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Lebek T, Malaguti M, Boezio GL, Zoupi L, Briscoe J, Elfick A, Lowell S. PUFFFIN: an ultra-bright, customisable, single-plasmid system for labelling cell neighbourhoods. EMBO J 2024:10.1038/s44318-024-00154-w. [PMID: 38997504 DOI: 10.1038/s44318-024-00154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 07/14/2024] Open
Abstract
Cell communication coordinates developmental processes, maintains homeostasis, and contributes to disease. Therefore, understanding the relationship between cells in a shared environment is crucial. Here we introduce Positive Ultra-bright Fluorescent Fusion For Identifying Neighbours (PUFFFIN), a cell neighbour-labelling system based upon secretion and uptake of positively supercharged fluorescent protein s36GFP. We fused s36GFP to mNeonGreen or to a HaloTag, facilitating ultra-bright, sensitive, colour-of-choice labelling. Secretor cells transfer PUFFFIN to neighbours while retaining nuclear mCherry, making identification, isolation, and investigation of live neighbours straightforward. PUFFFIN can be delivered to cells, tissues, or embryos on a customisable single-plasmid construct composed of interchangeable components with the option to incorporate any transgene. This versatility enables the manipulation of cell properties, while simultaneously labelling surrounding cells, in cell culture or in vivo. We use PUFFFIN to ask whether pluripotent cells adjust the pace of differentiation to synchronise with their neighbours during exit from naïve pluripotency. PUFFFIN offers a simple, sensitive, customisable approach to profile non-cell-autonomous responses to natural or induced changes in cell identity or behaviour.
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Affiliation(s)
- Tamina Lebek
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3FF, UK
| | | | - Lida Zoupi
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Edinburgh, EH8 9XD, UK
| | | | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH8 3DW, UK
- UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK.
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2
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Xue E, Lee ACK, Chow KT, Ng DKP. Promotion and Detection of Cell-Cell Interactions through a Bioorthogonal Approach. J Am Chem Soc 2024; 146:17334-17347. [PMID: 38767615 PMCID: PMC11212048 DOI: 10.1021/jacs.4c04317] [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: 03/27/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Manipulation of cell-cell interactions via cell surface modification is crucial in tissue engineering and cell-based therapy. To be able to monitor intercellular interactions, it can also provide useful information for understanding how the cells interact and communicate. We report herein a facile bioorthogonal strategy to promote and monitor cell-cell interactions. It involves the use of a maleimide-appended tetrazine-caged boron dipyrromethene (BODIPY)-based fluorescent probe and a maleimide-substituted bicyclo[6.1.0]non-4-yne (BCN) to modify the membrane of macrophage (RAW 264.7) and cancer (HT29, HeLa, and A431) cells, respectively, via maleimide-thiol conjugation. After modification, the two kinds of cells interact strongly through inverse electron-demand Diels-Alder reaction of the surface tetrazine and BCN moieties. The coupling also disrupts the tetrazine quenching unit, restoring the fluorescence emission of the BODIPY core on the cell-cell interface, and promotes phagocytosis. Hence, this approach can promote and facilitate the detection of intercellular interactions, rendering it potentially useful for macrophage-based immunotherapy.
