1
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Cheng X, Yang W, Lin W, Mei F. Paradoxes of Cellular SUMOylation Regulation: A Role of Biomolecular Condensates? Pharmacol Rev 2023; 75:979-1006. [PMID: 37137717 PMCID: PMC10441629 DOI: 10.1124/pharmrev.122.000784] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
Protein SUMOylation is a major post-translational modification essential for maintaining cellular homeostasis. SUMOylation has long been associated with stress responses as a diverse array of cellular stress signals are known to trigger rapid alternations in global protein SUMOylation. In addition, while there are large families of ubiquitination enzymes, all small ubiquitin-like modifiers (SUMOs) are conjugated by a set of enzymatic machinery comprising one heterodimeric SUMO-activating enzyme, a single SUMO-conjugating enzyme, and a small number of SUMO protein ligases and SUMO-specific proteases. How a few SUMOylation enzymes specifically modify thousands of functional targets in response to diverse cellular stresses remains an enigma. Here we review recent progress toward understanding the mechanisms of SUMO regulation, particularly the potential roles of liquid-liquid phase separation/biomolecular condensates in regulating cellular SUMOylation during cellular stresses. In addition, we discuss the role of protein SUMOylation in pathogenesis and the development of novel therapeutics targeting SUMOylation. SIGNIFICANCE STATEMENT: Protein SUMOylation is one of the most prevalent post-translational modifications and plays a vital role in maintaining cellular homeostasis in response to stresses. Protein SUMOylation has been implicated in human pathogenesis, such as cancer, cardiovascular diseases, neurodegeneration, and infection. After more than a quarter century of extensive research, intriguing enigmas remain regarding the mechanism of cellular SUMOylation regulation and the therapeutic potential of targeting SUMOylation.
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Affiliation(s)
- Xiaodong Cheng
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Wenli Yang
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Wei Lin
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Fang Mei
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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2
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Salas-Lloret D, Jansen NS, Nagamalleswari E, van der Meulen C, Gracheva E, de Ru AH, Otte HAM, van Veelen PA, Pichler A, Goedhart J, Vertegaal AC, González-Prieto R. SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. SCIENCE ADVANCES 2023; 9:eadh2073. [PMID: 37531430 PMCID: PMC10396300 DOI: 10.1126/sciadv.adh2073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
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Affiliation(s)
- Daniel Salas-Lloret
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Nicolette S. Jansen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Coen van der Meulen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ekaterina Gracheva
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - H. Anne Marie Otte
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Andrea Pichler
- Max Plank Institute for Immunobiology and Epigenetics, Freiburg, Germany
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | | | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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3
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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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4
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Garza-Domínguez R, Torres-Quiroz F. Evolutionary Signals in Coronaviral Structural Proteins Suggest Possible Complex Mechanisms of Post-Translational Regulation in SARS-CoV-2 Virus. Viruses 2022; 14:v14112469. [PMID: 36366566 PMCID: PMC9696223 DOI: 10.3390/v14112469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Post-translational regulation of proteins has emerged as a central topic of research in the field of functional proteomics. Post-translational modifications (PTMs) dynamically control the activities of proteins and are involved in a wide range of biological processes. Crosstalk between different types of PTMs represents a key mechanism of regulation and signaling. Due to the current pandemic of the novel and dangerous SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) virus, here we present an in silico analysis of different types of PTMs in structural proteins of coronaviruses. A dataset of PTM sites was studied at three levels: conservation analysis, mutational analysis and crosstalk analysis. We identified two sets of PTMs which could have important functional roles in the regulation of the structural proteins of coronaviruses. Additionally, we found seven interesting signals of potential crosstalk events. These results reveal a higher level of complexity in the mechanisms of post-translational regulation of coronaviral proteins and provide new insights into the adaptation process of the SARS-CoV-2 virus.
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5
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The Role of SUMO E3 Ligases in Signaling Pathway of Cancer Cells. Int J Mol Sci 2022; 23:ijms23073639. [PMID: 35408996 PMCID: PMC8998487 DOI: 10.3390/ijms23073639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Small ubiquitin-like modifier (SUMO)ylation is a reversible post-translational modification that plays a crucial role in numerous aspects of cell physiology, including cell cycle regulation, DNA damage repair, and protein trafficking and turnover, which are of importance for cell homeostasis. Mechanistically, SUMOylation is a sequential multi-enzymatic process where SUMO E3 ligases recruit substrates and accelerate the transfer of SUMO onto targets, modulating their interactions, localization, activity, or stability. Accumulating evidence highlights the critical role of dysregulated SUMO E3 ligases in processes associated with the occurrence and development of cancers. In the present review, we summarize the SUMO E3 ligases, in particular, the novel ones recently identified, and discuss their regulatory roles in cancer pathogenesis.
