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George J, Mittal S, Kadamberi IP, Pradeep S, Chaluvally-Raghavan P. Optimized proximity ligation assay (PLA) for detection of RNA-protein complex interactions in cell lines. STAR Protoc 2022; 3:101340. [PMID: 35620072 PMCID: PMC9127197 DOI: 10.1016/j.xpro.2022.101340] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Conventional proximity ligation assay (PLA) suffers from target specificity issues that curtail their accuracy on interpreting proximal interactions in cell biology. Here, we present a reliable and sensitive approach by including a fluorochrome-labeled mRNA fragment along with biotin-labeled RNA probe and a target-specific antibody, which were used to generate proximal ligation signals through linear connectors in intact cells. This protocol will be particularly useful for studying the proximal interactions between RNA binding proteins (RBPs) and their target mRNAs in cells. For complete details on the use and execution of this protocol, please refer to George et al. (2021). FXR1 binds to the AU-rich elements (ARE) within cMYC 3′UTR Use of fluorescence-labeled mRNA improves the specificity of PLA reaction Linear connectors linked to the probes produce high levels of PLA signals
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2
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Li Y, Liu S, Cao L, Luo Y, Du H, Li S, Zhang Z, Guo X, Tian W, Wong CC, You F. CBRPP: a new RNA-centric method to study RNA-protein interactions. RNA Biol 2021; 18:1608-1621. [PMID: 33596778 DOI: 10.1101/2020.04.09.033290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
RNA and protein are interconnected biomolecules that can influence each other's life cycles and functions through physical interactions. Abnormal RNA-protein interactions lead to cell dysfunctions and human diseases. Therefore, mapping networks of RNA-protein interactions is crucial for understanding cellular processes and pathogenesis of related diseases. Different practical protein-centric methods for studying RNA-protein interactions have been reported, but few robust RNA-centric methods exist. Here, we developed CRISPR-based RNA proximity proteomics (CBRPP), a new RNA-centric method to identify proteins associated with an endogenous RNA of interest in native cellular context without pre-editing of the target RNA, cross-linking or RNA-protein complexes manipulation in vitro. CBRPP is based on a fusion of dCas13 and proximity-based labelling (PBL) enzyme. dCas13 can deliver PBL enzyme to the target RNA with high specificity, while PBL enzyme labels the surrounding proteins of the target RNA, which are then identified by mass spectrometry.
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Affiliation(s)
- Yunfei Li
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Shengde Liu
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Lili Cao
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Yujie Luo
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Hongqiang Du
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Siji Li
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Zeming Zhang
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Xuefei Guo
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Wenmin Tian
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Beijing, China
| | - Catherine Cl Wong
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Beijing, China
| | - Fuping You
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
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3
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Li Y, Liu S, Cao L, Luo Y, Du H, Li S, Zhang Z, Guo X, Tian W, Wong CC, You F. CBRPP: a new RNA-centric method to study RNA-protein interactions. RNA Biol 2021; 18:1608-1621. [PMID: 33596778 DOI: 10.1080/15476286.2021.1873620] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA and protein are interconnected biomolecules that can influence each other's life cycles and functions through physical interactions. Abnormal RNA-protein interactions lead to cell dysfunctions and human diseases. Therefore, mapping networks of RNA-protein interactions is crucial for understanding cellular processes and pathogenesis of related diseases. Different practical protein-centric methods for studying RNA-protein interactions have been reported, but few robust RNA-centric methods exist. Here, we developed CRISPR-based RNA proximity proteomics (CBRPP), a new RNA-centric method to identify proteins associated with an endogenous RNA of interest in native cellular context without pre-editing of the target RNA, cross-linking or RNA-protein complexes manipulation in vitro. CBRPP is based on a fusion of dCas13 and proximity-based labelling (PBL) enzyme. dCas13 can deliver PBL enzyme to the target RNA with high specificity, while PBL enzyme labels the surrounding proteins of the target RNA, which are then identified by mass spectrometry.
