1
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Schulte S, Shin B, Rothenberg EV, Pierce NA. Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction. ACS Chem Biol 2024; 19:280-288. [PMID: 38232374 PMCID: PMC10877569 DOI: 10.1021/acschembio.3c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/18/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Signal amplification based on the mechanism of hybridization chain reaction (HCR) facilitates spatial exploration of gene regulatory networks by enabling multiplex, quantitative, high-resolution imaging of RNA and protein targets. Here, we extend these capabilities to the imaging of protein:protein complexes, using proximity-dependent cooperative probes to conditionally generate a single amplified signal if and only if two target proteins are colocalized within the sample. HCR probes and amplifiers combine to provide automatic background suppression throughout the protocol, ensuring that even if reagents bind nonspecifically in the sample, they will not generate amplified background. We demonstrate protein:protein imaging with a high signal-to-background ratio in human cells, mouse proT cells, and highly autofluorescent formalin-fixed paraffin-embedded (FFPE) human breast tissue sections. Further, we demonstrate multiplex imaging of three different protein:protein complexes simultaneously and validate that HCR enables accurate and precise relative quantitation of protein:protein complexes with subcellular resolution in an anatomical context. Moreover, we establish a unified framework for simultaneous multiplex, quantitative, high-resolution imaging of RNA, protein, and protein:protein targets, with one-step, isothermal, enzyme-free HCR signal amplification performed for all target classes simultaneously.
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Affiliation(s)
- Samuel
J. Schulte
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Boyoung Shin
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Ellen V. Rothenberg
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Niles A. Pierce
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Division
of Engineering and Applied Science, California
Institute of Technology, Pasadena, California 91125, United States
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2
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Wenson L, Leino M, Jarvius M, Heldin J, Koos B, Söderberg O. The method developer's guide to oligonucleotide design. Expert Rev Proteomics 2024; 21:65-80. [PMID: 38363709 DOI: 10.1080/14789450.2024.2318565] [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: 10/25/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
INTRODUCTION Development of new methods is essential to make great leaps in science, opening up new avenues for research, but the process behind method development is seldom described. AREAS COVERED Over the last twenty years we have been developing several new methods, such as in situ PLA, proxHCR, and MolBoolean, using oligonucleotide-conjugated antibodies to visualize protein-protein interactions. Herein, we describe the rationale behind the oligonucleotide systems of these methods. The main objective of this paper is to provide researchers with a description on how we thought when we designed those methods. We also describe in detail how the methods work and how one should interpret results. EXPERT OPINION Understanding how the methods work is important in selecting an appropriate method for your experiments. We also hope that this paper may be an inspiration for young researchers to enter the field of method development. Seeing a problem is a motivation to develop a solution.
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Affiliation(s)
- Leonie Wenson
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Mattias Leino
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Malin Jarvius
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Johan Heldin
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Björn Koos
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum-Langendreer, Ruhr-Universität Bochum, Bochum, Germany
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
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3
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Zhang L, He M, Wang P, Yu J, Li D. A protocol to investigate the effects of lncRNAs on in vivo protein-protein interactions using proximity ligation assay. STAR Protoc 2023; 4:102757. [PMID: 38043056 PMCID: PMC10701416 DOI: 10.1016/j.xpro.2023.102757] [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: 09/01/2023] [Revised: 11/01/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023] Open
Abstract
A large variety of cellular signals are triggered and transmitted by protein-protein interactions (PPIs). Long noncoding RNAs regulate PPIs by enhancing or destabilizing these interactions. Here, we use the proximity ligation assay technique to determine PPIs between p53 and SET regulated by long intergenic noncoding RNA 324 (LINC00324). We detail procedures for establishing LINC00324 knockdown and overexpression U2OS and HepG2 cells followed by in situ PLA protocol. This approach has many potential applications for the study of cellular factors that regulate PPIs. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2023).1.
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Affiliation(s)
- Ling Zhang
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China
| | - Mengfan He
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China
| | - Peizhen Wang
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China
| | - Jianfeng Yu
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China; Department of Life Science and Technology, Changshu Institute of Technology, 99 South Third Ring Road, Suzhou 215500, China
| | - Dawei Li
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China.
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4
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Fenstermaker TK, Petruk S, Kovermann SK, Brock HW, Mazo A. RNA polymerase II associates with active genes during DNA replication. Nature 2023; 620:426-433. [PMID: 37468626 DOI: 10.1038/s41586-023-06341-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
The transcriptional machinery is thought to dissociate from DNA during replication. Certain proteins, termed epigenetic marks, must be transferred from parent to daughter DNA strands in order to maintain the memory of transcriptional states1,2. These proteins are believed to re-initiate rebuilding of chromatin structure, which ultimately recruits RNA polymerase II (Pol II) to the newly replicated daughter strands. It is believed that Pol II is recruited back to active genes only after chromatin is rebuilt3,4. However, there is little experimental evidence addressing the central questions of when and how Pol II is recruited back to the daughter strands and resumes transcription. Here we show that immediately after passage of the replication fork, Pol II in complex with other general transcription proteins and immature RNA re-associates with active genes on both leading and lagging strands of nascent DNA, and rapidly resumes transcription. This suggests that the transcriptionally active Pol II complex is retained in close proximity to DNA, with a Pol II-PCNA interaction potentially underlying this retention. These findings indicate that the Pol II machinery may not require epigenetic marks to be recruited to the newly synthesized DNA during the transition from DNA replication to resumption of transcription.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sina K Kovermann
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hugh W Brock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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5
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Vistain L, Van Phan H, Keisham B, Jordi C, Chen M, Reddy ST, Tay S. Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing. Nat Methods 2022; 19:1578-1589. [PMID: 36456784 DOI: 10.1038/s41592-022-01684-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 10/13/2022] [Indexed: 12/04/2022]
Abstract
We present proximity sequencing (Prox-seq) for simultaneous measurement of proteins, protein complexes and mRNAs in thousands of single cells. Prox-seq combines proximity ligation assay with single-cell sequencing to measure proteins and their complexes from all pairwise combinations of targeted proteins, providing quadratically scaled multiplexing. We validate Prox-seq and analyze a mixture of T cells and B cells to show that it accurately identifies these cell types and detects well-known protein complexes. Next, by studying human peripheral blood mononuclear cells, we discover that naïve CD8+ T cells display the protein complex CD8-CD9. Finally, we study protein interactions during Toll-like receptor (TLR) signaling in human macrophages. We observe the formation of signal-specific protein complexes, find CD36 co-receptor activity and additive signal integration under lipopolysaccharide (TLR4) and Pam2CSK4 (TLR2) stimulation, and show that quantification of protein complexes identifies signaling inputs received by macrophages. Prox-seq provides access to an untapped measurement modality for single-cell phenotyping and can discover uncharacterized protein interactions in different cell types.