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6
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Li Y, Huang Y, Li T. PTM-X: Prediction of Post-Translational Modification Crosstalk Within and Across Proteins. Methods Mol Biol 2022; 2499:275-283. [PMID: 35696086 DOI: 10.1007/978-1-0716-2317-6_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Posttranslational modifications (PTMs), which are processes of adding covalent groups in protein amino acids after the translation, play an important role in regulating proteins' localization, degradation, and functions. Different PTMs both within a single protein and across multiple proteins can work together or regulate reciprocally, known as PTM cross talk. However, high-throughput experimental identifications of PTM cross talk are lack due to technical limitations. In this chapter, we review in silico prediction approaches and illustrate the usage of PTM-X, a suite of recently proposed machine learning methods to predict both intra- and interprotein PTM cross talk.
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Affiliation(s)
- Yuxuan Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yuanhua Huang
- Department of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
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7
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Aroankins TS, Murali SK, Fenton RA, Wu Q. The Hydrogen-Coupled Oligopeptide Membrane Cotransporter Pept2 is SUMOylated in Kidney Distal Convoluted Tubule Cells. Front Mol Biosci 2021; 8:790606. [PMID: 34881291 PMCID: PMC8646034 DOI: 10.3389/fmolb.2021.790606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Protein post-translational modification by the Small Ubiquitin-like MOdifier (SUMO) on lysine residues is a reversible process highly important for transcription and protein stability. In the kidney, SUMOylation appears to be important for the cellular response to aldosterone. Therefore, in this study, we generated a SUMOylation profile of the aldosterone-sensitive kidney distal convoluted tubule (DCT) as a basis for understanding SUMOylation events in this cell type. Using mass spectrometry-based proteomics, 1037 SUMO1 and 552 SUMO2 sites, corresponding to 546 SUMO1 and 356 SUMO2 proteins, were identified from a modified mouse kidney DCT cell line (mpkDCT). SUMOylation of the renal hydrogen-coupled oligopeptide and drug co-transporter (Pept2) at one site (K139) was found to be highly regulated by aldosterone. Using immunolabelling of mouse kidney sections Pept2 was localized to DCT cells in vivo. Aldosterone stimulation of mpkDCT cell lines expressing wild-type Pept2 or mutant K139R-Pept2, post-transcriptionally increased Pept2 expression up to four-fold. Aldosterone decreased wild-type Pept2 abundance in the apical membrane domain of mpkDCT cells, but this response was absent in K139R-Pept2 expressing cells. In summary, we have generated a SUMOylation landscape of the mouse DCT and determined that SUMOylation plays an important role in the physiological regulation of Pept2 trafficking by aldosterone.
