease pathways, and assistance in the diagnosis, prognosis, and development of new therapeutic options for eye pathologies.
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Affiliation(s)
- Guillermo Solís-Fernández
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Molecular Imaging and Photonics Division, Chemistry Department, Faculty of Sciences, KU Leuven, Leuven, Belgium
| | - Ana Montero-Calle
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Miren Alonso-Navarro
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Miguel Ángel Fernandez-Torres
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Victoria Eugenia Lledó
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - María Garranzo-Asensio
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Rodrigo Barderas
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Guzman-Aranguez
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain.
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4
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Qi H, Wang F, Tao SC. Proteome microarray technology and application: higher, wider, and deeper. Expert Rev Proteomics 2019; 16:815-827. [PMID: 31469014 DOI: 10.1080/14789450.2019.1662303] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Introduction: Protein microarray is a powerful tool for both biological study and clinical research. The most useful features of protein microarrays are their miniaturized size (low reagent and sample consumption), high sensitivity and their capability for parallel/high-throughput analysis. The major focus of this review is functional proteome microarray. Areas covered: For proteome microarray, this review will discuss some recently constructed proteome microarrays and new concepts that have been used for constructing proteome microarrays and data interpretation in past few years, such as PAGES, M-NAPPA strategy, VirD technology, and the first protein microarray database. this review will summarize recent proteomic scale applications and address the limitations and future directions of proteome microarray technology. Expert opinion: Proteome microarray is a powerful tool for basic biological and clinical research. It is expected to see improvements in the currently used proteome microarrays and the construction of more proteome microarrays for other species by using traditional strategies or novel concepts. It is anticipated that the maximum number of features on a single microarray and the number of possible applications will be increased, and the information that can be obtained from proteome microarray experiments will more in-depth in the future.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University , Shanghai , China
| | - Fei Wang
- School of Pharmacy, Shanghai Jiao Tong University , Shanghai , China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University , Shanghai , China
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5
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Garranzo-Asensio M, Montero-Calle A, Solís-Fernández G, Barderas R, Guzman-Aranguez A. Protein Microarrays: Valuable Tools for Ocular Diseases Research. Curr Med Chem 2019; 27:4549-4566. [PMID: 31244416 DOI: 10.2174/0929867326666190627131300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/07/2019] [Accepted: 05/14/2019] [Indexed: 11/22/2022]
Abstract
The eye is a complex organ comprised of several compartments with exclusive and specialized properties that reflect their diverse functions. Although the prevalence of eye pathologies is increasing, mainly because of its correlation with aging and of generalized lifestyle changes, the pathogenic molecular mechanisms of many common ocular diseases remain poorly understood. Therefore, there is an unmet need to delve into the pathogenesis, diagnosis, and treatment of eye diseases to preserve ocular health and reduce the incidence of visual impairment or blindness. Proteomics analysis stands as a valuable tool for deciphering protein profiles related to specific ocular conditions. In turn, such profiles can lead to real breakthroughs in the fields of ocular science and ophthalmology. Among proteomics techniques, protein microarray technology stands out by providing expanded information using very small volumes of samples. In this review, we present a brief summary of the main types of protein microarrays and their application for the identification of protein changes in chronic ocular diseases such as dry eye, glaucoma, age-related macular degeneration, or diabetic retinopathy. The validation of these specific protein alterations could provide new biomarkers, disclose eye diseases pathways, and help in the diagnosis and development of novel therapies for eye pathologies.
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Affiliation(s)
- María Garranzo-Asensio
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, C/Arcos de Jalon 118, Madrid 28037, Spain
| | - Ana Montero-Calle
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Guillermo Solís-Fernández
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rodrigo Barderas
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Guzman-Aranguez
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, C/Arcos de Jalon 118, Madrid 28037, Spain
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6
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Song G, Chen L, Zhang B, Song Q, Yu Y, Moore C, Wang TL, Shih IM, Zhang H, Chan DW, Zhang Z, Zhu H. Proteome-wide Tyrosine Phosphorylation Analysis Reveals Dysregulated Signaling Pathways in Ovarian Tumors. Mol Cell Proteomics 2019; 18:448-460. [PMID: 30523211 PMCID: PMC6398206 DOI: 10.1074/mcp.ra118.000851] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/20/2018] [Indexed: 11/06/2022] Open
Abstract
The recent accomplishment of comprehensive proteogenomic analysis of high-grade serous ovarian carcinoma (HGSOC) tissues reveals cancer associated molecular alterations were not limited to variations among DNA, and mRNA/protein expression, but are a result of complex reprogramming of signaling pathways/networks mediated by the protein and post-translational modification (PTM) interactomes. A systematic, multiplexed approach interrogating enzyme-substrate relationships in the context of PTMs is fundamental in understanding the dynamics of these pathways, regulation of cellular processes, and their roles in disease processes. Here, as part of Clinical Proteomic Tumor Analysis Consortium (CPTAC) project, we established a multiplexed PTM assay (tyrosine phosphorylation, and lysine acetylation, ubiquitylation and SUMOylation) method to identify protein probes' PTMs on the human proteome array. Further, we focused on the tyrosine phosphorylation and identified 19 kinases are potentially responsible for the dysregulated signaling pathways observed in HGSOC. Additionally, elevated kinase activity was observed when 14 ovarian cancer cell lines or tumor tissues were subjected to test the autophosphorylation status of PTK2 (pY397) and PTK2B (pY402) as a proxy for kinase activity. Taken together, this report demonstrates that PTM signatures based on lysate reactions on human proteome array is a powerful, unbiased approach to identify dysregulated PTM pathways in tumors.