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Affiliation(s)
- Luke Vistain
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Bijentimala Keisham
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Christian Jordi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
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6
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Sharanek A, Raco L, Soleimani VD, Jahani-Asl A. In situ detection of protein-protein interaction by proximity ligation assay in patient derived brain tumor stem cells. STAR Protoc 2022; 3:101554. [PMID: 35880130 PMCID: PMC9307678 DOI: 10.1016/j.xpro.2022.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Improper or aberrant protein-protein interactions can lead to severe human diseases including cancer. Here, we describe an adapted proximity ligation assay (PLA) protocol for the assessment of galectin-1-HOXA5 interaction in brain tumor stem cells (BTSCs). We detail the steps for culturing and preparation of BTSCs followed by PLA and detection of protein interactions in situ using fluorescent microscopy. This PLA protocol is optimized specifically for BTSCs and includes key controls for effective result analysis. For complete details on the use and execution of this protocol, please refer to Sharanek et al. (2021). Proximity ligation assay to detect protein-protein interaction in BTSCs Optimized plating conditions for BTSC preparation using minute starting material Inclusion of appropriate controls for the PLA to ensure specificity and precision Alternative reagents and buffers to allow user to adapt the protocol to their needs
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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7
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Suraritdechachai S, Lakkanasirorat B, Uttamapinant C. Molecular probes for cellular imaging of post-translational proteoforms. RSC Chem Biol 2022; 3:201-219. [PMID: 35360891 PMCID: PMC8826509 DOI: 10.1039/d1cb00190f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.
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Affiliation(s)
- Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Benya Lakkanasirorat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
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8
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Iwabuchi E, Miki Y, Sasano H. The Visualization of Protein-Protein Interactions in Breast Cancer: Deployment Study in Pathological Examination. Acta Histochem Cytochem 2021; 54:177-183. [PMID: 35023880 PMCID: PMC8727844 DOI: 10.1267/ahc.21-00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/14/2021] [Indexed: 11/22/2022] Open
Abstract
The therapeutic strategy is determined by protein expression using immunohistochemistry of estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2 (HER2) in formalin-fixed paraffin-embedded (FFPE) breast cancer tissues. However, few proteins function independently, and many of them functions due to protein-protein interactions (PPIs) with other proteins. Therefore, it is important to focus on PPIs. This review summarizes the PPIs of ER and HER2 in breast cancer, especially those using a proximity ligation assay that can visualize PPIs in FFPE tissues. In particular, assessing the interaction of CEACAM6 with HER2 may serve as a surrogate marker for the efficacy of trastuzumab in patients with breast cancer. Therefore, in this review, the technique used to detect the interaction of CEACAM6 and HER2 in routinely processed pathological specimens will be applied to the clinical practice of drug selection. We showed the possibility as a novel pathological examination method using PPIs.
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Affiliation(s)
- Erina Iwabuchi
- Department of Pathology, Tohoku University Graduate School of Medicine
| | - Yasuhiro Miki
- Department of Disaster Obstetrics and Gynecology, International Research Institute of Disaster Science (IRIDes), Tohoku University
| | - Hironobu Sasano
- Department of Pathology, Tohoku University Graduate School of Medicine
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9
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Multiplex protein profiling method for extracellular vesicle protein detection. Sci Rep 2021; 11:12477. [PMID: 34127763 PMCID: PMC8203679 DOI: 10.1038/s41598-021-92012-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/21/2021] [Indexed: 12/21/2022] Open
Abstract
Extracellular vesicles (EVs) are small nanometer-sized membrane sacs secreted into biological fluids by all cells. EVs encapsulate proteins, RNAs and metabolites from its origin cell and play important roles in intercellular communication events. Over the past decade, EVs have become a new emerging source for cancer diagnostics. One of the challenges in the study of EVs and there utility as diagnostic biomarkers is the amount of EVs needed for traditional protein analysis methods. Here, we present a new immuno-PCR method that takes advantage of commercially available TotalSeq antibodies containing DNA conjugated oligos to identify immobilized protein analysts using real-time qPCR. Using this method, we demonstrate that multiple EV surface proteins can be profiled simultaneously with high sensitivity and specificity. This approach was also successfully applied to similar protocol using cell and serum samples. We further described the development of a micro-size exclusion chromatography method, where we were able to detect EV surface proteins with as little as 10 μL of human serum when combined with immuno-PCR. Overall, these results show that the immuno-PCR method results in rapid detection of multiple EV markers from small sample volumes in a single tube.
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10
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Francés-Soriano L, Leino M, Dos Santos MC, Kovacs D, Borbas KE, Söderberg O, Hildebrandt N. In Situ Rolling Circle Amplification Förster Resonance Energy Transfer (RCA-FRET) for Washing-Free Real-Time Single-Protein Imaging. Anal Chem 2021; 93:1842-1850. [PMID: 33356162 DOI: 10.1021/acs.analchem.0c04828] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescence signal enhancement via isothermal nucleic acid amplification is an important approach for sensitive imaging of intra- or extracellular nucleic acid or protein biomarkers. Rolling circle amplification (RCA) is frequently applied for fluorescence in situ imaging but faces limitations concerning multiplexing, dynamic range, and the required multiple washing steps before imaging. Here, we show that Förster resonance energy transfer (FRET) between fluorescent dyes and between lanthanide (Ln) complexes and dyes that hybridize to β-actin-specific RCA products in HaCaT cells can afford washing-free imaging of single β-actin proteins. Proximity-dependent FRET could be monitored directly after or during (real-time monitoring) dye or Ln DNA probe incubation and could efficiently distinguish between photoluminescence from β-actin-specific RCA and DNA probes freely diffusing in solution or nonspecifically attached to cells. Moreover, time-gated FRET imaging with the Ln-dye FRET pairs efficiently suppressed sample autofluorescence and improved the signal-to-background ratio. Our results present an important proof of concept of RCA-FRET imaging with a strong potential to advance in situ RCA toward easier sample preparation, higher-order multiplexing, autofluorescence-free detection, and increased dynamic range by real-time monitoring of in situ RCA.
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Affiliation(s)
- Laura Francés-Soriano
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Mattias Leino
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, 75124 Uppsala, Sweden
| | - Marcelina Cardoso Dos Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Daniel Kovacs
- Department of Chemistry, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - K Eszter Borbas
- Department of Chemistry, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, 75124 Uppsala, Sweden
| | - Niko Hildebrandt
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
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11
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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: 1.3] [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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12
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SYNPLA, a method to identify synapses displaying plasticity after learning. Proc Natl Acad Sci U S A 2020; 117:3214-3219. [PMID: 31974314 DOI: 10.1073/pnas.1919911117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Which neural circuits undergo synaptic changes when an animal learns? Although it is widely accepted that changes in synaptic strength underlie many forms of learning and memory, it remains challenging to connect changes in synaptic strength at specific neural pathways to specific behaviors and memories. Here we introduce SYNPLA (synaptic proximity ligation assay), a synapse-specific, high-throughput, and potentially brain-wide method capable of detecting circuit-specific learning-induced synaptic plasticity.
