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Miyazawa K, Itoh Y, Fu H, Miyazono K. Receptor-activated transcription factors and beyond: multiple modes of Smad2/3-dependent transmission of TGF-β signaling. J Biol Chem 2024; 300:107256. [PMID: 38569937 PMCID: PMC11063908 DOI: 10.1016/j.jbc.2024.107256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Transforming growth factor β (TGF-β) is a pleiotropic cytokine that is widely distributed throughout the body. Its receptor proteins, TGF-β type I and type II receptors, are also ubiquitously expressed. Therefore, the regulation of various signaling outputs in a context-dependent manner is a critical issue in this field. Smad proteins were originally identified as signal-activated transcription factors similar to signal transducer and activator of transcription proteins. Smads are activated by serine phosphorylation mediated by intrinsic receptor dual specificity kinases of the TGF-β family, indicating that Smads are receptor-restricted effector molecules downstream of ligands of the TGF-β family. Smad proteins have other functions in addition to transcriptional regulation, including post-transcriptional regulation of micro-RNA processing, pre-mRNA splicing, and m6A methylation. Recent technical advances have identified a novel landscape of Smad-dependent signal transduction, including regulation of mitochondrial function without involving regulation of gene expression. Therefore, Smad proteins are receptor-activated transcription factors and also act as intracellular signaling modulators with multiple modes of function. In this review, we discuss the role of Smad proteins as receptor-activated transcription factors and beyond. We also describe the functional differences between Smad2 and Smad3, two receptor-activated Smad proteins downstream of TGF-β, activin, myostatin, growth and differentiation factor (GDF) 11, and Nodal.
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Affiliation(s)
- Keiji Miyazawa
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan.
| | - Yuka Itoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hao Fu
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kohei Miyazono
- Department of Applied Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Cancer Invasion and Metastasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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2
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Sarma U, Ripka L, Anyaegbunam UA, Legewie S. Modeling Cellular Signaling Variability Based on Single-Cell Data: The TGFβ-SMAD Signaling Pathway. Methods Mol Biol 2023; 2634:215-251. [PMID: 37074581 DOI: 10.1007/978-1-0716-3008-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Nongenetic heterogeneity is key to cellular decisions, as even genetically identical cells respond in very different ways to the same external stimulus, e.g., during cell differentiation or therapeutic treatment of disease. Strong heterogeneity is typically already observed at the level of signaling pathways that are the first sensors of external inputs and transmit information to the nucleus where decisions are made. Since heterogeneity arises from random fluctuations of cellular components, mathematical models are required to fully describe the phenomenon and to understand the dynamics of heterogeneous cell populations. Here, we review the experimental and theoretical literature on cellular signaling heterogeneity, with special focus on the TGFβ/SMAD signaling pathway.
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Affiliation(s)
- Uddipan Sarma
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Lorenz Ripka
- Institute of Molecular Biology (IMB), Mainz, Germany
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Uchenna Alex Anyaegbunam
- Institute of Molecular Biology (IMB), Mainz, Germany
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Mainz, Germany.
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany.
- Stuttgart Research Center for Systems Biology, University of Stuttgart, Stuttgart, Germany.
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3
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Lönn P, Al-Amin RA, Doulabi EM, Heldin J, Gallini R, Björkesten J, Oelrich J, Kamali-Moghaddam M, Landegren U. Image-based high-throughput mapping of TGF-β-induced phosphocomplexes at a single-cell level. Commun Biol 2021; 4:1284. [PMID: 34773084 PMCID: PMC8590043 DOI: 10.1038/s42003-021-02798-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
Protein interactions and posttranslational modifications orchestrate cellular responses to e.g. cytokines and drugs, but it has been difficult to monitor these dynamic events in high-throughput. Here, we describe a semi-automated system for large-scale in situ proximity ligation assays (isPLA), combining isPLA in microtiter wells with automated microscopy and computer-based image analysis. Phosphorylations and interactions are digitally recorded along with subcellular morphological features. We investigated TGF-β-responsive Smad2 linker phosphorylations and complex formations over time and across millions of individual cells, and we relate these events to cell cycle progression and local cell crowding via measurements of DNA content and nuclear size of individual cells, and of their relative positions. We illustrate the suitability of this protocol to screen for drug effects using phosphatase inhibitors. Our approach expands the scope for image-based single cell analyses by combining observations of protein interactions and modifications with morphological details of individual cells at high throughput. To improve our ability to monitor cellular responses to e.g. cytokines or drugs, Lönn et al have developed a semi-automated system for large-scale in situ proximity ligation assays (isPLA) in HaCAT keratinocyte cells. Their approach expands the scope for image-based single cell analyses by combining observations of protein interactions and modifications with morphological details of individual cells at high throughput.
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Affiliation(s)
- Peter Lönn
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Rasel A Al-Amin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ehsan Manouchehri Doulabi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Heldin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Radiosa Gallini
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Björkesten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Oelrich
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Lindskog C, Backman M, Zieba A, Asplund A, Uhlén M, Landegren U, Pontén F. Proximity Ligation Assay as a Tool for Antibody Validation in Human Tissues. J Histochem Cytochem 2020; 68:515-529. [PMID: 32602410 DOI: 10.1369/0022155420936384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Immunohistochemistry (IHC) is the accepted standard for spatial analysis of protein expression in tissues. IHC is widely used for cancer diagnostics and in basic research. The development of new antibodies to proteins with unknown expression patterns has created a demand for thorough validation. We have applied resources from the Human Protein Atlas project and the Antibody Portal at National Cancer Institute to generate protein expression data for 12 proteins across 39 cancer cell lines and 37 normal human tissue types. The outcome of IHC on consecutive sections from both cell and tissue microarrays using two independent antibodies for each protein was compared with in situ proximity ligation (isPLA), where binding by both antibodies is required to generate detection signals. Semi-quantitative scores from IHC and isPLA were compared with expression of the corresponding 12 transcripts across all cell lines and tissue types. Our results show a more consistent correlation between mRNA levels and isPLA as compared to IHC. The main benefits of isPLA include increased detection specificity and decreased unspecific staining compared to IHC. We conclude that implementing isPLA as a complement to IHC for analysis of protein expression and in antibody validation pipelines can lead to more accurate localization of proteins in tissue.