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Affiliation(s)
- Evelyn
Y. Xue
- Department
of Chemistry, The Chinese University of
Hong Kong, Shatin,
N.T., Hong Kong, China
| | - Alan Chun Kit Lee
- School
of Life Sciences, The Chinese University
of Hong Kong, Shatin, N.T., Hong Kong, China
- Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Kwan T. Chow
- Department
of Biomedical Sciences, City University
of Hong Kong, Kowloon, Hong Kong, China
| | - Dennis K. P. Ng
- Department
of Chemistry, The Chinese University of
Hong Kong, Shatin,
N.T., Hong Kong, China
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3
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Kozyreva ZV, Demina PA, Sapach AY, Terentyeva DA, Gusliakova OI, Abramova AM, Goryacheva IY, Trushina DB, Sukhorukov GB, Sindeeva OA. Multiple dyes applications for fluorescent convertible polymer capsules as macrophages tracking labels. Heliyon 2024; 10:e30680. [PMID: 38813172 PMCID: PMC11133507 DOI: 10.1016/j.heliyon.2024.e30680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/31/2024] [Accepted: 05/01/2024] [Indexed: 05/31/2024] Open
Abstract
Tracing individual cell pathways among the whole population is crucial for understanding their behavior, cell communication, migration dynamics, and fate. Optical labeling is one approach for tracing individual cells, but it typically requires genetic modification to induce the generation of photoconvertible proteins. Nevertheless, this approach has limitations and is not applicable to certain cell types. For instance, genetic modification often leads to the death of macrophages. This study aims to develop an alternative method for labeling macrophages by utilizing photoconvertible micron-sized capsules capable of easy internalization and prolonged retention within cells. Thermal treatment in a polyvinyl alcohol gel medium is employed for the scalable synthesis of capsules with a wide range of fluorescent dyes, including rhodamine 6G, pyronin B, fluorescein, acridine yellow, acridine orange, thiazine red, and previously reported rhodamine B. The fluorescence brightness, photostability, and photoconversion ability of the capsules are evaluated using confocal laser scanning microscopy. Viability, uptake, mobility, and photoconversion studies are conducted on RAW 264.7 and bone marrow-derived macrophages, serving as model cell lines. The production yield of the capsules is increased due to the use of polyvinyl alcohol gel, eliminating the need for conventional filtration steps. Capsules entrapping rhodamine B and rhodamine 6G meet all requirements for intracellular use in individual cell tracking. Mass spectrometry analysis reveals a sequence of deethylation steps that result in blue shifts in the dye spectra upon irradiation. Cellular studies on macrophages demonstrate robust uptake of the capsules. The capsules exhibit minimal cytotoxicity and have a negligible impact on cell motility. The successful photoconversion of RhB-containing capsules within cells highlights their potential as alternatives to photoconvertible proteins for individual cell labeling, with promising applications in personalized medicine.
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Affiliation(s)
- Zhanna V. Kozyreva
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, 30 b.1 Bolshoy Boulevard, 121205, Moscow, Russia
| | - Polina A. Demina
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012, Saratov, Russia
| | - Anastasiia Yu Sapach
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, 30 b.1 Bolshoy Boulevard, 121205, Moscow, Russia
| | - Daria A. Terentyeva
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, 30 b.1 Bolshoy Boulevard, 121205, Moscow, Russia
| | - Olga I. Gusliakova
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, 30 b.1 Bolshoy Boulevard, 121205, Moscow, Russia
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012, Saratov, Russia
| | - Anna M. Abramova
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012, Saratov, Russia
| | - Irina Yu Goryacheva
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, 30 b.1 Bolshoy Boulevard, 121205, Moscow, Russia
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012, Saratov, Russia
| | - Daria B. Trushina
- Institute of Molecular Theranostics, Sechenov University, 8-2 Trubetskaya Str., 119991, Moscow, Russia
| | - Gleb B. Sukhorukov
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, 30 b.1 Bolshoy Boulevard, 121205, Moscow, Russia
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Life Improvement by Future Technologies (LIFT) Center, Skolkovo, 143025, Moscow, Russia
| | - Olga A. Sindeeva
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, 30 b.1 Bolshoy Boulevard, 121205, Moscow, Russia
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4
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Maffuid K, Cao Y. Utilizing a Proximity Dependent Labeling Strategy to Study Cancer-Immune Intercellular Interactions In Vitro and In Vivo. J Pharmacol Exp Ther 2024; 389:246-253. [PMID: 37770200 PMCID: PMC11125784 DOI: 10.1124/jpet.123.001761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/11/2023] [Indexed: 10/03/2023] Open
Abstract
Immune cells play a critical role in surveilling and defending against cancer, emphasizing the importance of understanding how they interact and communicate with cancer cells to determine cancer status, treatment response, and the formation of the tumor microenvironment (TME). To this end, we conducted a study demonstrating the effectiveness of an enzyme-mediated intercellular proximity labeling (EXCELL) method, which utilizes a modified version of the sortase A enzyme known as mgSrtA, in detecting and characterizing immune-tumor cell interactions. The mgSrtA enzyme is expressed on the membrane of tumor cells, which is able to label immune cells that interact with tumor cells in a proximity-dependent manner. Our research indicates that the EXCELL technique can detect and characterize immune-tumor cell interactions in a time- and concentration-dependent manner, both in vitro and in vivo, without requiring pre-engineering of the immune cells. We also highlight its ability to detect various types of immune cell subpopulations in vivo that have migrated out of the tumor into the spleen, providing insights into the role of peripheral T-cell recruitment in tumor progression. Overall, our findings suggest that the EXCELL method has great potential for improving our understanding of immune cell dynamics within the TME, ultimately leading to more potent pharmacological effects and cancer immunotherapy strategies. SIGNIFICANCE STATEMENT: The enzyme-mediated intercellular proximity labeling method holds promise for detecting immune cell interactions with cancer cells, both in vitro and in vivo. It has important implications for studying immune tumor cell dynamics and potentially uncovering novel subtypes of immune cells within the tumor microenvironment, both prior to and during immunotherapeutic interventions.