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Affiliation(s)
- Yunfei Li
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Shengde Liu
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Lili Cao
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Yujie Luo
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Hongqiang Du
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Siji Li
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Zeming Zhang
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Xuefei Guo
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Wenmin Tian
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Beijing, China
| | - Catherine Cl Wong
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Beijing, China
| | - Fuping You
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
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4
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Blanchard EL, Argyropoulou D, Zurla C, Bhosle SM, Vanover D, Santangelo PJ. Quantification and Localization of Protein-RNA Interactions in Patient-Derived Archival Tumor Tissue. Cancer Res 2019; 79:5418-5431. [PMID: 31481502 DOI: 10.1158/0008-5472.can-19-1094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/24/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022]
Abstract
Abnormal post-transcriptional regulation induced by alterations of mRNA-protein interactions is critical during tumorigenesis and cancer progression and is a hallmark of cancer cells. A more thorough understanding is needed to develop treatments and foresee outcomes. Cellular and mouse tumor models are insufficient for vigorous investigation as they lack consistency and translatability to humans. Moreover, to date, studies in human tumor tissue are predominately limited to expression analysis of proteins and mRNA, which do not necessarily provide information about the frequency of mRNA-protein interactions. Here, we demonstrate novel optimization of a method that is based on FISH and proximity ligation techniques to quantify mRNA interactions with RNA-binding proteins relevant for tumorigenesis and cancer progression in archival patient-derived tumor tissue. This method was validated for multiple mRNA-protein pairs in several cellular models and in multiple types of archival human tumor samples. Furthermore, this approach allowed high-throughput analysis of mRNA-protein interactions across a wide range of tumor types and stages through tumor microarrays. This method is quantitative, specific, and sensitive for detecting interactions and their localization at both the individual cell and whole-tissue scales with single interaction sensitivity. This work presents an important tool in investigating post-transcriptional regulation in cancer on a high-throughput scale, with great potential for translatability into any applications where mRNA-protein interactions are of interest. SIGNIFICANCE: This work presents an approach to sensitively, specifically, and quantitatively detect and localize native mRNA and protein interactions for analysis of abnormal post-transcriptional regulation in patient-derived archival tumor samples.
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Affiliation(s)
- Emmeline L Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Danae Argyropoulou
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Sushma M Bhosle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
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5
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Blanchard EL, Loomis KH, Bhosle SM, Vanover D, Baumhof P, Pitard B, Zurla C, Santangelo PJ. Proximity Ligation Assays for In Situ Detection of Innate Immune Activation: Focus on In Vitro-Transcribed mRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 14:52-66. [PMID: 30579042 PMCID: PMC6304375 DOI: 10.1016/j.omtn.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 01/04/2023]
Abstract
The characterization of innate immune activation is crucial for vaccine and therapeutic development, including RNA-based vaccines, a promising approach. Current measurement methods quantify type I interferon and inflammatory cytokine production, but they do not allow for the isolation of individual pathways, do not provide kinetic activation or spatial information within tissues, and cannot be translated into clinical studies. Here we demonstrated the use of proximity ligation assays (PLAs) to detect pattern recognition receptor (PRR) activation in cells and in tissue samples. First, we validated PLA's sensitivity and specificity using well-characterized soluble agonists. Next, we characterized PRR activation from in vitro-transcribed (IVT) mRNAs, as well as the effect of sequence and base modifications in vitro. Finally, we established the measurement of PRR activation in tissue sections via PLA upon IVT mRNA intramuscular (i.m.) injection in mice. Overall, our results indicate that PLA is a valuable, versatile, and sensitive tool to monitor PRR activation for vaccine, adjuvant, and therapeutic screening.
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Affiliation(s)
- Emmeline L Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Building, Atlanta, GA 30332, USA
| | - Kristin H Loomis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Building, Atlanta, GA 30332, USA
| | - Sushma M Bhosle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Building, Atlanta, GA 30332, USA
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Building, Atlanta, GA 30332, USA
| | | | - Bruno Pitard
- In-Cell-Art, 21 rue de la Noue Bras de Fer, 44200 Nantes, France
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Building, Atlanta, GA 30332, USA
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Building, Atlanta, GA 30332, USA.
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6
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Loomis KH, Lindsay KE, Zurla C, Bhosle SM, Vanover DA, Blanchard EL, Kirschman JL, Bellamkonda RV, Santangelo PJ. In Vitro Transcribed mRNA Vaccines with Programmable Stimulation of Innate Immunity. Bioconjug Chem 2018; 29:3072-3083. [PMID: 30067354 DOI: 10.1021/acs.bioconjchem.8b00443] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In vitro transcribed (IVT) mRNA is an appealing platform for next generation vaccines, as it can be manufactured rapidly at large scale to meet emerging pathogens. However, its performance as a robust vaccine is strengthened by supplemental immune stimulation, which is typically provided by adjuvant formulations that facilitate delivery and stimulate immune responses. Here, we present a strategy for increasing translation of a model IVT mRNA vaccine while simultaneously modulating its immune-stimulatory properties in a programmable fashion, without relying on delivery vehicle formulations. Substitution of uridine with the modified base N1-methylpseudouridine reduces the intrinsic immune stimulation of the IVT mRNA and enhances antigen translation. Tethering adjuvants to naked IVT mRNA through antisense nucleotides boosts the immunostimulatory properties of adjuvants in vitro, without impairing transgene production or adjuvant activity. In vivo, intramuscular injection of tethered IVT mRNA-TLR7 agonists leads to enhanced local immune responses, and to antigen-specific cell-mediated and humoral responses. We believe this system represents a potential platform compatible with any adjuvant of interest to enable specific programmable stimulation of immune responses.