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Affiliation(s)
- Takwa S Aroankins
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Department of Anesthesiology and Intensive Care, Sahlgrenska University Hospital, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | | | - Robert A Fenton
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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8
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de Pins B, Mendes T, Giralt A, Girault JA. The Non-receptor Tyrosine Kinase Pyk2 in Brain Function and Neurological and Psychiatric Diseases. Front Synaptic Neurosci 2021; 13:749001. [PMID: 34690733 PMCID: PMC8527176 DOI: 10.3389/fnsyn.2021.749001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/14/2021] [Indexed: 12/28/2022] Open
Abstract
Pyk2 is a non-receptor tyrosine kinase highly enriched in forebrain neurons. Pyk2 is closely related to focal adhesion kinase (FAK), which plays an important role in sensing cell contacts with extracellular matrix and other extracellular signals controlling adhesion and survival. Pyk2 shares some of FAK’s characteristics including recruitment of Src-family kinases after autophosphorylation, scaffolding by interacting with multiple partners, and activation of downstream signaling pathways. Pyk2, however, has the unique property to respond to increases in intracellular free Ca2+, which triggers its autophosphorylation following stimulation of various receptors including glutamate NMDA receptors. Pyk2 is dephosphorylated by the striatal-enriched phosphatase (STEP) that is highly expressed in the same neuronal populations. Pyk2 localization in neurons is dynamic, and altered following stimulation, with post-synaptic and nuclear enrichment. As a signaling protein Pyk2 is involved in multiple pathways resulting in sometimes opposing functions depending on experimental models. Thus Pyk2 has a dual role on neurites and dendritic spines. With Src family kinases Pyk2 participates in postsynaptic regulations including of NMDA receptors and is necessary for specific types of synaptic plasticity and spatial memory tasks. The diverse functions of Pyk2 are also illustrated by its role in pathology. Pyk2 is activated following epileptic seizures or ischemia-reperfusion and may contribute to the consequences of these insults whereas Pyk2 deficit may contribute to the hippocampal phenotype of Huntington’s disease. Pyk2 gene, PTK2B, is associated with the risk for late-onset Alzheimer’s disease. Studies of underlying mechanisms indicate a complex contribution with involvement in amyloid toxicity and tauopathy, combined with possible functional deficits in neurons and contribution in microglia. A role of Pyk2 has also been proposed in stress-induced depression and cocaine addiction. Pyk2 is also important for the mobility of astrocytes and glioblastoma cells. The implication of Pyk2 in various pathological conditions supports its potential interest for therapeutic interventions. This is possible through molecules inhibiting its activity or increasing it through inhibition of STEP or other means, depending on a precise evaluation of the balance between positive and negative consequences of Pyk2 actions.
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Affiliation(s)
- Benoit de Pins
- Institut du Fer à Moulin, Paris, France.,Inserm UMR-S 1270, Paris, France.,Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France
| | - Tiago Mendes
- Institut du Fer à Moulin, Paris, France.,Inserm UMR-S 1270, Paris, France.,Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France
| | - Albert Giralt
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
| | - Jean-Antoine Girault
- Institut du Fer à Moulin, Paris, France.,Inserm UMR-S 1270, Paris, France.,Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France
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9
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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10
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Morozko EL, Smith-Geater C, Monteys AM, Pradhan S, Lim RG, Langfelder P, Kachemov M, Kulkarni JA, Zaifman J, Hill A, Stocksdale JT, Cullis PR, Wu J, Ochaba J, Miramontes R, Chakraborty A, Hazra TK, Lau A, St-Cyr S, Orellana I, Kopan L, Wang KQ, Yeung S, Leavitt BR, Reidling JC, Yang XW, Steffan JS, Davidson BL, Sarkar PS, Thompson LM. PIAS1 modulates striatal transcription, DNA damage repair, and SUMOylation with relevance to Huntington's disease. Proc Natl Acad Sci U S A 2021; 118:e2021836118. [PMID: 33468657 PMCID: PMC7848703 DOI: 10.1073/pnas.2021836118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA damage repair genes are modifiers of disease onset in Huntington's disease (HD), but how this process intersects with associated disease pathways remains unclear. Here we evaluated the mechanistic contributions of protein inhibitor of activated STAT-1 (PIAS1) in HD mice and HD patient-derived induced pluripotent stem cells (iPSCs) and find a link between PIAS1 and DNA damage repair pathways. We show that PIAS1 is a component of the transcription-coupled repair complex, that includes the DNA damage end processing enzyme polynucleotide kinase-phosphatase (PNKP), and that PIAS1 is a SUMO E3 ligase for PNKP. Pias1 knockdown (KD) in HD mice had a normalizing effect on HD transcriptional dysregulation associated with synaptic function and disease-associated transcriptional coexpression modules enriched for DNA damage repair mechanisms as did reduction of PIAS1 in HD iPSC-derived neurons. KD also restored mutant HTT-perturbed enzymatic activity of PNKP and modulated genomic integrity of several transcriptionally normalized genes. The findings here now link SUMO modifying machinery to DNA damage repair responses and transcriptional modulation in neurodegenerative disease.