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Affiliation(s)
- Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Max Backman
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Agata Zieba
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Cappelli C, Sepulveda H, Rivas S, Pola V, Urzúa U, Donoso G, Sagredo E, Carrero D, Casanova-Ortiz E, Sagredo A, González M, Manterola M, Nardocci G, Armisén R, Montecino M, Marcelain K. Ski Is Required for Tri-Methylation of H3K9 in Major Satellite and for Repression of Pericentromeric Genes: Mmp3, Mmp10 and Mmp13, in Mouse Fibroblasts. J Mol Biol 2020; 432:3222-3238. [PMID: 32198114 DOI: 10.1016/j.jmb.2020.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/23/2020] [Accepted: 03/11/2020] [Indexed: 11/27/2022]
Abstract
Several mechanisms directing a rapid transcriptional reactivation of genes immediately after mitosis have been described. However, little is known about the maintenance of repressive signals during mitosis. In this work, we address the role of Ski in the repression of gene expression during M/G1 transition in mouse embryonic fibroblasts (MEFs). We found that Ski localises as a distinct pair of dots at the pericentromeric region of mitotic chromosomes, and the absence of the protein is related to high acetylation and low tri-methylation of H3K9 in pericentromeric major satellite. Moreover, differential expression assays in early G1 cells showed that the presence of Ski is significantly associated with repression of genes localised nearby to pericentromeric DNA. In mitotic cells, chromatin immunoprecipitation assays confirmed the association of Ski to major satellite and the promoters of the most repressed genes: Mmp3, Mmp10 and Mmp13. These genes are at pericentromeric region of chromosome 9. In these promoters, the presence of Ski resulted in increased H3K9 tri-methylation levels. This Ski-dependent regulation is also observed during interphase. Consequently, Mmp activity is augmented in Ski-/- MEFs. Altogether, these data indicate that association of Ski with the pericentromeric region of chromosomes during mitosis is required to maintain the silencing bookmarks of underlying chromatin.
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Affiliation(s)
- Claudio Cappelli
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Instituto de Bioquimica y Microbiologia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Hugo Sepulveda
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Solange Rivas
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Víctor Pola
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Ulises Urzúa
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gerardo Donoso
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Eduardo Sagredo
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - David Carrero
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Emmanuel Casanova-Ortiz
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alfredo Sagredo
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marisel González
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marcia Manterola
- Instituto de Ciencias Biomédicas. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gino Nardocci
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Ricardo Armisén
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Martin Montecino
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Katherine Marcelain
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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Pang K, Hao L, Shi Z, Chen B, Pang H, Dong Y, Zhang Z, Dong B, Han C. Comprehensive gene expression analysis after ERH gene knockdown in human bladder cancer T24 cell lines. Gene 2020; 738:144475. [PMID: 32081697 DOI: 10.1016/j.gene.2020.144475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 01/07/2023]
Abstract
INTRODUCTION In this article, we utilized Ingenuity® Pathway Analysis (IPA®) bioinformatics analysis software and Metascape® bioinformatics analysis website tools to analyse the possible mechanism of ERH affecting tumourigenesis (proliferation and apoptosis) in bladder cancer (BC) T24 cells. METHODS The ERH gene was knocked down, and BC T24 cells were divided into ERH normal and knockdown groups. Affymetrix® gene expression microarrays were performed to obtain a differentially expressed gene list (DEGL) between the 2 groups. IPA® data analyses contain five modules: disease and function analysis, upstream analysis, regulator effects analysis, canonical pathway analysis and molecular network analysis. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were analysed by Metascape®. RESULTS The results of the gene expression profiling chip and the DEGL showed that 344 genes were upregulated and 254 genes were downregulated. The IPA® and Metascape® pathway analyses showed that the ERH gene may affect proliferation and apoptosis by affecting the apoptosis, cell cycle, Toll-like receptor (TLR), NF-κB or TGF-beta signalling pathways. Upstream analysis determined that the ERH gene may regulate TNF and NK-κB in the BC T24 cell lines. The ERH gene may be involved in the "cell death and survival" molecular network in BC T24 cells. ERH may be a regulator of KITLG through TNF. CONCLUSIONS The ERH gene may affect apoptosis through the TLR, NF-κB, TNF or TGF-beta signalling pathways in BC T24 cells, and may be a regulator of KITLG to ultimately activate the growth of malignant tumours.