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Affiliation(s)
- Kristin H Loomis
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
| | - Kevin E Lindsay
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
| | - Sushma M Bhosle
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
| | - Daryll A Vanover
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
| | - Emmeline L Blanchard
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
| | - Jonathan L Kirschman
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
| | - Ravi V Bellamkonda
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Krone Engineering Biosystems Building, 950 Atlantic Drive , Atlanta , Georgia 30332 , United States
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7
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Unifying in vitro and in vivo IVT mRNA expression discrepancies in skeletal muscle via mechanotransduction. Biomaterials 2018; 159:189-203. [PMID: 29331806 DOI: 10.1016/j.biomaterials.2018.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 12/30/2017] [Accepted: 01/06/2018] [Indexed: 12/23/2022]
Abstract
The translational efficiency of an in vitro transcribed (IVT) mRNA was measured upon delivery to primary skeletal muscle cells and to a mouse model system, towards the development of a predictive in vitro assay for the screening and validation of intramuscular mRNA-based vaccines. When IVT mRNA was delivered either naked or complexed with novel aminoglycoside-based delivery vehicles, significant differences in protein expression in vitro and in vivo were observed. We hypothesized that this previously anticipated discrepancy was due to differences in the mechanism of IVT mRNA endosomal entry and release following delivery. To address this, IVT mRNA was fluorescently labeled prior to delivery, to visualize its distribution. Colocalization with endosomal markers indicated that different entry pathways were utilized in vivo and in vitro, depending on the delivery vehicle, resulting in variations in protein expression levels. Since extracellular matrix stiffness (ECM) influences mRNA entry, trafficking and release, the effect of mechanotransduction on mRNA expression was investigated in vitro upon delivery of IVT mRNA alone, and complexed with delivery vehicles to skeletal muscle cells grown on ∼10 kPa hydrogels. This in vitro hydrogel model more accurately recapitulated the results obtained in vivo upon IM injection, indicating that this approach may assist in the characterization of mRNA based vaccines.
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8
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Kirschman JL, Bhosle S, Vanover D, Blanchard EL, Loomis KH, Zurla C, Murray K, Lam BC, Santangelo PJ. Characterizing exogenous mRNA delivery, trafficking, cytoplasmic release and RNA-protein correlations at the level of single cells. Nucleic Acids Res 2017; 45:e113. [PMID: 28449134 PMCID: PMC5499550 DOI: 10.1093/nar/gkx290] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/06/2017] [Accepted: 04/11/2017] [Indexed: 12/25/2022] Open
Abstract
The use of synthetic messenger ribonucleic acid (mRNA) to express specific proteins is a highly promising therapeutic and vaccine approach that avoids many safety issues associated with viral or DNA-based systems. However, in order to optimize mRNA designs and delivery, technology advancements are required to study fundamental mechanisms of mRNA uptake and localization at the single-cell and tissue level. Here, we present a single RNA sensitive fluorescent labeling method which allows us to label and visualize synthetic mRNA without significantly affecting function. This approach enabled single cell characterization of mRNA uptake and release kinetics from endocytic compartments, the measurement of mRNA/protein correlations, and motivated the investigation of mRNA induced cellular stress, all important mechanisms influencing protein production. In addition, we demonstrated this approach can facilitate near-infrared imaging of mRNA localization in vivo and in ex-vivo tissue sections, which will facilitate mRNA trafficking studies in pre-clinical models. Overall, we demonstrate the ability to study fundamental mechanisms necessary to optimize delivery and therapeutic strategies, in order to design the next generation of novel mRNA therapeutics and vaccines.
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Affiliation(s)
- Jonathan L. Kirschman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Sushma Bhosle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Emmeline L. Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Kristin H. Loomis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Kathryn Murray
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Blaine C. Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
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9
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A Novel Method to Quantify RNA-Protein Interactions In Situ Using FMTRIP and Proximity Ligation. Methods Mol Biol 2017; 1468:155-70. [PMID: 27662876 DOI: 10.1007/978-1-4939-4035-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA binding proteins (RBP) and small RNAs regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNAs) through their interactions with specific cis-acting elements within target RNAs. Here, we describe a novel method to detect protein-mRNA interactions, which combines FLAG-peptide modified, multiply-labeled tetravalent RNA imaging probes (FMTRIPs) with proximity ligation (PLA), and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein-mRNA interactions with single-interaction sensitivity.