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Affiliation(s)
- Eva L Morozko
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Charlene Smith-Geater
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Alejandro Mas Monteys
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Subrata Pradhan
- Department of Neurology, University of Texas Medical Branch, Galveston, TX 77555
| | - Ryan G Lim
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Peter Langfelder
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, CA 90095
| | - Marketta Kachemov
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Jayesh A Kulkarni
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Josh Zaifman
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Austin Hill
- Incisive Genetics Inc., Vancouver, BC, Canada V6A 0H9
| | | | - Pieter R Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
- NanoMedicines Innovation Network, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA 92697
| | - Joseph Ochaba
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Ricardo Miramontes
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Tapas K Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Alice Lau
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Sophie St-Cyr
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Iliana Orellana
- Sue and Bill Gross Stem Cell Institute, University of California, Irvine, CA 92697
| | - Lexi Kopan
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Keona Q Wang
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Sylvia Yeung
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Jack C Reidling
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - X William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095
| | - Joan S Steffan
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Partha S Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, TX 77555
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Leslie M Thompson
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697;
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
- Department of Biological Chemistry, University of California, Irvine, CA 92697
- Sue and Bill Gross Stem Cell Institute, University of California, Irvine, CA 92697
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11
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The Function of SUMOylation and Its Role in the Development of Cancer Cells under Stress Conditions: A Systematic Review. Stem Cells Int 2020; 2020:8835714. [PMID: 33273928 PMCID: PMC7683158 DOI: 10.1155/2020/8835714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Malignant tumors still pose serious threats to human health due to their high morbidity and mortality. Recurrence and metastasis are the most important factors affecting patient prognosis. Chemotherapeutic drugs and radiation used to treat these tumors mainly interfere with tumor metabolism, destroy DNA integrity, and inhibit protein synthesis. The upregulation of small ubiquitin-like modifier (SUMO) is a prevalent posttranslational modification (PTM) in various cancers and plays a critical role in tumor development. The dysregulation of SUMOylation can protect cancer cells from stresses exerted by external or internal stimuli. SUMOylation is a dynamic process finely regulated by SUMOylation enzymes and proteases to maintain a balance between SUMOylation and deSUMOylation. An increasing number of studies have reported that SUMOylation imbalance may contribute to cancer development, including metastasis, angiogenesis, invasion, and proliferation. High level of SUMOylation is required for cancer cells to survive internal or external stresses. Downregulation of SUMOylation may inhibit the development of cancer, making it an important potential clinical therapeutic target. Some studies have already begun to treat tumors by inhibiting the expression of SUMOylation family members, including SUMO E1 or E2. The tumor cells become more aggressive under internal and external stresses. The prevention of tumor development, metastasis, recurrence, and radiochemotherapy resistance by attenuating SUMOylation requires further exploration. This review focused on SUMOylation in tumor cells to discuss its effects on tumor suppressor proteins and oncoproteins as well as classical tumor pathways to identify new insights for cancer clinical therapy.
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12
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Syu GD, Dunn J, Zhu H. Developments and Applications of Functional Protein Microarrays. Mol Cell Proteomics 2020; 19:916-927. [PMID: 32303587 PMCID: PMC7261817 DOI: 10.1074/mcp.r120.001936] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/24/2020] [Indexed: 12/19/2022] Open
Abstract
Protein microarrays are crucial tools in the study of proteins in an unbiased, high-throughput manner, as they allow for characterization of up to thousands of individually purified proteins in parallel. The adaptability of this technology has enabled its use in a wide variety of applications, including the study of proteome-wide molecular interactions, analysis of post-translational modifications, identification of novel drug targets, and examination of pathogen-host interactions. In addition, the technology has also been shown to be useful in profiling antibody specificity, as well as in the discovery of novel biomarkers, especially for autoimmune diseases and cancers. In this review, we will summarize the developments that have been made in protein microarray technology in both in basic and translational research over the past decade. We will also introduce a novel membrane protein array, the GPCR-VirD array, and discuss the future directions of functional protein microarrays.
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Affiliation(s)
- Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan R.O.C..
| | - Jessica Dunn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231.
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13
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Protein inhibitor of activated STAT1 (PIAS1) inhibits IRF8 activation of Epstein-Barr virus lytic gene expression. Virology 2019; 540:75-87. [PMID: 31743858 DOI: 10.1016/j.virol.2019.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 11/23/2022]
Abstract
Epstein-Barr virus (EBV), a major human oncogenic pathogen, establishes life-long persistent infections. In latently infected B lymphocytes, the virus persists as an episome in the nucleus. Periodic reactivation of latent virus is controlled by both viral and cellular factors. Our recent studies showed that interferon regulatory factor 8 (IRF8) is required for EBV lytic reactivation while protein inhibitor of activated STAT1 (PIAS1) functions as an EBV restriction factor to block viral reactivation. Here, we show that IRF8 directly binds to the EBV genome and regulates EBV lytic gene expression together with PU.1 and EBV transactivator RTA. Furthermore, our study reveals that PIAS1 antagonizes IRF8/PU.1-mediated lytic gene activation through binding to and inhibiting IRF8. Together, our study establishes IRF8 as a transcriptional activator in promoting EBV reactivation and defines PIAS1 as an inhibitor of IRF8 to limit lytic gene expression.