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Affiliation(s)
- Guang Song
- From the ‡Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Li Chen
- §Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231
| | - Bai Zhang
- §Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231
| | - Qifeng Song
- From the ‡Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Yu Yu
- §Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231
| | - Cedric Moore
- From the ‡Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Tian-Li Wang
- §Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231
- ¶Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231
| | - Ie-Ming Shih
- ¶Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231
| | - Hui Zhang
- §Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231
| | - Daniel W Chan
- §Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231
| | - Zhen Zhang
- §Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231;
| | - Heng Zhu
- From the ‡Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205;
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7
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Eisenhardt N, Ilic D, Nagamalleswari E, Pichler A. Biochemical characterization of SUMO-conjugating enzymes by in vitro sumoylation assays. Methods Enzymol 2019; 618:167-185. [PMID: 30850051 DOI: 10.1016/bs.mie.2018.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The small ubiquitin-related modifier (SUMO) is a protein of ~10kDa that is covalently conjugated to its substrate proteins in an enzymatic process called sumoylation. This posttranslational modification is an essential regulatory mechanism that plays crucial roles in many cellular pathways. It allows rapid adaptation to environmental changes by switching protein functions due to alternate complex assemblies, changes in intracellular localization, enzymatic activity, or stability. SUMO conjugation is executed by the hierarchical action of E1, E2, and E3 enzymes. Both E2 and E3 enzymes contribute to substrate specificity but with E3 ligases being the more important for this. E1 and E2 activities are essential for all sumoylation reactions but usually-with a few exceptions-modify substrates only inefficiently. Hence, most substrates require the additional action of an E3 ligase or a cofactor. Here, we describe methods to distinguish a bona fide E3 ligase from a cofactor activity by using in vitro sumoylation assays.
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Affiliation(s)
- Nathalie Eisenhardt
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Dragana Ilic
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Easa Nagamalleswari
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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8
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Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nat Methods 2018; 15:330-338. [PMID: 29638227 PMCID: PMC6063793 DOI: 10.1038/nmeth.4632] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 01/25/2018] [Indexed: 01/08/2023]
Abstract
A key component of efforts to address the reproducibility crisis in biomedical research is the development of rigorously validated and renewable protein-affinity reagents. As part of the US National Institutes of Health (NIH) Protein Capture Reagents Program (PCRP), we have generated a collection of 1,406 highly validated immunoprecipitation- and/or immunoblotting-grade mouse monoclonal antibodies (mAbs) to 737 human transcription factors, using an integrated production and validation pipeline. We used HuProt human protein microarrays as a primary validation tool to identify mAbs with high specificity for their cognate targets. We further validated PCRP mAbs by means of multiple experimental applications, including immunoprecipitation, immunoblotting, chromatin immunoprecipitation followed by sequencing (ChIP-seq), and immunohistochemistry. We also conducted a meta-analysis that identified critical variables that contribute to the generation of high-quality mAbs. All validation data, protocols, and links to PCRP mAb suppliers are available at http://proteincapture.org.