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10
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Zhang W, Xie M, Shu MD, Steitz JA, DiMaio D. A proximity-dependent assay for specific RNA-protein interactions in intact cells. RNA (NEW YORK, N.Y.) 2016; 22:1785-1792. [PMID: 27659050 PMCID: PMC5066630 DOI: 10.1261/rna.058248.116] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/25/2016] [Indexed: 05/05/2023]
Abstract
The proximity ligation assay (PLA) is an immune staining method that detects protein-protein interactions in fixed cells. We describe here RNA-PLA, a simple adaptation of this technology that allows the detection of specific RNA-protein interactions in fixed cells by using a DNA oligonucleotide that hybridizes to a target RNA in combination with an antibody that recognizes the protein bound to the target RNA. Stable and transient RNA-protein interactions can be readily detected by generation of a fluorescent signal in discrete compartments in intact fixed cells with high specificity. We demonstrate that this approach requires the colocalization of the binding protein and its RNA target in the same cellular compartment, use of an oligonucleotide complementary to the target RNA, and the presence of a binding site for the protein in the target RNA.
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Affiliation(s)
- Wei Zhang
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8005, USA
| | - Mingyi Xie
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06520-208024, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-208024, USA
| | - Mei-Di Shu
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06520-208024, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-208024, USA
| | - Joan A Steitz
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06520-208024, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-208024, USA
- Yale Cancer Center, New Haven, Connecticut 06520-8028, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8005, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-208024, USA
- Yale Cancer Center, New Haven, Connecticut 06520-8028, USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut 06520-208040, USA
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11
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Zurla C, Jung J, Santangelo PJ. Can we observe changes in mRNA "state"? Overview of methods to study mRNA interactions with regulatory proteins relevant in cancer related processes. Analyst 2016; 141:548-62. [PMID: 26605378 PMCID: PMC4701657 DOI: 10.1039/c5an01959a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA binding proteins (RBP) regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNA) through their interactions with specific cis-acting elements within target RNAs. Post-transcriptional regulatory mechanisms are directly involved in the control of the immune response and stress response and their alterations play a crucial role in cancer related processes. In this review, we discuss mRNAs and RNA binding proteins relevant to tumorigenesis, current methodologies for detecting RNA interactions, and last, we describe a novel method to detect such interactions, which combines peptide modified, RNA imaging probes (FMTRIPs) with proximity ligation (PLA) and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein-mRNA interactions with single-interaction sensitivity in situ.
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Affiliation(s)
- C Zurla
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - J Jung
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - P J Santangelo
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
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12
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Ulke‐Lemée A, Turner SR, MacDonald JA. In situ Analysis of Smoothelin‐like 1 and Calmodulin Interactions in Smooth Muscle Cells by Proximity Ligation. J Cell Biochem 2015; 116:2667-75. [DOI: 10.1002/jcb.25215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/22/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Annegret Ulke‐Lemée
- Department of Biochemistry and Molecular BiologyCumming School of MedicineUniversity of CalgaryCalgaryAlbertaT2N 4Z6Canada
| | - Sara R. Turner
- Department of Biochemistry and Molecular BiologyCumming School of MedicineUniversity of CalgaryCalgaryAlbertaT2N 4Z6Canada
| | - Justin A. MacDonald
- Department of Biochemistry and Molecular BiologyCumming School of MedicineUniversity of CalgaryCalgaryAlbertaT2N 4Z6Canada
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13
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O’Connor JW, Gomez EW. Cell adhesion and shape regulate TGF-beta1-induced epithelial-myofibroblast transition via MRTF-A signaling. PLoS One 2013; 8:e83188. [PMID: 24340092 PMCID: PMC3858353 DOI: 10.1371/journal.pone.0083188] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/10/2013] [Indexed: 01/08/2023] Open
Abstract
Myofibroblasts, specialized cells that play important roles in wound healing and fibrosis, can develop from epithelial cells through an epithelial-mesenchymal transition (EMT). During EMT, epithelial cells detach from neighboring cells and acquire an elongated, mesenchymal-like morphology. These phenotypic changes are accompanied by changes in gene expression patterns including upregulation of a variety of cytoskeletal associated proteins which contribute to the ability of myofibroblasts to exert large contractile forces. Here, the relationship between cell shape and cytoskeletal tension and the expression of cytoskeletal proteins in transforming growth factor (TGF)-β1-induced EMT is determined. We find that culturing cells in conditions which permit cell spreading and increased contractility promotes the increased expression of myofibroblast markers and cytoskeletal associated proteins. In contrast, blocking cell spreading prevents transdifferentiation to the myofibroblast phenotype. Furthermore, we find that cell shape regulates the expression of cytoskeletal proteins by controlling the subcellular localization of myocardin related transcription factor (MRTF)-A. Pharmacological inhibition of cytoskeletal tension or MRTF-A signaling blocks the acquisition of a myofibroblast phenotype in spread cells while overexpression of MRTF-A promotes the expression of cytoskeletal proteins for all cell shapes. These data suggest that cell shape is a critical determinant of myofibroblast development from epithelial cells.
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Affiliation(s)
- Joseph W. O’Connor
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Esther W. Gomez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Bioengineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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