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14
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Wu Z, Huang R, Yuan L. Crosstalk of intracellular post-translational modifications in cancer. Arch Biochem Biophys 2019; 676:108138. [PMID: 31606391 DOI: 10.1016/j.abb.2019.108138] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/29/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022]
Abstract
Post-translational modifications (PTMs) have been reported to play pivotal roles in numerous cellular biochemical and physiological processes. Multiple PTMs can influence the actions of each other positively or negatively, termed as PTM crosstalk or PTM code. During recent years, development of identification strategies for PTMs co-occurrence has revealed abundant information of interplay between PTMs. Increasing evidence demonstrates that deregulation of PTMs crosstalk is involved in the genesis and development of various diseases. Insight into the complexity of PTMs crosstalk will help us better understand etiology and provide novel targets for drug therapy. In the present review, we will discuss the important functional roles of PTMs crosstalk in proteins associated with cancer diseases.
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Affiliation(s)
- Zheng Wu
- School of Kinesiology and Health, Capital University of Physical Education and Sports, Beijing, 100191, China.
| | - Rongting Huang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Liang Yuan
- Peking University International Hospital, Beijing, 102200, China
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15
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Zhang Y, Hirota T, Kuwata K, Oishi S, Gramani SG, Bode JW. Chemical Synthesis of Atomically Tailored SUMO E2 Conjugating Enzymes for the Formation of Covalently Linked SUMO-E2-E3 Ligase Ternary Complexes. J Am Chem Soc 2019; 141:14742-14751. [PMID: 31436980 DOI: 10.1021/jacs.9b06820] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
E2 conjugating enzymes are the key catalytic actors in the transfer of ubiquitin, SUMO, and other ubiquitin-like modifiers to their substrate proteins. Their high rates of transfer and promiscuous binding complicate studies of their interactions and binding partners. To access specific, covalently linked conjugates of the SUMO E2 conjugating enzyme Ubc9, we prepared synthetic variants bearing site-specific non-native modifications including the following: (1) replacement of Cys93 to 2,3-diaminopropionic acid to form the amide-linked stable E2-SUMO conjugate, which is known to have high affinity for E3 ligases; (2) a photoreactive group (diazirine) to trap E3 ligases upon UV irradiation; and (3) an N-terminal biotin for purification and detection. To construct these Ubc9 variants in a flexible, convergent manner, we combined the three leading methods: native chemical ligation (NCL), α-ketoacid-hydroxylamine (KAHA) ligation, and serine/threonine ligation (STL). Using the synthetic proteins, we demonstrated the selective formation of Ubc9-SUMO conjugates and the trapping of an E3 ligase (RanBP2) to form the stable, covalently linked SUMO1-Ubc9-RanBP2 ternary complex. The powerful combination of ligation methods-which minimizes challenges of functional group manipulations-will enable chemical probes based on E2 conjugating enzymes to trap E3 ligases and facilitate the synthesis of other protein classes.
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Affiliation(s)
- Yinfeng Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Subramanian G Gramani
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Jeffrey W Bode
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan.,Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich 8093 , Switzerland
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16
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Antfolk D, Antila C, Kemppainen K, Landor SKJ, Sahlgren C. Decoding the PTM-switchboard of Notch. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118507. [PMID: 31301363 PMCID: PMC7116576 DOI: 10.1016/j.bbamcr.2019.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/03/2019] [Accepted: 07/06/2019] [Indexed: 01/08/2023]
Abstract
The developmentally indispensable Notch pathway exhibits a high grade of pleiotropism in its biological output. Emerging evidence supports the notion of post-translational modifications (PTMs) as a modus operandi controlling dynamic fine-tuning of Notch activity. Although, the intricacy of Notch post-translational regulation, as well as how these modifications lead to multiples of divergent Notch phenotypes is still largely unknown, numerous studies show a correlation between the site of modification and the output. These include glycosylation of the extracellular domain of Notch modulating ligand binding, and phosphorylation of the PEST domain controlling half-life of the intracellular domain of Notch. Furthermore, several reports show that multiple PTMs can act in concert, or compete for the same sites to drive opposite outputs. However, further investigation of the complex PTM crosstalk is required for a complete understanding of the PTM-mediated Notch switchboard. In this review, we aim to provide a consistent and up-to-date summary of the currently known PTMs acting on the Notch signaling pathway, their functions in different contexts, as well as explore their implications in physiology and disease. Furthermore, we give an overview of the present state of PTM research methodology, and allude to a future with PTM-targeted Notch therapeutics.