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13
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Peckys DB, Hirsch D, Gaiser T, de Jonge N. Visualisation of HER2 homodimers in single cells from HER2 overexpressing primary formalin fixed paraffin embedded tumour tissue. Mol Med 2019; 25:42. [PMID: 31455202 PMCID: PMC6712713 DOI: 10.1186/s10020-019-0108-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022] Open
Abstract
Background HER2 is considered as one of the most important, predictive biomarkers in oncology. The diagnosis of HER2 positive cancer types such as breast- and gastric cancer is usually based on immunohistochemical HER2 staining of tumour tissue. However, the current immunohistochemical methods do not provide localized information about HER2’s functional state. In order to generate signals leading to cell growth and proliferation, the receptor spontaneously forms homodimers, a process that can differ between individual cancer cells. Materials and methods HER2 overexpressing tumour cells were dissociated from formalin-fixed paraffin-embedded (FFPE) patient’s biopsy sections, subjected to a heat-induced antigen retrieval procedure, and immobilized on microchips. HER2 was specifically labelled via a two-step protocol involving the incubation with an Affibody-biotin compound followed by the binding of a streptavidin coated quantum dot (QD) nanoparticle. Cells with membrane bound HER2 were identified using fluorescence microscopy, coated with graphene to preserve their hydrated state, and subsequently examined by scanning transmission electron microscopy (STEM) to obtain the locations at the single molecule level. Label position data was statistically analysed via the pair correlation function, yielding information about the presence of HER2 homodimers. Results Tumour cells from two biopsies, scored HER2 3+, and a HER2 negative control sample were examined. The specific labelling protocol was first tested for a sectioned tissue sample of HER2-overexpressing tumour. Subsequently, a protocol was optimized to study HER2 homodimerization in single cells dissociated from the tissue section. Electron microscopy data showed membrane bound HER2 in average densities of 201–689 proteins/μm2. An automated, statistical analysis of well over 200,000 of measured protein positions revealed the presence of HER2 homodimers in 33 and 55% of the analysed images for patient 1 and 2, respectively. Conclusions We introduced an electron microscopy method capable of measuring the positions of individually labelled HER2 proteins in patient tumour cells from which information about the functional status of the receptor was derived. This method could take HER2 testing a step further by examining HER2 homodimerization directly out of tumour tissue and may become important for adjusting a personalized antibody-based drug therapy. Electronic supplementary material The online version of this article (10.1186/s10020-019-0108-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana B Peckys
- Department of Biophysics, Saarland University, Homburg, Germany
| | - Daniela Hirsch
- Institute for Pathology, University Medical Center Mannheim, Ruprecht-Karls University of Heidelberg, Mannheim, Germany
| | - Timo Gaiser
- Institute for Pathology, University Medical Center Mannheim, Ruprecht-Karls University of Heidelberg, Mannheim, Germany
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, Campus D2-2, 66123, Saarbrücken, Germany. .,Department of Physics, Saarland University, Saarbrücken, Germany.
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14
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Karchugina S, Chernoff J. Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay. J Vis Exp 2018. [PMID: 30394375 DOI: 10.3791/57755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Regulated protein-protein interactions are a guiding principle for many signaling events, and the detection of such events is an important element in understanding how such pathways are organized and how they function. There are many methods to detect protein-protein interactions in cells, but relatively few can be used to detect interactions between endogenous proteins. One such method, the proximity ligation assay (PLA), has several advantages to recommend its use. Compared to other common methods of protein-protein interaction analysis, PLA has relatively high sensitivity and specificity, can be performed with minimal cell manipulation, and, in the protocol described herein, requires only two target-specific antibodies derived from different species (e.g., from mouse and rabbit) and one specialized reagent: a set of secondary antibodies that are covalently linked to specific oligonucleotides that, when brought in close proximity of one another, create an amplifiable platform for in situ PCR or rolling circle amplification. In this presentation, we show how to apply the PLA technique to visualize changes in MST1 and MST2 proximity in fixed cells. The technique described in this manuscript is particularly applicable for the analysis of cell signaling studies.
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15
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Klaesson A, Grannas K, Ebai T, Heldin J, Koos B, Leino M, Raykova D, Oelrich J, Arngården L, Söderberg O, Landegren U. Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes. Sci Rep 2018; 8:5400. [PMID: 29599435 PMCID: PMC5876389 DOI: 10.1038/s41598-018-23582-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 03/14/2018] [Indexed: 12/26/2022] Open
Abstract
We have redesigned probes for in situ proximity ligation assay (PLA), resulting in more efficient localized detection of target proteins. In situ PLA depends on recognition of target proteins by pairs of antibody-oligonucleotide conjugates (PLA probes), which jointly give rise to DNA circles that template localized rolling circle amplification reactions. The requirement for dual recognition of the target proteins improves selectivity by ignoring any cross-reactivity not shared by the antibodies, and it allows detection of protein-protein interactions and post-translational modifications. We herein describe an improved design of the PLA probes –UnFold probes – where all elements required for formation of circular DNA strands are incorporated in the probes. Premature interactions between the UnFold probes are prevented by including an enzymatic “unfolding” step in the detection reactions. This allows DNA circles to form by pairs of reagents only after excess reagents have been removed. We demonstrate the performance of UnFold probes for detection of protein-protein interactions and post-translational modifications in fixed cells and tissues, revealing considerably more efficient signal generation. We also apply the UnFold probes to detect IL-6 in solution phase after capture on solid supports, demonstrating increased sensitivity over both normal sandwich enzyme-linked immunosorbent assays and conventional PLA assays.
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Affiliation(s)
- Axel Klaesson
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Karin Grannas
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Tonge Ebai
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Heldin
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Björn Koos
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Mattias Leino
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Doroteya Raykova
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Johan Oelrich
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Linda Arngården
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden.
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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16
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Kang CC, Ward TM, Bockhorn J, Schiffman C, Huang H, Pegram MD, Herr AE. Electrophoretic cytopathology resolves ERBB2 forms with single-cell resolution. NPJ Precis Oncol 2018; 2:10. [PMID: 29872719 PMCID: PMC5871910 DOI: 10.1038/s41698-018-0052-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 02/10/2018] [Accepted: 02/20/2018] [Indexed: 12/20/2022] Open
Abstract
In addition to canonical oncoproteins, truncated isoforms and proteolysis products are implicated in both drug resistance and disease progression. In HER2-positive breast tumors, expression of truncated HER2 isoforms resulting from alternative translation and/or carboxy-terminal fragments (CTFs) resulting from proteolysis (collectively, t-erbB2) have been associated with shortened progression-free survival of patients. Thus, to advance clinical pathology and inform treatment decisions, we developed a high-selectivity cytopathology assay capable of distinguishing t-erbB2 from full-length HER2 expression without the need for isoform-specific antibodies. Our microfluidic, single-cell western blot, employs electrophoretic separations to resolve full-length HER2 from the smaller t-erbB2 in each ~28 pL single-cell lysate. Subsequently, a pan-HER2 antibody detects all resolved HER2 protein forms via immunoprobing. In analysis of eight breast tumor biopsies, we identified two tumors comprised of 15% and 40% t-erbB2-expressing cells. By single-cell western blotting of the t-erbB2-expressing cells, we observed statistically different ratios of t-erbB2 proteins to full-length HER2 expression. Further, target multiplexing and clustering analyses scrutinized signaling, including ribosomal S6, within the t-erbB2-expressing cell subpopulation. Taken together, cytometric assays that report both protein isoform profiles and signaling state offer cancer classification taxonomies with unique relevance to precisely describing drug resistance mechanisms in which oncoprotein isoforms/fragments are implicated.