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Affiliation(s)
- Kun Pang
- Department of Urology, The Third Affiliated Hospital of Soochow University, No. 185, Juqian Street, Changzhou City, Jiangsu Province, China; Department of Urology, Xuzhou Clinical School of Xuzhou Medical College, Xuzhou Central Hospital, No. 199 Jiefang South Road, Xuzhou, Jiangsu, China
| | - Lin Hao
- Department of Urology, The Third Affiliated Hospital of Soochow University, No. 185, Juqian Street, Changzhou City, Jiangsu Province, China; Department of Urology, Xuzhou Clinical School of Xuzhou Medical College, Xuzhou Central Hospital, No. 199 Jiefang South Road, Xuzhou, Jiangsu, China
| | - Zhenduo Shi
- Department of Urology, The Third Affiliated Hospital of Soochow University, No. 185, Juqian Street, Changzhou City, Jiangsu Province, China; Department of Urology, Xuzhou Clinical School of Xuzhou Medical College, Xuzhou Central Hospital, No. 199 Jiefang South Road, Xuzhou, Jiangsu, China
| | - Bo Chen
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical College, Xuzhou Central Hospital, No. 199 Jiefang South Road, Xuzhou, Jiangsu, China
| | - Huiqing Pang
- Department of Operating Room, Linyi Central Hospital, No. 17, Jiankang Road, Yishui, Shandong, China
| | - Yang Dong
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical College, Xuzhou Central Hospital, No. 199 Jiefang South Road, Xuzhou, Jiangsu, China
| | - Zhiguo Zhang
- Department of Urology, The Third Affiliated Hospital of Soochow University, No. 185, Juqian Street, Changzhou City, Jiangsu Province, China; Department of Urology, Xuzhou Clinical School of Xuzhou Medical College, Xuzhou Central Hospital, No. 199 Jiefang South Road, Xuzhou, Jiangsu, China
| | - Bingzheng Dong
- Department of Urology, The Third Affiliated Hospital of Soochow University, No. 185, Juqian Street, Changzhou City, Jiangsu Province, China; Department of Urology, Xuzhou Clinical School of Xuzhou Medical College, Xuzhou Central Hospital, No. 199 Jiefang South Road, Xuzhou, Jiangsu, China
| | - Conghui Han
- Department of Urology, The Third Affiliated Hospital of Soochow University, No. 185, Juqian Street, Changzhou City, Jiangsu Province, China; Department of Urology, Xuzhou Clinical School of Xuzhou Medical College, Xuzhou Central Hospital, No. 199 Jiefang South Road, Xuzhou, Jiangsu, China.
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7
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Tecalco-Cruz AC, Ríos-López DG, Vázquez-Victorio G, Rosales-Alvarez RE, Macías-Silva M. Transcriptional cofactors Ski and SnoN are major regulators of the TGF-β/Smad signaling pathway in health and disease. Signal Transduct Target Ther 2018; 3:15. [PMID: 29892481 PMCID: PMC5992185 DOI: 10.1038/s41392-018-0015-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 02/16/2018] [Accepted: 03/15/2018] [Indexed: 12/19/2022] Open
Abstract
The transforming growth factor-β (TGF-β) family plays major pleiotropic roles by regulating many physiological processes in development and tissue homeostasis. The TGF-β signaling pathway outcome relies on the control of the spatial and temporal expression of >500 genes, which depend on the functions of the Smad protein along with those of diverse modulators of this signaling pathway, such as transcriptional factors and cofactors. Ski (Sloan-Kettering Institute) and SnoN (Ski novel) are Smad-interacting proteins that negatively regulate the TGF-β signaling pathway by disrupting the formation of R-Smad/Smad4 complexes, as well as by inhibiting Smad association with the p300/CBP coactivators. The Ski and SnoN transcriptional cofactors recruit diverse corepressors and histone deacetylases to repress gene transcription. The TGF-β/Smad pathway and coregulators Ski and SnoN clearly regulate each other through several positive and negative feedback mechanisms. Thus, these cross-regulatory processes finely modify the TGF-β signaling outcome as they control the magnitude and duration of the TGF-β signals. As a result, any alteration in these regulatory mechanisms may lead to disease development. Therefore, the design of targeted therapies to exert tight control of the levels of negative modulators of the TGF-β pathway, such as Ski and SnoN, is critical to restore cell homeostasis under the specific pathological conditions in which these cofactors are deregulated, such as fibrosis and cancer. Proteins that repress molecular signaling through the transforming growth factor-beta (TGF-β) pathway offer promising targets for treating cancer and fibrosis. Marina Macías-Silva and colleagues from the National Autonomous University of Mexico in Mexico City review the ways in which a pair of proteins, called Ski and SnoN, interact with downstream mediators of TGF-β to inhibit the effects of this master growth factor. Aberrant levels of Ski and SnoN have been linked to diverse range of diseases involving cell proliferation run amok, and therapies that regulate the expression of these proteins could help normalize TGF-β signaling to healthier physiological levels. For decades, drug companies have tried to target the TGF-β pathway, with limited success. Altering the activity of these repressors instead could provide a roundabout way of remedying pathogenic TGF-β activity in fibrosis and oncology.
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Affiliation(s)
- Angeles C Tecalco-Cruz
- 1Instituto de Investigaciones Biomédicas at Universidad Nacional Autónoma de México, Mexico city, 04510 Mexico
| | - Diana G Ríos-López
- 2Instituto de Fisiología Celular at Universidad Nacional Autónoma de México, Mexico city, 04510 Mexico
| | | | - Reyna E Rosales-Alvarez
- 2Instituto de Fisiología Celular at Universidad Nacional Autónoma de México, Mexico city, 04510 Mexico
| | - Marina Macías-Silva
- 2Instituto de Fisiología Celular at Universidad Nacional Autónoma de México, Mexico city, 04510 Mexico
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8
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In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation. Mod Pathol 2018; 31:253-263. [PMID: 28937142 DOI: 10.1038/modpathol.2017.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 05/28/2017] [Accepted: 05/29/2017] [Indexed: 02/07/2023]
Abstract
Antibodies are important tools in anatomical pathology and research, but the quality of in situ protein detection by immunohistochemistry greatly depends on the choice of antibodies and the abundance of the targeted proteins. Many antibodies used in scientific research do not meet requirements for specificity and sensitivity. Accordingly, methods that improve antibody performance and produce quantitative data can greatly advance both scientific investigations and clinical diagnostics based on protein expression and in situ localization. We demonstrate here protocols for antibody labeling that allow specific protein detection in tissues via bright-field in situ proximity ligation assays, where each protein molecule must be recognized by two antibodies. We further demonstrate that single polyclonal antibodies or purified serum preparations can be used for these dual recognition assays. The requirement for protein recognition by pairs of antibody conjugates can significantly improve specificity of protein detection over single-binder assays.