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Affiliation(s)
- Daniel Antfolk
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Christian Antila
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Kati Kemppainen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Sebastian K-J Landor
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.
| | - Cecilia Sahlgren
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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17
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Liu Y, Fan P, Zhang S, Wang Y, Liu D. Prioritization and comprehensive analysis of genes related to major depressive disorder. Mol Genet Genomic Med 2019; 7:e659. [PMID: 30968596 PMCID: PMC6565567 DOI: 10.1002/mgg3.659] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/30/2019] [Accepted: 03/04/2019] [Indexed: 12/28/2022] Open
Abstract
Background Major depressive disorder (MDD) is a serious mental health problem in modern society, which is difficult to identify and diagnose in the early stages. Despite strong evidence supporting the heritability of MDD, progresses in large‐scale and individual genetic studies remain preliminary. Methods In this study, a multi‐data source‐based prioritization (MDSP) method was proposed, and an appropriate threshold was determined for the optimization of depression‐related genes (DEPgenes). Analyses on Gene Ontology biological processes, KEGG pathway and the specific pathway crosstalk network were further proposed. Results A total of 143 DEPgenes were identified and the MDD‐specific network was constructed for the pathogenesis investigation and therapeutic methods development of MDD. Comparing with existing research strategies, the genetic optimization and analysis results were confirmed to be reliable. Finally, the pathway enrichment and crosstalk analyses revealed two unique pathway interaction modules that were significantly enriched with MDD genes. The related core pathways of neuroactive ligand‐receptor interaction and dopaminergic synapse supported the neuropathology hypothesis of MDD. And the pathways of serotonergic synapse and morphine addiction indicated the mechanism of drug addiction caused by serotonin used in the treatment. Conclusions This work provided a reference for the study of MDD, although future validation by extensive experimentation is still required.
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Affiliation(s)
- Yi Liu
- ICUFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinP.R. China
| | - Pengfei Fan
- Organ Transplant CenterTianjin First Central HospitalTianjinP.R. China
| | - Shiyuan Zhang
- ICUFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinP.R. China
| | - Yidan Wang
- Clinical Practice Teaching CenterTianjin University of Traditional Chinese MedicineTianjinP.R. China
| | - Dan Liu
- Acupuncture DepartmentFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinP.R. China
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18
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Zhao X. SUMO-Mediated Regulation of Nuclear Functions and Signaling Processes. Mol Cell 2019; 71:409-418. [PMID: 30075142 DOI: 10.1016/j.molcel.2018.07.027] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022]
Abstract
Since the discovery of SUMO twenty years ago, SUMO conjugation has become a widely recognized post-translational modification that targets a myriad of proteins in many processes. Great progress has been made in understanding the SUMO pathway enzymes, substrate sumoylation, and the interplay between sumoylation and other regulatory mechanisms in a variety of contexts. As these research directions continue to generate insights into SUMO-based regulation, several mechanisms by which sumoylation and desumoylation can orchestrate large biological effects are emerging. These include the ability to target multiple proteins within the same cellular structure or process, respond dynamically to external and internal stimuli, and modulate signaling pathways involving other post-translational modifications. Focusing on nuclear function and intracellular signaling, this review highlights a broad spectrum of historical data and recent advances with the aim of providing an overview of mechanisms underlying SUMO-mediated global effects to stimulate further inquiry into intriguing roles of SUMO.