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Affiliation(s)
- Chi-Chih Kang
- 1Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720 USA
| | - Toby M Ward
- 2Division of Medical Oncology, Department of Medicine, Stanford University, Stanford, CA 94305 USA
| | - Jessica Bockhorn
- 2Division of Medical Oncology, Department of Medicine, Stanford University, Stanford, CA 94305 USA
| | - Courtney Schiffman
- 3Division of Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA 94720 USA
| | - Haiyan Huang
- 4Department of Statistics, University of California Berkeley, Berkeley, CA 94720 USA
| | - Mark D Pegram
- 2Division of Medical Oncology, Department of Medicine, Stanford University, Stanford, CA 94305 USA
| | - Amy E Herr
- 1Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720 USA
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17
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Li T, Hodgson JW, Petruk S, Mazo A, Brock HW. Additional sex combs interacts with enhancer of zeste and trithorax and modulates levels of trimethylation on histone H3K4 and H3K27 during transcription of hsp70. Epigenetics Chromatin 2017; 10:43. [PMID: 28927461 PMCID: PMC5605996 DOI: 10.1186/s13072-017-0151-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/13/2017] [Indexed: 11/10/2022] Open
Abstract
Background Maintenance of cell fate determination requires the Polycomb group for repression; the trithorax group for gene activation; and the enhancer of trithorax and Polycomb (ETP) group for both repression and activation. Additional sex combs (Asx) is a genetically identified ETP for the Hox loci, but the molecular basis of its dual function is unclear. Results We show that in vitro, Asx binds directly to the SET domains of the histone methyltransferases (HMT) enhancer of zeste [E(z)] (H3K27me3) and Trx (H3K4me3) through a bipartite interaction site separated by 846 amino acid residues. In Drosophila S2 cell nuclei, Asx interacts with E(z) and Trx in vivo. Drosophila Asx is required for repression of heat-shock gene hsp70 and is recruited downstream of the hsp70 promoter. Changes in the levels of H3K4me3 and H3K27me3 downstream of the hsp70 promoter in Asx mutants relative to wild type show that Asx regulates H3K4 and H3K27 trimethylation. Conclusions We propose that during transcription Asx modulates the ratio of H3K4me3 to H3K27me3 by selectively recruiting the antagonistic HMTs, E(z) and Trx or other nucleosome-modifying enzymes to hsp70. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0151-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taosui Li
- Department of Zoology, Life Sciences Institute, University of British Columbia, 2350 Health Science Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jacob W Hodgson
- Department of Zoology, Life Sciences Institute, University of British Columbia, 2350 Health Science Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Hugh W Brock
- Department of Zoology, Life Sciences Institute, University of British Columbia, 2350 Health Science Mall, Vancouver, BC, V6T 1Z4, Canada.
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18
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Peckys DB, Korf U, Wiemann S, de Jonge N. Liquid-phase electron microscopy of molecular drug response in breast cancer cells reveals irresponsive cell subpopulations related to lack of HER2 homodimers. Mol Biol Cell 2017; 28:mbc.E17-06-0381. [PMID: 28794264 PMCID: PMC5687022 DOI: 10.1091/mbc.e17-06-0381] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 12/31/2022] Open
Abstract
The development of drug resistance in cancer poses a major clinical problem. An example is human epidermal growth factor receptor 2 (HER2) overexpressing breast cancer often treated with anti-HER2 antibody therapies, such as trastuzumab. Since drug resistance is rooted mainly in tumor cell heterogeneity, we examined the drug effect in different subpopulations of SKBR3 breast cancer cells, and compared the results with a drug resistant cell line, HCC1954. Correlative light microscopy and liquid-phase scanning transmission electron microscopy (STEM) were used to quantitatively analyze HER2 responses upon drug binding, whereby many tens of whole cells were imaged. Trastuzumab was found to selectively cross-link and down regulate HER2 homodimers from the plasma membranes of bulk cancer cells. In contrast, HER2 resided mainly as monomers in rare subpopulations of resting- and cancer stem cells (CSCs), and these monomers were not internalized after drug binding. The HER2 distribution was hardly influenced by trastuzumab for the HCC1954 cells. These findings show that resting cells and CSCs are irresponsive to the drug, and thus point towards a molecular explanation behind the origin of drug resistance. This analytical method is broadly applicable to study membrane protein interactions in the intact plasma membrane, while accounting for cell heterogeneity.
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Affiliation(s)
- Diana B Peckys
- Department of Biophysics, Saarland University, D-66421 Homburg, Germany
| | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
- Department of Physics, Saarland University, 66123 Saarbrücken, Germany
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19
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Löf L, Arngården L, Ebai T, Landegren U, Söderberg O, Kamali-Moghaddam M. Detection of Extracellular Vesicles Using Proximity Ligation Assay with Flow Cytometry Readout-ExoPLA. ACTA ACUST UNITED AC 2017; 81:4.8.1-4.8.10. [PMID: 28678418 DOI: 10.1002/cpcy.22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Extracellular vesicles (EVs) are continuously released by most cells, and they carry surface markers of their cells of origin. Found in all body fluids, EVs function as conveyers of cellular information, and evidence implicates them as markers of disease. These characteristics make EVs attractive diagnostic targets. However, detection and characterization of EVs is challenging due to their small size. We've established a method, called ExoPLA, that allows individual EVs to be detected and characterized at high specificity and sensitivity. Based on the in situ proximity ligation assay (in situ PLA), proximal oligonucleotide-conjugated antibodies bound to their targets on the surfaces of the EVs allow formation of circular products that can be fluorescently labeled by rolling circle amplification. The intense fluorescent signals produced in this assay allow detection and enumeration of individual EVs by flow cytometry. We describe the procedures for ExoPLA, along with expected results and troubleshooting. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Liza Löf
- Department of Immunology, Genetics & Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Linda Arngården
- Department of Immunology, Genetics & Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tonge Ebai
- Department of Immunology, Genetics & Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics & Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics & Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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20
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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: 5.0] [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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21
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DE JONGE N. Membrane protein stoichiometry studied in intact mammalian cells using liquid-phase electron microscopy. J Microsc 2017; 269:134-142. [DOI: 10.1111/jmi.12570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/15/2017] [Accepted: 03/25/2017] [Indexed: 02/02/2023]
Affiliation(s)
- N. DE JONGE
- Leibniz Institute for New Materials; Saarbrücken Germany
- Department of Physics; University of Saarland; Saarbrücken Germany
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22
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Verset L, Tommelein J, Decaestecker C, De Vlieghere E, Bracke M, Salmon I, De Wever O, Demetter P. ADAM-17/FHL2 colocalisation suggests interaction and role of these proteins in colorectal cancer. Tumour Biol 2017; 39:1010428317695024. [PMID: 28349819 DOI: 10.1177/1010428317695024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
FHL2 is a multifunctional scaffolding protein; its expression is associated with poor prognosis in colorectal cancer. ADAM-17 is a metalloprotease implicated in ectodomain shedding. FHL2 regulates ADAM-17 plasma membrane localisation, and FHL2 deficiency leads to decreased activity of ADAM-17 in mouse macrophages. Presence and relationship of the ADAM-17/FHL2 complex with colorectal cancer progression is unknown. We studied FHL2 and ADAM-17 expression in several colon cancer cell lines by immunocytochemistry and western blot. To highlight the interaction between both molecules, we used the Duolink® kit for proximity ligation assay on SW480 cells. We also performed proximity ligation assay on biopsies and surgical specimens of colorectal adenocarcinoma and on matched normal mucosa. Furthermore, biopsies of colorectal adenoma with matched normal mucosa were selected. For quantification, pictures of the malignant, adenomatous and normal tissues were taken. Proximity ligation assay signals were quantified. Mean numbers of proximity ligation assay signals and of proximity ligation assay signals/nucleus were calculated. All cell lines showed FHL2 immunoreactivity; strongest positivity was observed in SW480 cells. ADAM-17 was expressed in all cell lines. Proximity ligation assay signals were present in SW480 cells. Quantitative analysis revealed that the interaction between FHL2 and ADAM-17 is more frequent in malignant than in normal tissue (p = 0.005). The mean number of ADAM-17/FHL2 proximity ligation assay signals was higher in colorectal adenocarcinoma than in adenoma with low-grade dysplasia (p = 0.0004). FHL2 interacts with ADAM-17 in normal, dysplastic and malignant colon epithelial cells. Colocalisation of these proteins is more frequent in malignant than in normal and dysplastic cells, suggesting a role for ADAM-17/FHL2 complex in the development of colorectal cancer.