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9
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Strasen J, Sarma U, Jentsch M, Bohn S, Sheng C, Horbelt D, Knaus P, Legewie S, Loewer A. Cell-specific responses to the cytokine TGFβ are determined by variability in protein levels. Mol Syst Biol 2018; 14:e7733. [PMID: 29371237 PMCID: PMC5787704 DOI: 10.15252/msb.20177733] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The cytokine TGFβ provides important information during embryonic development, adult tissue homeostasis, and regeneration. Alterations in the cellular response to TGFβ are involved in severe human diseases. To understand how cells encode the extracellular input and transmit its information to elicit appropriate responses, we acquired quantitative time-resolved measurements of pathway activation at the single-cell level. We established dynamic time warping to quantitatively compare signaling dynamics of thousands of individual cells and described heterogeneous single-cell responses by mathematical modeling. Our combined experimental and theoretical study revealed that the response to a given dose of TGFβ is determined cell specifically by the levels of defined signaling proteins. This heterogeneity in signaling protein expression leads to decomposition of cells into classes with qualitatively distinct signaling dynamics and phenotypic outcome. Negative feedback regulators promote heterogeneous signaling, as a SMAD7 knock-out specifically affected the signal duration in a subpopulation of cells. Taken together, we propose a quantitative framework that allows predicting and testing sources of cellular signaling heterogeneity.
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Affiliation(s)
- Jette Strasen
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Uddipan Sarma
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Marcel Jentsch
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Bohn
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Caibin Sheng
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Daniel Horbelt
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Petra Knaus
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | | | - Alexander Loewer
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany .,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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10
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Lucarelli P, Schilling M, Kreutz C, Vlasov A, Boehm ME, Iwamoto N, Steiert B, Lattermann S, Wäsch M, Stepath M, Matter MS, Heikenwälder M, Hoffmann K, Deharde D, Damm G, Seehofer D, Muciek M, Gretz N, Lehmann WD, Timmer J, Klingmüller U. Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression. Cell Syst 2018; 6:75-89.e11. [DOI: 10.1016/j.cels.2017.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 06/23/2017] [Accepted: 11/14/2017] [Indexed: 12/11/2022]
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11
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Ebai T, Souza de Oliveira FM, Löf L, Wik L, Schweiger C, Larsson A, Keilholtz U, Haybaeck J, Landegren U, Kamali-Moghaddam M. Analytically Sensitive Protein Detection in Microtiter Plates by Proximity Ligation with Rolling Circle Amplification. Clin Chem 2017; 63:1497-1505. [DOI: 10.1373/clinchem.2017.271833] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 05/04/2017] [Indexed: 12/31/2022]
Abstract
Abstract
BACKGROUND
Detecting proteins at low concentrations in plasma is crucial for early diagnosis. Current techniques in clinical routine, such as sandwich ELISA, provide sensitive protein detection because of a dependence on target recognition by pairs of antibodies, but detection of still lower protein concentrations is often called for. Proximity ligation assay with rolling circle amplification (PLARCA) is a modified proximity ligation assay (PLA) for analytically specific and sensitive protein detection via binding of target proteins by 3 antibodies, and signal amplification via rolling circle amplification (RCA) in microtiter wells, easily adapted to instrumentation in use in hospitals.
METHODS
Proteins captured by immobilized antibodies were detected using a pair of oligonucleotide-conjugated antibodies. Upon target recognition these PLA probes guided oligonucleotide ligation, followed by amplification via RCA of circular DNA strands that formed in the reaction. The RCA products were detected by horseradish peroxidase-labeled oligonucleotides to generate colorimetric reaction products with readout in an absorbance microplate reader.
RESULTS
We compared detection of interleukin (IL)-4, IL-6, IL-8, p53, and growth differentiation factor 15 (GDF-15) by PLARCA and conventional sandwich ELISA or immuno-RCA. PLARCA detected lower concentrations of proteins and exhibited a broader dynamic range compared to ELISA and iRCA using the same antibodies. IL-4 and IL-6 were detected in clinical samples at femtomolar concentrations, considerably lower than for ELISA.
CONCLUSIONS
PLARCA offers detection of lower protein levels and increased dynamic ranges compared to ELISA. The PLARCA procedure may be adapted to routine instrumentation available in hospitals and research laboratories.
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Affiliation(s)
- Tonge Ebai
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Liza Löf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lotta Wik
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Caroline Schweiger
- Charité Comprehensive Cancer Center, University of Berlin, Berlin, Germany
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Anders Larsson
- Department of Medical Sciences, Biochemical Structure and Function, Uppsala University, Uppsala, Sweden
| | - Ulrich Keilholtz
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Johannes Haybaeck
- Charité Comprehensive Cancer Center, University of Berlin, Berlin, Germany
- Department of Pathology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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12
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Close Encounters - Probing Proximal Proteins in Live or Fixed Cells. Trends Biochem Sci 2017; 42:504-515. [PMID: 28566215 DOI: 10.1016/j.tibs.2017.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 12/30/2022]
Abstract
The well-oiled machinery of the cellular proteome operates via variable expression, modifications, and interactions of proteins, relaying genomic and transcriptomic information to coordinate cellular functions. In recent years, a number of techniques have emerged that serve to identify sets of proteins acting in close proximity in the course of orchestrating cellular activities. These proximity-dependent assays, including BiFC, BioID, APEX, FRET, and isPLA, have opened up new avenues to examine protein interactions in live or fixed cells. We review herein the current status of proximity-dependent in situ techniques. We compare the advantages and limitations of the methods, underlining recent progress and the growing importance of these techniques in basic research, and we discuss their potential as tools for drug development and diagnostics.