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Affiliation(s)
- Xiaolan Zhao
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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19
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Tomasi ML, Ramani K. SUMOylation and phosphorylation cross-talk in hepatocellular carcinoma. Transl Gastroenterol Hepatol 2018; 3:20. [PMID: 29780898 DOI: 10.21037/tgh.2018.04.04] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/11/2018] [Indexed: 01/22/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a primary malignancy of the liver and occurs predominantly in patients with underlying chronic liver disease and cirrhosis. The large spectrum of protein post-translational modification (PTM) includes numerous critical signaling events that occur during neoplastic transformation. PTMs occur to nearly all proteins and increase the functional diversity of proteins. We have reviewed the role of two major PTMs, SUMOylation and phosphorylation, in the altered signaling of key players in HCC. SUMOylation is a PTM that involves addition of a small ubiquitin-like modifiers (SUMO) group to proteins. It is known to regulate protein stability, protein-protein interactions, trafficking and transcriptional activity. The major pathways that are regulated by SUMOylation and may influence HCC are regulation of transcription, cell growth pathways associated with B-cell lymphoma 2 (Bcl-2) and methionine adenosyltransferases (MAT), oxidative stress pathways [nuclear erythroid 2-related factor 2 (Nrf2)], tumor suppressor pathways (p53), hypoxia-inducible signaling [hypoxia-inducible factor-1 (HIF-1)], glucose and lipid metabolism, nuclear factor kappa B (NF-κB) and β-Catenin signaling. Phosphorylation is an extensively studied PTM in HCC. The mitogen-activated protein kinase (MAPK), phosphatidyl inositol/AK-strain transforming (PI3K/AKT), and C-SRC pathways have been extensively studied for deregulation of kinases and alteration in signaling of targets through phosphorylation of their substrates. Cross-talk between phosphorylation and SUMOylation is known to influence transcriptional activity of proteins and protein-protein interactions. In HCC, several SUMOylation-dependent phosphorylation events have been studied such as MAPK activation and c-SRC activity that have been reviewed in this work. The drastic effects of site-specific phosphorylation or SUMOylation on enzyme activity of signaling players and its effect on growth and tumorigenesis suggests that these PTMs are novel targets for therapeutic intervention in HCC.
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Affiliation(s)
- Maria Lauda Tomasi
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Komal Ramani
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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20
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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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21
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Cox E, Hwang W, Uzoma I, Hu J, Guzzo CM, Jeong J, Matunis MJ, Qian J, Zhu H, Blackshaw S. Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex. Mol Cell Proteomics 2017; 16:812-823. [PMID: 28254775 PMCID: PMC5417823 DOI: 10.1074/mcp.m116.063719] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/14/2017] [Indexed: 12/23/2022] Open
Abstract
SUMOylation is a critical regulator of a broad range of cellular processes, and is thought to do so in part by modulation of protein interaction. To comprehensively identify human proteins whose interaction is modulated by SUMOylation, we developed an in vitro binding assay using human proteome microarrays to identify targets of SUMO1 and SUMO2. We then integrated these results with protein SUMOylation and protein-protein interaction data to perform network motif analysis. We focused on a single network motif we termed a SUMOmodPPI (SUMO-modulated Protein-Protein Interaction) that included the INO80 chromatin remodeling complex subunits TFPT and INO80E. We validated the SUMO-binding activity of INO80E, and showed that TFPT is a SUMO substrate both in vitro and in vivo We then demonstrated a key role for SUMOylation in mediating the interaction between these two proteins, both in vitro and in vivo By demonstrating a key role for SUMOylation in regulating the INO80 chromatin remodeling complex, this work illustrates the power of bioinformatics analysis of large data sets in predicting novel biological phenomena.
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Affiliation(s)
- Eric Cox
- From the ‡Biochemistry, Cellular and Molecular Biology Graduate Program
- §Solomon H. Snyder Department of Neuroscience
- ¶Department of Pharmacology and Molecular Sciences
| | | | - Ijeoma Uzoma
- ¶Department of Pharmacology and Molecular Sciences
| | | | - Catherine M Guzzo
- **Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Junseop Jeong
- ¶Department of Pharmacology and Molecular Sciences
- ‡‡Center for High-Throughput Biology
| | - Michael J Matunis
- **Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Heng Zhu
- ¶Department of Pharmacology and Molecular Sciences
- ‡‡Center for High-Throughput Biology
| | - Seth Blackshaw
- §Solomon H. Snyder Department of Neuroscience,
- ‡‡Center for High-Throughput Biology
- §§Institute for Cell Engineering
- ¶¶Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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