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Affiliation(s)
- Laurine Verset
- 1 Department of Pathology, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Joke Tommelein
- 2 Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Gent, Belgium.,3 Cancer Research Institute Ghent (CRIG), Gent, Belgium
| | - Christine Decaestecker
- 4 Centre for Microscopy and Molecular Imaging (CMMI), Digital Image Analysis in Pathology (DIAPATH), Gosselies, Belgium
| | - Elly De Vlieghere
- 2 Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Gent, Belgium.,3 Cancer Research Institute Ghent (CRIG), Gent, Belgium
| | - Marc Bracke
- 2 Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Gent, Belgium.,3 Cancer Research Institute Ghent (CRIG), Gent, Belgium
| | - Isabelle Salmon
- 1 Department of Pathology, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium.,4 Centre for Microscopy and Molecular Imaging (CMMI), Digital Image Analysis in Pathology (DIAPATH), Gosselies, Belgium
| | - Olivier De Wever
- 2 Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Gent, Belgium.,3 Cancer Research Institute Ghent (CRIG), Gent, Belgium
| | - Pieter Demetter
- 1 Department of Pathology, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
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23
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Kroneis T, Jonasson E, Andersson D, Dolatabadi S, Ståhlberg A. Global preamplification simplifies targeted mRNA quantification. Sci Rep 2017; 7:45219. [PMID: 28332609 PMCID: PMC5362892 DOI: 10.1038/srep45219] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/20/2017] [Indexed: 01/09/2023] Open
Abstract
The need to perform gene expression profiling using next generation sequencing and quantitative real-time PCR (qPCR) on small sample sizes and single cells is rapidly expanding. However, to analyse few molecules, preamplification is required. Here, we studied global and target-specific preamplification using 96 optimised qPCR assays. To evaluate the preamplification strategies, we monitored the reactions in real-time using SYBR Green I detection chemistry followed by melting curve analysis. Next, we compared yield and reproducibility of global preamplification to that of target-specific preamplification by qPCR using the same amount of total RNA. Global preamplification generated 9.3-fold lower yield and 1.6-fold lower reproducibility than target-specific preamplification. However, the performance of global preamplification is sufficient for most downstream applications and offers several advantages over target-specific preamplification. To demonstrate the potential of global preamplification we analysed the expression of 15 genes in 60 single cells. In conclusion, we show that global preamplification simplifies targeted gene expression profiling of small sample sizes by a flexible workflow. We outline the pros and cons for global preamplification compared to target-specific preamplification.
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Affiliation(s)
- Thomas Kroneis
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden.,Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Harrachgasse 21, 8010, Graz, Austria
| | - Emma Jonasson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
| | - Daniel Andersson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
| | - Soheila Dolatabadi
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
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24
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Burns TJ, Frei AP, Gherardini PF, Bava FA, Batchelder JE, Yoshiyasu Y, Yu JM, Groziak AR, Kimmey SC, Gonzalez VD, Fantl WJ, Nolan GP. High-throughput precision measurement of subcellular localization in single cells. Cytometry A 2017; 91:180-189. [PMID: 28094900 DOI: 10.1002/cyto.a.23054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 01/21/2023]
Abstract
To quantify visual and spatial information in single cells with a throughput of thousands of cells per second, we developed Subcellular Localization Assay (SLA). This adaptation of Proximity Ligation Assay expands the capabilities of flow cytometry to include data relating to localization of proteins to and within organelles. We used SLA to detect the nuclear import of transcription factors across cell subsets in complex samples. We further measured intranuclear re-localization of target proteins across the cell cycle and upon DNA damage induction. SLA combines multiple single-cell methods to bring about a new dimension of inquiry and analysis in complex cell populations. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Tyler J Burns
- Department of Cancer Biology, Stanford University School of Medicine, Stanford, California
| | - Andreas P Frei
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Pier F Gherardini
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Felice A Bava
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Jake E Batchelder
- Immunology and Microbial Pathogenesis, Joan and Sanford I. Weill Medical College of Cornell University, New York, New York
| | - Yuki Yoshiyasu
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Julie M Yu
- Department of Biological Sciences, University of California Berkeley, Berkeley, California
| | | | - Samuel C Kimmey
- Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Veronica D Gonzalez
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Wendy J Fantl
- Stanford Comprehensive Cancer Institute and Department of Obstetrics and Gynecology, Stanford University, Stanford, California
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, California
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25
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Iwabuchi E, Miki Y, Ono K, Onodera Y, Suzuki T, Hirakawa H, Ishida T, Ohuchi N, Sasano H. In situ detection of estrogen receptor dimers in breast carcinoma cells in archival materials using proximity ligation assay (PLA). J Steroid Biochem Mol Biol 2017; 165:159-169. [PMID: 27264933 DOI: 10.1016/j.jsbmb.2016.05.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/05/2016] [Accepted: 05/23/2016] [Indexed: 01/20/2023]
Abstract
Estrogen receptor (ER) is required for carcinoma cell proliferation in the great majority of breast cancer and also functions as a dimer. ER dimeric proteins have been largely identified by BRET/FRET analyses but their in situ visualization have not yet been reported. Recently, in situ Proximity Ligation Assay (PLA) has been developed as the methods detecting protein interactions in situ. Therefore, in this study we firstly demonstrated the dimerization of ERα in breast carcinoma cell lines and tissues using PLA. The human breast carcinoma cell lines MCF-7, T-47D and MDA-MB-231 were used in this study. Cells were treated with ER agonist or antagonist and fixed in 4% PFA, and ER dimers were subsequently detected using PLA. The evaluation of ER dimers in breast carcinoma cell lines were quantified by measuring the area of dots localized in the nuclei using image analysis. We also firstly demonstrated the visualization of ER dimer patterns in 10% formalin-fixed paraffin-embedded tissues of breast cancer using PLA technique. Estradiol (E2) administration induced ERα homodimers in the nuclei of MCF-7 and T-47D but not in ER-negative MDA-MB-231. 4-OH tamoxifen also induced ERα homodimers but the subcellular localization of these ERα homodimers was predominant in cytoplasm instead of the nuclei induced by E2 treatment. ICI182,780 treatment did decrease the number of formation of ERα homodimers in MCF-7. In breast cancer patients, ERα PLA score was significantly correlated positively with ERα- or PgR (progesterone receptor) immunohistochemical scores and inversely with Ki-67-labeling index, respectively. We also demonstrated the ERα/β heterodimer as well as ERα homodimers in both breast carcinoma cell lines and surgical pathology specimens. In summary, we did firstly succeed in the visualization of ER dimeric proteins using PLA method. The evaluation of ER dimer patterns could provide pivotal information as to the prediction of response to endocrine therapy of breast cancer patients.