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Abstract
How signaling pathways function reliably despite cellular variation remains a question in many systems. In the transforming growth factor-β (Tgf-β) pathway, exposure to ligand stimulates nuclear localization of Smad proteins, which then regulate target gene expression. Examining Smad3 dynamics in live reporter cells, we found evidence for fold-change detection. Although the level of nuclear Smad3 varied across cells, the fold change in the level of nuclear Smad3 was a more precise outcome of ligand stimulation. The precision of the fold-change response was observed throughout the signaling duration and across Tgf-β doses, and significantly increased the information transduction capacity of the pathway. Using single-molecule FISH, we further observed that expression of Smad3 target genes (ctgf, snai1, and wnt9a) correlated more strongly with the fold change, rather than the level, of nuclear Smad3. These findings suggest that some target genes sense Smad3 level relative to background, as a strategy for coping with cellular noise.
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Koos B, Söderberg O. Designing and Applying Proximity-Dependent Hybridization Chain Reaction. ACTA ACUST UNITED AC 2016; 85:19.28.1-19.28.13. [PMID: 27479504 DOI: 10.1002/cpps.9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Proximity-dependent hybridization chain reaction (proxHCR) is a novel technique for detection of protein interaction, post-translational modifications (PTMs), or protein expression. The method is based upon antibodies targeting the proteins of interest that are covalently conjugated to DNA oligonucleotides, which enables the induction of a hybridization chain reaction (HCR) to generate a fluorescent signal visible under a microscope. In contrast to the in situ proximity ligation assay (in situ PLA), which is another method that utilizes antibody-DNA conjugates to detect protein interactions, proxHCR does not require enzymatic steps. This makes proxHCR an inexpensive alternative to in situ PLA. Another potential advantage might be that proxHCR could more readily be adapted for use in automated staining procedures and in point-of-care devices, as all reagents can be stored at room temperature. This unit describes how the oligonucleotide system for proxHCR can be designed and a protocol for how to perform proxHCR is presented. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Björn Koos
- Max Planck Institute for Molecular Physiology, Department of Systemic Cell Biology, Dortmund, Germany
| | - Ola Söderberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
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15
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Blokzijl A, Zieba A, Hust M, Schirrmann T, Helmsing S, Grannas K, Hertz E, Moren A, Chen L, Söderberg O, Moustakas A, Dübel S, Landegren U. Single Chain Antibodies as Tools to Study transforming growth factor-β-Regulated SMAD Proteins in Proximity Ligation-Based Pharmacological Screens. Mol Cell Proteomics 2016; 15:1848-56. [PMID: 26929218 DOI: 10.1074/mcp.m115.055756] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Indexed: 02/06/2023] Open
Abstract
The cellular heterogeneity seen in tumors, with subpopulations of cells capable of resisting different treatments, renders single-treatment regimens generally ineffective. Accordingly, there is a great need to increase the repertoire of drug treatments from which combinations may be selected to efficiently target sets of pathological processes, while suppressing the emergence of resistance mutations. In this regard, members of the TGF-β signaling pathway may furnish new, valuable therapeutic targets. In the present work, we developed in situ proximity ligation assays (isPLA) to monitor the state of the TGF-β signaling pathway. Moreover, we extended the range of suitable affinity reagents for this analysis by developing a set of in-vitro-derived human antibody fragments (single chain fragment variable, scFv) that bind SMAD2 (Mothers against decapentaplegic 2), 3, 4, and 7 using phage display. These four proteins are all intracellular mediators of TGF-β signaling. We also developed an scFv specific for SMAD3 phosphorylated in the linker domain 3 (p179 SMAD3). This phosphorylation has been shown to inactivate the tumor suppressor function of SMAD3. The single chain affinity reagents developed in the study were fused tocrystallizable antibody fragments (Fc-portions) and expressed as dimeric IgG-like molecules having Fc domains (Yumabs), and we show that they represent valuable reagents for isPLA.Using these novel assays, we demonstrate that p179 SMAD3 forms a complex with SMAD4 at increased frequency during division and that pharmacological inhibition of cyclin-dependent kinase 4 (CDK4)(1) reduces the levels of p179SMAD3 in tumor cells. We further show that the p179SMAD3-SMAD4 complex is bound for degradation by the proteasome. Finally, we developed a chemical screening strategy for compounds that reduce the levels of p179SMAD3 in tumor cells with isPLA as a read-out, using the p179SMAD3 scFv SH544-IIC4. The screen identified two kinase inhibitors, known inhibitors of the insulin receptor, which decreased levels of p179SMAD3/SMAD4 complexes, thereby demonstrating the suitability of the recombinant affinity reagents applied in isPLA in screening for inhibitors of cell signaling.