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Affiliation(s)
- Anand Venkataraman
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kun Yang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Paolo Mita
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zheng Kuang
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Lin Xue
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Devlina Ghosh
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shuang Liu
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - Sarah Keegan
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Richard Saul
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Hongyan Zhang
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Guang Song
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jessica McDade
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sooyeon Yoo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seva G Khambadkone
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jimmy de Melo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Milanka Stevanovic
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lizhi Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Atul Tandon
- NeoBiotechnologies, Inc., Union City, California, USA
| | - Elliot Campbell
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Stephen Anderson
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Jef D Boeke
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Fenyö
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Gordon Whiteley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Heng Zhu
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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9
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Guo J, Chen D, Gao X, Hu X, Zhou Y, Wu C, Wang Y, Chen J, Pei R, Chen X. Protein Inhibitor of Activated STAT2 Restricts HCV Replication by Modulating Viral Proteins Degradation. Viruses 2017; 9:v9100285. [PMID: 28973998 PMCID: PMC5691636 DOI: 10.3390/v9100285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 09/27/2017] [Accepted: 09/27/2017] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) replication in cells is controlled by many host factors. In this report, we found that protein inhibitor of activated STAT2 (PIAS2), which is a small ubiquitin-like modifier (SUMO) E3 ligase, restricted HCV replication. During infection, HCV core, NS3 and NS5A protein expression, as well as the viral assembly and budding efficiency were enhanced when endogenous PIAS2 was knocked down, whereas exogenous PIAS2 expression decreased HCV core, NS3, and NS5A protein expression and the viral assembly and budding efficiency. PIAS2 did not influence the viral entry, RNA replication, and protein translation steps of the viral life cycle. When expressed together with SUMO1, PIAS2 reduced the HCV core, NS3 and NS5A protein levels expressed from individual plasmids through the proteasome pathway in a ubiquitin-independent manner; the stability of these proteins in the HCV infectious system was enhanced when PIAS2 was knocked down. Furthermore, we found that the core was SUMOylated at amino acid K78, and PIAS2 enhanced the SUMOylation level of the core.
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Affiliation(s)
- Jing Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Dan Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaoxiao Gao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Yuan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Chunchen Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Yun Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Jizheng Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Rongjuan Pei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Xinwen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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10
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Newman RH, Zhang J. Integrated Strategies to Gain a Systems-Level View of Dynamic Signaling Networks. Methods Enzymol 2017; 589:133-170. [PMID: 28336062 DOI: 10.1016/bs.mie.2017.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In order to survive and function properly in the face of an ever changing environment, cells must be able to sense changes in their surroundings and respond accordingly. Cells process information about their environment through complex signaling networks composed of many discrete signaling molecules. Individual pathways within these networks are often tightly integrated and highly dynamic, allowing cells to respond to a given stimulus (or, as is typically the case under physiological conditions, a combination of stimuli) in a specific and appropriate manner. However, due to the size and complexity of many cellular signaling networks, it is often difficult to predict how cellular signaling networks will respond under a particular set of conditions. Indeed, crosstalk between individual signaling pathways may lead to responses that are nonintuitive (or even counterintuitive) based on examination of the individual pathways in isolation. Therefore, to gain a more comprehensive view of cell signaling processes, it is important to understand how signaling networks behave at the systems level. This requires integrated strategies that combine quantitative experimental data with computational models. In this chapter, we first examine some of the progress that has recently been made toward understanding the systems-level regulation of cellular signaling networks, with a particular emphasis on phosphorylation-dependent signaling networks. We then discuss how genetically targetable fluorescent biosensors are being used together with computational models to gain unique insights into the spatiotemporal regulation of signaling networks within single, living cells.
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Affiliation(s)
- Robert H Newman
- North Carolina Agricultural and Technical State University, Greensboro, NC, United States.
| | - Jin Zhang
- University of California, San Diego, San Diego, CA, United States.
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11
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Atak A, Mukherjee S, Jain R, Gupta S, Singh VA, Gahoi N, K P M, Srivastava S. Protein microarray applications: Autoantibody detection and posttranslational modification. Proteomics 2016; 16:2557-2569. [PMID: 27452627 DOI: 10.1002/pmic.201600104] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/09/2016] [Accepted: 07/19/2016] [Indexed: 12/18/2022]
Abstract
The discovery of DNA microarrays was a major milestone in genomics; however, it could not adequately predict the structure or dynamics of underlying protein entities, which are the ultimate effector molecules in a cell. Protein microarrays allow simultaneous study of thousands of proteins/peptides, and various advancements in array technologies have made this platform suitable for several diagnostic and functional studies. Antibody arrays enable researchers to quantify the abundance of target proteins in biological fluids and assess PTMs by using the antibodies. Protein microarrays have been used to assess protein-protein interactions, protein-ligand interactions, and autoantibody profiling in various disease conditions. Here, we summarize different microarray platforms with focus on its biological and clinical applications in autoantibody profiling and PTM studies. We also enumerate the potential of tissue microarrays to validate findings from protein arrays as well as other approaches, highlighting their significance in proteomics.
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Affiliation(s)
- Apurva Atak
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shuvolina Mukherjee
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rekha Jain
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shabarni Gupta
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vedita Anand Singh
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Nikita Gahoi
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Manubhai K P
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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