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Affiliation(s)
- Erina Iwabuchi
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasuhiro Miki
- Department of Disaster Obstetrics and Gynecology, International Research Institute of Disaster Science (IRIDes), Tohoku University, Sendai, Japan
| | - Katsuhiko Ono
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshiaki Onodera
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Takanori Ishida
- Department of Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Noriaki Ohuchi
- Department of Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hironobu Sasano
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan.
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26
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Gomes I, Sierra S, Devi LA. Detection of Receptor Heteromerization Using In Situ Proximity Ligation Assay. CURRENT PROTOCOLS IN PHARMACOLOGY 2016; 75:2.16.1-2.16.31. [PMID: 27960030 PMCID: PMC5758307 DOI: 10.1002/cpph.15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although G protein-coupled receptor (GPCR) heteromerization has been extensively demonstrated in vitro using heterologous cells that overexpress epitope-tagged receptors, their presence in endogenous systems is less well established. This is because a criterion to identify receptor heteromerization is the demonstration that the two interacting receptors are present not only in the same cell but also in the same subcellular compartment in close enough proximity to allow for direct receptor-receptor interaction. This has been difficult to study in native tissues due to a lack of sensitive and selective tools not only capable of detecting low-abundance proteins but also of demonstrating that they are in sufficiently close proximity to interact. The latter can be achieved using a proximity ligation assay (PLA). Detailed in this unit are protocols for demonstrating the presence of GPCR heteromers in endogenous cells as well as animal and human tissues, the controls required for these assays, and troubleshooting tips. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ivone Gomes
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Salvador Sierra
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lakshmi A Devi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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27
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Abstract
The invention of the microscope has been fundamental for the understanding of tissue architecture and subcellular structures. With the advancement of higher magnification microscopes came the development of various molecular biology tools such as Förster resonance energy transfer (FRET) and in situ proximity ligation assay (in situ PLA) to monitor protein interactions. Microscopy has become a commonly used method for the investigation of molecular events within the cell, for the identification of key players in signaling networks, and the activation of these pathways. Multiple approaches are available for functional analyses in single cells. They provide information not only on the localization of proteins at a given time point, but also on their expression levels and activity states, allowing us to pinpoint hallmarks of different cellular identities within tissues in health and disease. Clever solutions to increase the sensitivity of molecular tools, the possibilities for multiplexing, as well as image resolution have recently been introduced; however, these methods have their pros and cons. Therefore, one needs to carefully consider the biological question of interest along with the nature of the sample before choosing the most suitable method or combination of methods. Herein, we review a few of the most exciting microscopy-based molecular techniques for proteomic analysis and cover the benefits as well as the disadvantages of their use.
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Löf L, Ebai T, Dubois L, Wik L, Ronquist KG, Nolander O, Lundin E, Söderberg O, Landegren U, Kamali-Moghaddam M. Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout. Sci Rep 2016; 6:34358. [PMID: 27681459 PMCID: PMC5041182 DOI: 10.1038/srep34358] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/09/2016] [Indexed: 12/28/2022] Open
Abstract
Flow cytometry is a powerful method for quantitative and qualitative analysis of individual cells. However, flow cytometric analysis of extracellular vesicles (EVs), and the proteins present on their surfaces has been hampered by the small size of the EVs – in particular for the smallest EVs, which can be as little as 40 nm in diameter, the limited number of antigens present, and their low refractive index. We addressed these limitations for detection and characterization of EV by flow cytometry through the use of multiplex and multicolor in situ proximity ligation assays (in situ PLA), allowing each detected EV to be easily recorded over background noise using a conventional flow cytometer. By targeting sets of proteins on the surface that are specific for distinct classes of EVs, the method allows for selective recognition of populations of EVs in samples containing more than one type of EVs. The method presented herein opens up for analyses of EVs using flow cytometry for their characterization and quantification.
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Affiliation(s)
- Liza Löf
- Department of Immunology, Genetics &Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Tonge Ebai
- Department of Immunology, Genetics &Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Louise Dubois
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Lotta Wik
- Department of Immunology, Genetics &Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - K Göran Ronquist
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Olivia Nolander
- Department of Immunology, Genetics &Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Emma Lundin
- Department of Immunology, Genetics &Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Ola Söderberg
- Department of Immunology, Genetics &Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics &Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics &Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
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In situ characterization of the mTORC1 during adipogenesis of human adult stem cells on chip. Proc Natl Acad Sci U S A 2016; 113:E4143-50. [PMID: 27382182 DOI: 10.1073/pnas.1601207113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Mammalian target of rapamycin (mTOR) is a central kinase integrating nutrient, energy, and metabolite signals. The kinase forms two distinct complexes: mTORC1 and mTORC2. mTORC1 plays an essential but undefined regulatory function for regeneration of adipose tissue. Analysis of mTOR in general is hampered by the complexity of regulatory mechanisms, including protein interactions and/or phosphorylation, in an ever-changing cellular microenvironment. Here, we developed a microfluidic large-scale integration chip platform for culturing and differentiating human adipose-derived stem cells (hASCs) in 128 separated microchambers under standardized nutrient conditions over 3 wk. The progression of the stem cell differentiation was measured by determining the lipid accumulation rates in hASC cultures. For in situ protein analytics, we developed a multiplex in situ proximity ligation assay (mPLA) that can detect mTOR in its two complexes selectively in single cells and implemented it on the same chip. With this combined technology, it was possible to reveal that the mTORC1 is regulated in its abundance, phosphorylation state, and localization in coordination with lysosomes during adipogenesis. High-content image analysis and parameterization of the in situ PLA signals in over 1 million cells cultured on four individual chips showed that mTORC1 and lysosomes are temporally and spatially coordinated but not in its composition during adipogenesis.
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Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods 2016; 13:269-75. [PMID: 26808670 PMCID: PMC4767631 DOI: 10.1038/nmeth.3742] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/16/2015] [Indexed: 12/20/2022]
Abstract
Precise gene expression measurement has been fundamental to developing an advanced understanding of the roles of biological networks in health and disease. To enable detection of expression signatures specific to individual cells we developed PLAYR (Proximity Ligation Assay for RNA). PLAYR enables highly multiplexed quantification of transcripts in single cells by flow- and mass-cytometry and is compatible with standard antibody staining of proteins. With mass cytometry, this currently enables simultaneous quantification of more than 40 different mRNAs and proteins. The technology was demonstrated in primary cells to be capable of quantifying multiple gene expression transcripts while the identity and the functional state of each analyzed cell was defined based on the expression of other transcripts or proteins. PLAYR now enables high throughput deep phenotyping of cells to readily expand beyond protein epitopes to include RNA expression, thereby opening a new venue on the characterization of cellular metabolism.