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Affiliation(s)
- Andries Blokzijl
- From the ‡Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 85, Sweden; **YUMAB GmbH, Rebenring 33 Braunschweig 38106, Germany
| | - Agata Zieba
- From the ‡Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 85, Sweden;
| | - Michael Hust
- ‖Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstr. 7, Braunschweig 38106, Germany
| | - Thomas Schirrmann
- ‖Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstr. 7, Braunschweig 38106, Germany; **YUMAB GmbH, Rebenring 33 Braunschweig 38106, Germany
| | - Saskia Helmsing
- ‖Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstr. 7, Braunschweig 38106, Germany
| | - Karin Grannas
- From the ‡Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 85, Sweden
| | - Ellen Hertz
- From the ‡Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 85, Sweden
| | - Anita Moren
- §Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-751 24, Sweden
| | - Lei Chen
- From the ‡Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 85, Sweden
| | - Ola Söderberg
- From the ‡Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 85, Sweden
| | - Aristidis Moustakas
- §Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-751 24, Sweden, ¶Dept. of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 23, Sweden
| | - Stefan Dübel
- ‖Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstr. 7, Braunschweig 38106, Germany
| | - Ulf Landegren
- From the ‡Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 85, Sweden
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16
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Vanhatupa S, Ojansivu M, Autio R, Juntunen M, Miettinen S. Bone Morphogenetic Protein-2 Induces Donor-Dependent Osteogenic and Adipogenic Differentiation in Human Adipose Stem Cells. Stem Cells Transl Med 2015; 4:1391-402. [PMID: 26494778 DOI: 10.5966/sctm.2015-0042] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/10/2015] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED Bone morphogenetic protein-2 (BMP-2) is a growth factor used to stimulate bone regeneration in clinical applications. However, there are contradicting reports on the functionality of BMP-2 in human adipose stem cells (hASCs), which are frequently used in tissue engineering. In this study, we analyzed the effects of BMP-2 on SMAD1/5 signaling, proliferation, and differentiation in hASCs. Our results indicated that BMP-2 induced dose-dependent (25-100 ng/ml) activation of SMAD signaling. Furthermore, the cell proliferation analysis revealed that BMP-2 (100 ng/ml) consistently decreased the proliferation in all the cell lines studied. However, the analysis of the differentiation potential revealed that BMP-2 (100 ng/ml) exhibited a donor-dependent dual role, inducing both osteogenic and adipogenic differentiation in hASCs. The quantitative alkaline phosphatase (qALP) activity and mineralization levels were clearly enhanced in particular donor cell lines by BMP-2 stimulus. On the contrary, in other cell lines, qALP and mineralization levels were diminished and the lipid formation was enhanced. The current study also suggests that hASCs have accelerated biochemical responsiveness to BMP-2 stimulus in human serum-supplemented culture medium compared with fetal bovine serum. The production origin of the BMP-2 growth factor is also important for its response: BMP-2 produced in mammalian cells enhanced signaling and differentiation responses compared with BMP-2 produced in Escherichia coli. These results explain the existing contradiction in the reported BMP-2 studies and indicate the variability in the functional end mechanism of BMP-2-stimulated hASCs. SIGNIFICANCE This study examined how bone morphogenetic protein-2 (BMP-2) modulates the SMAD signaling mechanism and the proliferation and differentiation outcome of human adipose stem cells (hASCs) derived from several donors. The results indicate that BMP-2 triggers molecular SMAD signaling mechanisms in hASCs and regulates differentiation processes in human serum-culture conditions. Importantly, BMP-2 has dual activity, inducing osteogenic and adipogenic differentiation, subject to hASC donor line studied. These findings explain contradictory previous results and highlight the importance of further studies to understand how signaling pathways guide mesenchymal stem cell functions at the molecular level.
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Affiliation(s)
- Sari Vanhatupa
- Adult Stem Cell Research Group, University of Tampere, Tampere, Finland BioMediTech, University of Tampere, Tampere, Finland Science Center, Tampere University Hospital, Tampere, Finland
| | - Miina Ojansivu
- Adult Stem Cell Research Group, University of Tampere, Tampere, Finland BioMediTech, University of Tampere, Tampere, Finland Science Center, Tampere University Hospital, Tampere, Finland
| | - Reija Autio
- School of Health Sciences, University of Tampere, Tampere, Finland
| | - Miia Juntunen
- Adult Stem Cell Research Group, University of Tampere, Tampere, Finland BioMediTech, University of Tampere, Tampere, Finland Science Center, Tampere University Hospital, Tampere, Finland
| | - Susanna Miettinen
- Adult Stem Cell Research Group, University of Tampere, Tampere, Finland BioMediTech, University of Tampere, Tampere, Finland Science Center, Tampere University Hospital, Tampere, Finland
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17
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Buonato JM, Lan IS, Lazzara MJ. EGF augments TGFβ-induced epithelial-mesenchymal transition by promoting SHP2 binding to GAB1. J Cell Sci 2015; 128:3898-909. [PMID: 26359300 DOI: 10.1242/jcs.169599] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 09/03/2015] [Indexed: 01/17/2023] Open
Abstract
In many epithelial cells, epidermal growth factor (EGF) augments the epithelial-mesenchymal transition (EMT) that occurs when cells are treated with transforming growth factor β (TGFβ). We demonstrate that this augmentation requires activation of SH2 domain-containing phosphatase-2 (SHP2; also known as PTPN11), a proto-oncogene. In lung and pancreatic cancer cell lines, reductions in E-cadherin expression, increases in vimentin expression and increases in cell scatter rates were larger when cells were treated with TGFβ and EGF versus TGFβ or EGF alone. SHP2 knockdown promoted epithelial characteristics basally and antagonized EMT in response to TGFβ alone or in combination with EGF. Whereas EGF promoted SHP2 binding to tyrosine phosphorylated GAB1, which promotes SHP2 activity, TGFβ did not induce SHP2 association with phosphotyrosine-containing proteins. Knockdown of endogenous SHP2 and reconstitution with an SHP2 mutant with impaired phosphotyrosine binding ability eliminated the EGF-mediated EMT augmentation that was otherwise restored with wild-type SHP2 reconstitution. These results demonstrate roles for basal and ligand-induced SHP2 activity in EMT and further motivate efforts to identify specific ways to inhibit SHP2, given the role of EMT in tumor dissemination and chemoresistance.
