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Parfenyev SE, Shabelnikov SV, Tolkunova EN, Barlev NA, Mittenberg AG. p53 Affects Zeb1 Interactome of Breast Cancer Stem Cells. Int J Mol Sci 2023; 24:9806. [PMID: 37372954 DOI: 10.3390/ijms24129806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
P53 is a critical tumor suppressor that protects the integrity of genome and prevents cells from malignant transformation, including metastases. One of the driving forces behind the onset of metastases is the epithelial to mesenchymal transition (EMT) program. Zeb1 is one of the key transcription factors that govern EMT (TF-EMT). Therefore, the interaction and mutual influence of p53 and Zeb1 plays a critical role in carcinogenesis. Another important feature of tumors is their heterogeneity mediated by the presence of so-called cancer stem cells (CSCs). To this end, we have developed a novel fluorescent reporter-based approach to enrich the population of CSCs in MCF7 cells with inducible expression of Zeb1. Using these engineered cell lines, we studied the effect of p53 on Zeb1 interactomes isolated from both CSCs and regular cancer cells. By employing co-immunoprecipitations followed by mass spectrometry, we found that the composition of Zeb1 interactome was affected not only by the p53 status but also by the level of Oct4/Sox2 expression, indicating that stemness likely affects the specificity of Zeb1 interactions. This study, together with other proteomic studies of TF-EMT interactomes, provides a framework for future molecular analyses of biological functions of Zeb1 at all stages of oncogenesis.
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Affiliation(s)
- Sergey E Parfenyev
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Sergey V Shabelnikov
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Elena N Tolkunova
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Nickolai A Barlev
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana 20000, Kazakhstan
| | - Alexey G Mittenberg
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
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Sunna S, Bowen C, Zeng H, Rayaprolu S, Kumar P, Bagchi P, Dammer EB, Guo Q, Duong DM, Bitarafan S, Natu A, Wood L, Seyfried NT, Rangaraju S. Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines. Mol Cell Proteomics 2023; 22:100546. [PMID: 37061046 PMCID: PMC10205547 DOI: 10.1016/j.mcpro.2023.100546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
Different brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level can provide biological and therapeutic insights. To overcome the barriers of conventional isolation-based methods for cell type-specific proteomics, in vivo proteomic labeling with proximity-dependent biotinylation of cytosolic proteins using biotin ligase TurboID, coupled with mass spectrometry (MS) of labeled proteins, emerged as a powerful strategy for cell type-specific proteomics in the native state of cells without the need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID approach are representative of the whole-cell proteome and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing cytosolic TurboID to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. TurboID labeled endolysosome, translation, vesicle, and signaling proteins in BV2 microglia and synaptic, neuron projection, and microtubule proteins in N2A neurons. TurboID expression and biotinylation minimally impacted homeostatic cellular proteomes of BV2 and N2A cells and did not affect lipopolysaccharide-mediated cytokine production or resting cellular respiration in BV2 cells. MS analysis of the microglial biotin-labeled proteins captured the impact of lipopolysaccharide treatment (>500 differentially abundant proteins) including increased canonical proinflammatory proteins (Il1a, Irg1, and Oasl1) and decreased anti-inflammatory proteins (Arg1 and Mgl2).
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Affiliation(s)
- Sydney Sunna
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Christine Bowen
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Hollis Zeng
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Prateek Kumar
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Eric B Dammer
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Qi Guo
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Duc M Duong
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Sara Bitarafan
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Aditya Natu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Levi Wood
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA.
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Yheskel M, Sidoli S, Secombe J. Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. Epigenetics Chromatin 2023; 16:8. [PMID: 36803422 PMCID: PMC9938590 DOI: 10.1186/s13072-023-00481-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to demethylase-independent gene regulatory functions that remain less characterized. To expand our understanding of the mechanisms that contribute to KDM5-mediated transcription regulation, we used TurboID proximity labeling to identify KDM5-interacting proteins. RESULTS Using Drosophila melanogaster, we enriched for biotinylated proteins from KDM5-TurboID-expressing adult heads using a newly generated control for DNA-adjacent background in the form of dCas9:TurboID. Mass spectrometry analyses of biotinylated proteins identified both known and novel candidate KDM5 interactors, including members of the SWI/SNF and NURF chromatin remodeling complexes, the NSL complex, Mediator, and several insulator proteins. CONCLUSIONS Combined, our data shed new light on potential demethylase-independent activities of KDM5. In the context of KDM5 dysregulation, these interactions may play key roles in the alteration of evolutionarily conserved transcriptional programs implicated in human disorders.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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