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31
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Abstract
Spatiotemporal aspects of protein-tyrosine phosphatase (PTP) activity and interaction partners for many PTPs are elusive. We describe here an elegant and relatively simple method, in situ proximity ligation assay (in situ PLA), which can be used to address these issues. The possibility to detect endogenous unmodified proteins in situ and to visualize individual interactions with spatial resolution is the major advantage of this technique. We provide protocols suitable to monitor association of the transmembrane PTPs PTPRJ/DEP-1/CD148 and PTPRB/VE-PTP with their substrates, the receptor tyrosine kinases FMS-like tyrosine kinase 3 (FLT3/CD135), and Tie2 and vascular endothelial growth factor receptor 2 (VEGFR2), respectively. Detailed description of method development and reagents as well as highlighting of critical factors will enable the reader to apply the method successfully to other PTP-protein interactions.
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32
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Peckys DB, de Jonge N. Studying the Stoichiometry of Epidermal Growth Factor Receptor in Intact Cells using Correlative Microscopy. J Vis Exp 2015. [PMID: 26383083 PMCID: PMC4692600 DOI: 10.3791/53186] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This protocol describes the labeling of epidermal growth factor receptor (EGFR) on COS7 fibroblast cells, and subsequent correlative fluorescence microscopy and environmental scanning electron microscopy (ESEM) of whole cells in hydrated state. Fluorescent quantum dots (QDs) were coupled to EGFR via a two-step labeling protocol, providing an efficient and specific protein labeling, while avoiding label-induced clustering of the receptor. Fluorescence microscopy provided overview images of the cellular locations of the EGFR. The scanning transmission electron microscopy (STEM) detector was used to detect the QD labels with nanoscale resolution. The resulting correlative images provide data of the cellular EGFR distribution, and the stoichiometry at the single molecular level in the natural context of the hydrated intact cell. ESEM-STEM images revealed the receptor to be present as monomer, as homodimer, and in small clusters. Labeling with two different QDs, i.e., one emitting at 655 nm and at 800 revealed similar characteristic results.
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Affiliation(s)
| | - Niels de Jonge
- INM-Leibniz Institute for New Materials; Department of Physics, University of Saarland;
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Peckys DB, Korf U, de Jonge N. Local variations of HER2 dimerization in breast cancer cells discovered by correlative fluorescence and liquid electron microscopy. SCIENCE ADVANCES 2015; 1:e1500165. [PMID: 26601217 PMCID: PMC4646781 DOI: 10.1126/sciadv.1500165] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/03/2015] [Indexed: 05/17/2023]
Abstract
The formation of HER2 homodimers plays an important role in breast cancer aggressiveness and progression; however, little is known about its localization. We have studied the intra- and intercellular variation of HER2 at the single-molecule level in intact SKBR3 breast cancer cells. Whole cells were visualized in hydrated state with correlative fluorescence microscopy and environmental scanning electron microscopy (ESEM). The locations of individual HER2 receptors were detected using an anti-HER2 affibody in combination with a quantum dot (QD), a fluorescent nanoparticle. Fluorescence microscopy revealed considerable differences of HER2 membrane expression between individual cells and between different membrane regions of the same cell (that is, membrane ruffles and flat areas). Subsequent ESEM of the corresponding cellular regions provided images of individually labeled HER2 receptors. The high spatial resolution of 3 nm and the close proximity between the QD and the receptor allowed quantifying the stoichiometry of HER2 complexes, distinguishing between monomers, dimers, and higher-order clusters. Downstream data analysis based on calculating the pair correlation function from receptor positions showed that cellular regions exhibiting membrane ruffles contained a substantial fraction of HER2 in homodimeric state. Larger-order clusters were also present. Membrane areas with homogeneous membrane topography, on the contrary, displayed HER2 in random distribution. Second, HER2 homodimers appeared to be absent from a small subpopulation of cells exhibiting a flat membrane topography, possibly resting cells. Local differences in homodimer presence may point toward functional differences with possible relevance for studying metastasis and drug response.
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Affiliation(s)
- Diana B. Peckys
- INM—Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Niels de Jonge
- INM—Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
- Department of Physics, University of Saarland, Campus A5 1, 66123 Saarbrücken, Germany
- Corresponding author. E-mail:
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Larijani B, Perani M, Alburai'si K, Parker PJ. Functional proteomic biomarkers in cancer. Ann N Y Acad Sci 2015; 1346:1-6. [PMID: 25801208 DOI: 10.1111/nyas.12749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Beyond penetrant germline and somatic mutations, there are substantial challenges in extrapolating phenotypes from linear DNA sequences and transcriptomics. This brings a molecular pathology emphasis to the properties of the main players responsible for executing actions, proteins. The proteomic attribute most frequently determined in pathology is (relative) content, but for many candidate biomarkers this is not the most important feature to understand. In keeping pace with the depth of knowledge of the mechanisms underlying pathologies, we need to ask more sophisticated questions about the state of proteins, for example, their oligomerization status, modification status, and location. This demands hitherto nonroutine approaches to proteomics, which we will discuss in this brief perspective.
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Affiliation(s)
- Banafshe Larijani
- Cell Biophysics Laboratory, Ikerbasque, Basque Foundation for Science and Unidad de Biofísica (CSIC-UPV/EHU), Leioa, Spain
| | - Michela Perani
- King's College London, Guy's Campus, London, United Kingdom
| | | | - Peter J Parker
- King's College London, Guy's Campus, London, United Kingdom
- London Research Institute Cancer Research UK, Lincoln's Inn Fields, London, United Kingdom
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35
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Koos B, Kamali-Moghaddam M, David L, Sobrinho-Simões M, Dimberg A, Nilsson M, Wählby C, Söderberg O. Next-Generation Pathology—Surveillance of Tumor Microecology. J Mol Biol 2015; 427:2013-22. [DOI: 10.1016/j.jmb.2015.02.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 11/30/2022]
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36
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Greenwood C, Ruff D, Kirvell S, Johnson G, Dhillon HS, Bustin SA. Proximity assays for sensitive quantification of proteins. BIOMOLECULAR DETECTION AND QUANTIFICATION 2015; 4:10-6. [PMID: 27077033 PMCID: PMC4822221 DOI: 10.1016/j.bdq.2015.04.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 12/22/2022]
Abstract
Proximity assays are immunohistochemical tools that utilise two or more DNA-tagged aptamers or antibodies binding in close proximity to the same protein or protein complex. Amplification by PCR or isothermal methods and hybridisation of a labelled probe to its DNA target generates a signal that enables sensitive and robust detection of proteins, protein modifications or protein-protein interactions. Assays can be carried out in homogeneous or solid phase formats and in situ assays can visualise single protein molecules or complexes with high spatial accuracy. These properties highlight the potential of proximity assays in research, diagnostic, pharmacological and many other applications that require sensitive, specific and accurate assessments of protein expression.