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Affiliation(s)
- Janine M Buonato
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ingrid S Lan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew J Lazzara
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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18
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Grannas K, Arngården L, Lönn P, Mazurkiewicz M, Blokzijl A, Zieba A, Söderberg O. Crosstalk between Hippo and TGFβ: Subcellular Localization of YAP/TAZ/Smad Complexes. J Mol Biol 2015; 427:3407-15. [PMID: 25937570 DOI: 10.1016/j.jmb.2015.04.015] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/23/2015] [Accepted: 04/25/2015] [Indexed: 10/23/2022]
Abstract
The Hippo pathway plays a crucial role in growth control, proliferation and tumor suppression. Activity of the signaling pathway is associated with cell density sensing and tissue organization. Furthermore, the Hippo pathway helps to coordinate cellular processes through crosstalk with growth-factor-mediated signaling pathways such as TGFβ. Here we have examined the localization of interactions between proteins of the Hippo pathway (YAP/TAZ) and TGFβ (Smad2/3) signaling pathway by using in situ proximity ligation assays. We investigated the formation of protein complexes between YAP/TAZ and Smad2/3 and examined how these interactions were affected by TGFβ stimulation and cell density in HaCaT keratinocytes and in Smad4-deficient HT29 colon cancer cells. We demonstrate that TGFβ induces formation of YAP/TAZ-Smad2/3 complexes in HaCaT cells. Under sparse cell conditions, the complexes were detected to a higher degree and were predominantly located in the nucleus, while under dense culture conditions, the complexes were fewer and mainly located in the cytoplasm. Surprisingly, we could not detect any YAP/TAZ-Smad2/3 complexes in HT29 cells. To examine if Smad4 deficiency was responsible for the absence of interactions, we treated HaCaT cells with siRNA targeting Smad4. However, we could still observe complex formation in the siRNA-treated cells, suggesting that Smad4 is not essential for the YAP-Smad2/3 interaction. In conclusion, this study shows localized, density-dependent formation of YAP/TAZ-Smad2/3 complexes in HaCaT cells and provides evidence supporting a crosstalk between the Hippo and the TGFβ signaling pathways.
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Affiliation(s)
- Karin Grannas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Linda Arngården
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Peter Lönn
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Magdalena Mazurkiewicz
- Department of Oncology-Pathology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Andries Blokzijl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Agata Zieba
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Ola Söderberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden.
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19
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Nyati S, Schinske-Sebolt K, Pitchiaya S, Chekhovskiy K, Chator A, Chaudhry N, Dosch J, Van Dort ME, Varambally S, Kumar-Sinha C, Nyati MK, Ray D, Walter NG, Yu H, Ross BD, Rehemtulla A. The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-β signaling. Sci Signal 2015; 8:ra1. [PMID: 25564677 DOI: 10.1126/scisignal.2005379] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Transforming growth factor-β (TGF-β) signaling regulates cell proliferation and differentiation, which contributes to development and disease. Upon binding TGF-β, the type I receptor (TGFBRI) binds TGFBRII, leading to the activation of the transcription factors SMAD2 and SMAD3. Using an RNA interference screen of the human kinome and a live-cell reporter for TGFBR activity, we identified the kinase BUB1 (budding uninhibited by benzimidazoles-1) as a key mediator of TGF-β signaling. BUB1 interacted with TGFBRI in the presence of TGF-β and promoted the heterodimerization of TGFBRI and TGFBRII. Additionally, BUB1 interacted with TGFBRII, suggesting the formation of a ternary complex. Knocking down BUB1 prevented the recruitment of SMAD3 to the receptor complex, the phosphorylation of SMAD2 and SMAD3 and their interaction with SMAD4, SMAD-dependent transcription, and TGF-β-mediated changes in cellular phenotype including epithelial-mesenchymal transition (EMT), migration, and invasion. Knockdown of BUB1 also impaired noncanonical TGF-β signaling mediated by the kinases AKT and p38 MAPK (mitogen-activated protein kinase). The ability of BUB1 to promote TGF-β signaling depended on the kinase activity of BUB1. A small-molecule inhibitor of the kinase activity of BUB1 (2OH-BNPP1) and a kinase-deficient mutant of BUB1 suppressed TGF-β signaling and formation of the ternary complex in various normal and cancer cell lines. 2OH-BNPP1 administration to mice bearing lung carcinoma xenografts reduced the amount of phosphorylated SMAD2 in tumor tissue. These findings indicated that BUB1 functions as a kinase in the TGF-β pathway in a role beyond its established function in cell cycle regulation and chromosome cohesion.
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Affiliation(s)
- Shyam Nyati
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, MI 48109, USA. Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katerina Chekhovskiy
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Areeb Chator
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nauman Chaudhry
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph Dosch
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcian E Van Dort
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA. Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mukesh Kumar Nyati
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dipankar Ray
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, MI 48109, USA. Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongtao Yu
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brian Dale Ross
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alnawaz Rehemtulla
- Center for Molecular Imaging, University of Michigan, Ann Arbor, MI 48109, USA. Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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E-Cadherin and EpCAM expression by NSCLC tumour cells associate with normal fibroblast activation through a pathway initiated by integrin αvβ6 and maintained through TGFβ signalling. Oncogene 2014; 34:704-16. [PMID: 24488011 DOI: 10.1038/onc.2013.600] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/20/2013] [Accepted: 12/13/2013] [Indexed: 12/27/2022]
Abstract
Fibroblasts in the tumour stroma (cancer-associated fibroblasts) influence tumour progression and response to therapeutics; little is known about the mechanisms through which the tumour cell co-opts a normal fibroblast. To study the activation of fibroblasts by tumour cells, a panel of non-small cell lung cancer (NSCLC) cell lines and normal human dermal fibroblasts were co-cultured. A subset of the NSCLC cells induced an activated cancer-associated fibroblast-like fibroblast phenotype defined by induction of fibroblast α-smooth muscle actin expression. Tumour cells that activated fibroblasts were associated with E-Cadherin and EpCAM expression and expression of integrin αvβ6. Co-culture of activating tumour cells with fibroblasts resulted in induction of transcripts associated with tumour cell invasion and growth, TGFβ1 and TGFBR1, SERPINE-1, BMP6, SPHK1 and MMP9. Fibroblast activation was inhibited by an αvβ6/8 integrin blocking antibody (264RAD) and a small molecule inhibitor of the TGF-beta type I receptor activin-like kinase (ALK5) (SB431542), demonstrating that transactivation of the TGFβ pathway initiates fibroblast activation. Both integrin and ALK5 antagonists inhibited initiation. Only ALK5 was effective when added after 3 days of co-culture. This suggests that although activation is αvβ6-dependent, once fibroblasts are activated alternative TGFβ pathway regulators maintain an activation loop. In co-culture activating cells had reduced sensitivity to selumetinib, AZD8931 and afatinib compared with mono-culture. In contrast, non-activating cells were insensitive to selumetinib and AZD8931 in both mono-culture and co-culture. In conclusion NSCLC cell lines, positive for E-Cadherin, EpCAM and αvβ6 expression, activate normal fibroblasts through avβ6/TGFβ signalling in vitro, and influence both gene expression and response to therapeutic agents.
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21
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Role of Individual MARK Isoforms in Phosphorylation of Tau at Ser262 in Alzheimer’s Disease. Neuromolecular Med 2013; 15:458-69. [DOI: 10.1007/s12017-013-8232-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 04/24/2013] [Indexed: 12/28/2022]
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22
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Tgf-β1 inhibits Cftr biogenesis and prevents functional rescue of ΔF508-Cftr in primary differentiated human bronchial epithelial cells. PLoS One 2013; 8:e63167. [PMID: 23671668 PMCID: PMC3650079 DOI: 10.1371/journal.pone.0063167] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 03/28/2013] [Indexed: 11/19/2022] Open
Abstract
CFTR is an integral transmembrane glycoprotein and a cAMP-activated Cl(-) channel. Mutations in the CFTR gene lead to Cystic Fibrosis (CF)-an autosomal recessive disease with majority of the morbidity and mortality resulting from airway infection, inflammation, and fibrosis. The most common disease-associated mutation in the CFTR gene-deletion of Phe508 (ΔF508) leads to a biosynthetic processing defect of CFTR. Correction of the defect and delivery of ΔF508-CFTR to the cell surface has been highly anticipated as a disease modifying therapy. Compared to promising results in cultured cell this approach was much less effective in CF patients in an early clinical trial. Although the cause of failure to rescue ΔF508-CFTR in the clinical trial has not been determined, presence of factor(s) that interfere with the rescue in vivo could be considered. The cytokine TGF-β1 is frequently elevated in CF patients. TGF-β1 has pleiotropic effects in different disease models and genetic backgrounds and little is known about TGF-β1 effects on CFTR in human airway epithelial cells. Moreover, there are no published studies examining TGF-β1 effects on the functional rescue of ΔF508-CFTR. Here we found that TGF-β1 inhibits CFTR biogenesis by reducing mRNA levels and protein abundance in primary differentiated human bronchial epithelial (HBE) cells from non-CF individuals. TGF-β1 inhibits CFTR biogenesis without compromising the epithelial phenotype or integrity of HBE cells. TGF-β1 also inhibits biogenesis and impairs the functional rescue of ΔF508-CFTR in HBE cells from patients homozygous for the ΔF508 mutation. Our data indicate that activation of TGF-β1 signaling may inhibit CFTR function in non-CF individuals and may interfere with therapies directed at correcting the processing defect of ΔF508-CFTR in CF patients.
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23
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Differential regulation of Smad3 and of the type II transforming growth factor-β receptor in mitosis: implications for signaling. PLoS One 2012; 7:e43459. [PMID: 22927969 PMCID: PMC3425481 DOI: 10.1371/journal.pone.0043459] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/24/2012] [Indexed: 01/17/2023] Open
Abstract
The response to transforming growth factor-β (TGF-β) depends on cellular context. This context is changed in mitosis through selective inhibition of vesicle trafficking, reduction in cell volume and the activation of mitotic kinases. We hypothesized that these alterations in cell context may induce a differential regulation of Smads and TGF-β receptors. We tested this hypothesis in mesenchymal-like ovarian cancer cells, arrested (or not) in mitosis with 2-methoxyestradiol (2ME2). In mitosis, without TGF-β stimulation, Smad3 was phosphorylated at the C-terminus and linker regions and localized to the mitotic spindle. Phosphorylated Smad3 interacted with the negative regulators of Smad signaling, Smurf2 and Ski, and failed to induce a transcriptional response. Moreover, in cells arrested in mitosis, Smad3 levels were progressively reduced. These phosphorylations and reduction in the levels of Smad3 depended on ERK activation and Mps1 kinase activity, and were abrogated by increasing the volume of cells arrested in mitosis with hypotonic medium. Furthermore, an Mps1-dependent phosphorylation of GFP-Smad3 was also observed upon its over-expression in interphase cells, suggesting a mechanism of negative regulation which counters increases in Smad3 concentration. Arrest in mitosis also induced a block in the clathrin-mediated endocytosis of the type II TGF-β receptor (TβRII). Moreover, following the stimulation of mitotic cells with TGF-β, the proteasome-mediated attenuation of TGF-β receptor activity, the degradation and clearance of TβRII from the plasma membrane, and the clearance of the TGF-β ligand from the medium were compromised, and the C-terminus phosphorylation of Smad3 was prolonged. We propose that the reduction in Smad3 levels, its linker phosphorylation, and its association with negative regulators (observed in mitosis prior to ligand stimulation) represent a signal attenuating mechanism. This mechanism is balanced by the retention of active TGF-β receptors at the plasma membrane. Together, both mechanisms allow for a regulated cellular response to TGF-β stimuli in mitosis.
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