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Affiliation(s)
- Christina Greenwood
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - David Ruff
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Sara Kirvell
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Gemma Johnson
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Harvinder S Dhillon
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Stephen A Bustin
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
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37
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Application guide for omics approaches to cell signaling. Nat Chem Biol 2015; 11:387-97. [DOI: 10.1038/nchembio.1809] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/31/2015] [Indexed: 01/18/2023]
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38
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Smith MA, Hall R, Fisher K, Haake SM, Khalil F, Schabath MB, Vuaroqueaux V, Fiebig HH, Altiok S, Chen YA, Haura EB. Annotation of human cancers with EGFR signaling-associated protein complexes using proximity ligation assays. Sci Signal 2015; 8:ra4. [PMID: 25587191 DOI: 10.1126/scisignal.2005906] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Strategies to measure functional signaling-associated protein complexes have the potential to augment current molecular biomarker assays, such as genotyping and expression profiling, used to annotate diseases. Aberrant activation of epidermal growth factor receptor (EGFR) signaling contributes to diverse cancers. We used a proximity ligation assay (PLA) to detect EGFR in a complex with growth factor receptor-bound protein 2 (GRB2), the major signaling adaptor for EGFR. We used multiple lung cancer cell lines to develop and characterize EGFR:GRB2 PLA and correlated this assay with established biochemical measures of EGFR signaling. In a panel of patient-derived xenografts in mice, the intensity of EGFR:GRB2 PLA correlated with the reduction in tumor size in response to the EGFR inhibitor cetuximab. In tumor biopsies from three cohorts of lung cancer patients, positive EGFR:GRB2 PLA was observed in patients with and without EGFR mutations, and the intensity of EGFR:GRB2 PLA was predictive of overall survival in an EGFR inhibitor-treated cohort. Thus, we established the feasibility of using PLA to measure EGFR signaling-associated protein complexes in patient-based materials, suggesting the potential for similar assays for a broader array of receptor tyrosine kinases and other key signaling molecules.
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Affiliation(s)
- Matthew A Smith
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Richard Hall
- Graduate Medical Education, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kate Fisher
- Department of Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Scott M Haake
- Graduate Medical Education, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Farah Khalil
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | | | | | - Soner Altiok
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Yian Ann Chen
- Department of Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
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39
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Ohno M, Karagiannis P, Taniguchi Y. Protein expression analyses at the single cell level. Molecules 2014; 19:13932-47. [PMID: 25197931 PMCID: PMC6270791 DOI: 10.3390/molecules190913932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/13/2014] [Accepted: 08/29/2014] [Indexed: 01/07/2023] Open
Abstract
The central dogma of molecular biology explains how genetic information is converted into its end product, proteins, which are responsible for the phenotypic state of the cell. Along with the protein type, the phenotypic state depends on the protein copy number. Therefore, quantification of the protein expression in a single cell is critical for quantitative characterization of the phenotypic states. Protein expression is typically a dynamic and stochastic phenomenon that cannot be well described by standard experimental methods. As an alternative, fluorescence imaging is being explored for the study of protein expression, because of its high sensitivity and high throughput. Here we review key recent progresses in fluorescence imaging-based methods and discuss their application to proteome analysis at the single cell level.
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Affiliation(s)
- Masae Ohno
- Laboratory for Single Cell Gene Dynamics, Quantitative Biology Center, RIKEN Address, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Peter Karagiannis
- Laboratory for Single Cell Gene Dynamics, Quantitative Biology Center, RIKEN Address, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Yuichi Taniguchi
- Laboratory for Single Cell Gene Dynamics, Quantitative Biology Center, RIKEN Address, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
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40
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Pacchiana R, Abbate M, Armato U, Dal Prà I, Chiarini A. Combining immunofluorescence with in situ proximity ligation assay: a novel imaging approach to monitor protein–protein interactions in relation to subcellular localization. Histochem Cell Biol 2014; 142:593-600. [DOI: 10.1007/s00418-014-1244-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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Junker J, van Oudenaarden A. Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology. Cell 2014; 157:8-11. [DOI: 10.1016/j.cell.2014.02.010] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Indexed: 10/25/2022]
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42
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Gremel G, Grannas K, Sutton LA, Pontén F, Zieba A. In situ Protein Detection for Companion Diagnostics. Front Oncol 2013; 3:271. [PMID: 24199171 PMCID: PMC3814083 DOI: 10.3389/fonc.2013.00271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 10/17/2013] [Indexed: 01/29/2023] Open
Abstract
The emergence of targeted therapies for cancer has created a need for the development of companion diagnostic tests. Assays developed in recent years are aimed at determining both the effectiveness and safety of specific drugs for a defined group of patients, thus, enabling the more efficient design of clinical trials and also supporting physicians when making treatment-related decisions. Immunohistochemistry (IHC) is a widely accepted method for protein expression analyses in human tissues. Immunohistochemical assays, used to localize and quantitate relative protein expression levels within a morphological context, are frequently used as companion diagnostics during clinical trials and also following drug approval. Herein, we describe established immunochemistry-based methods and their application in routine diagnostics. We also explore the possibility of using IHC to detect specific protein mutations in addition to DNA-based tests. Finally, we review alternative protein binders and proximity ligation assays and discuss their potential to facilitate the development of novel, targeted therapies against cancer.
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Affiliation(s)
- Gabriela Gremel
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala , Sweden
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43
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Protein biomarker validation via proximity ligation assays. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:933-9. [PMID: 23933049 DOI: 10.1016/j.bbapap.2013.07.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/15/2013] [Accepted: 07/29/2013] [Indexed: 11/24/2022]
Abstract
The ability to detect minute amounts of specific proteins or protein modifications in blood as biomarkers for a plethora of human pathological conditions holds great promise for future medicine. Despite a large number of plausible candidate protein biomarkers published annually, the translation to clinical use is impeded by factors such as the required size of the initial studies, and limitations of the technologies used. The proximity ligation assay (PLA) is a versatile molecular tool that has the potential to address some obstacles, both in validation of biomarkers previously discovered using other techniques, and for future routine clinical diagnostic needs. The enhanced specificity of PLA extends the opportunities for large-scale, high-performance analyses of proteins. Besides advantages in the form of minimal sample consumption and an extended dynamic range, the PLA technique allows flexible assay reconfiguration. The technology can be adapted for detecting protein complexes, proximity between proteins in extracellular vesicles or in circulating tumor cells, and to address multiple post-translational modifications in the same protein molecule. We discuss herein requirements for biomarker validation, and how PLA may play an increasing role in this regard. We describe some recent developments of the technology, including proximity extension assays, the use of recombinant affinity reagents suitable for use in proximity assays, and the potential for single cell proteomics. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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44
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Analysis of protein interactions in situ by proximity ligation assays. Curr Top Microbiol Immunol 2013; 377:111-26. [PMID: 23921974 DOI: 10.1007/82_2013_334] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The fate of the cell is governed by interactions among proteins, nucleic acids, and other biomolecules. It is vital to look at these interactions in a cellular environment if we want to increase our understanding of cellular processes. Herein we will describe how the in situ proximity ligation assay (in situ PLA) can be used to visualize protein interactions in fixed cells and tissues. In situ PLA is a novel technique that uses DNA, together with DNA modifying processes such as ligation, cleavage, and polymerization, as tools to create surrogate markers for protein interactions of interest. Different in situ PLA designs make it possible not only to detect protein-protein interactions but also post-translational modifications and interactions of proteins with nucleic acids. Flexibility in DNA probe design and the multitude of different DNA modifying enzymes provide the basis for modifications of the method to make it suitable to use in many applications. Furthermore, examples of how in situ PLA can be combined with other methods for a comprehensive view of the cellular activity status are discussed.
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