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Affiliation(s)
- Kaitlyn Maffuid
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.M., Y.C.) and Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (Y.C.)
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.M., Y.C.) and Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (Y.C.)
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5
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Potter N, Latour S, Wong ECN, Winnik MA, Jackson HW, McGuigan AP, Nitz M. Design Parameters for a Mass Cytometry Detectable HaloTag Ligand. Bioconjug Chem 2024; 35:80-91. [PMID: 38112314 DOI: 10.1021/acs.bioconjchem.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Mass cytometry permits the high dimensional analysis of complex biological samples; however, some techniques are not yet integrated into the mass cytometry workflow due to reagent availability. The use of self-labeling protein systems, such as HaloTag, are one such application. Here, we describe the design and implementation of the first mass cytometry ligands for use with HaloTag. "Click"-amenable HaloTag warheads were first conjugated onto poly(l-lysine) or poly(acrylic acid) polymers that were then functionalized with diethylenetriaminepentaacetic acid (DTPA) lutetium metal chelates. Kinetic analysis of the HaloTag labeling rates demonstrated that the structure appended to the 1-chlorohexyl warhead was key to success. A construct with a diethylene glycol spacer appended to a benzamide gave similar rates (kobs ∼ 102 M-1 s-1), regardless of the nature of the polymer. Comparison of the polymer with a small molecule chelate having rapid HaloTag labeling kinetics (kobs ∼ 104 M-1 s-1) suggests the polymers significantly reduced the HaloTag labeling rate. HEK293T cells expressing surface-exposed GFP-HaloTag fusions were labeled with the polymeric constructs and 175Lu content measured by cytometry by time-of-flight (CyTOF). Robust labeling was observed; however, significant nonspecific binding of the constructs to cells was also present. Heavily pegylated polymers demonstrated that nonspecific binding could be reduced to allow cells bearing the HaloTag protein to be distinguished from nonexpressing cells.
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Affiliation(s)
- Nicole Potter
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Simon Latour
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Edmond C N Wong
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mitchell A Winnik
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Hartland W Jackson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Ontario Institute of Cancer Research, 661 University Avenue, Toronto, Ontario M5S 0A3, Canada
| | - Alison P McGuigan
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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6
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Malaguti M, Lebek T, Blin G, Lowell S. Enabling neighbour labelling: using synthetic biology to explore how cells influence their neighbours. Development 2024; 151:dev201955. [PMID: 38165174 PMCID: PMC10820747 DOI: 10.1242/dev.201955] [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] [Received: 09/08/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
Cell-cell interactions are central to development, but exploring how a change in any given cell relates to changes in the neighbour of that cell can be technically challenging. Here, we review recent developments in synthetic biology and image analysis that are helping overcome this problem. We highlight the opportunities presented by these advances and discuss opportunities and limitations in applying them to developmental model systems.
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Affiliation(s)
- Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Tamina Lebek
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Guillaume Blin
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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7
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Lee D, Latour S, Emblem M, Clark HJ, Santos JT, Jang J, McGuigan AP, Nitz M. Characterization of an N-Allylglyoxylamide-Based Bioorthogonal Nitrone Trap. Bioconjug Chem 2023; 34:2358-2365. [PMID: 38051144 DOI: 10.1021/acs.bioconjchem.3c00463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Aldehydes are attractive bioorthogonal coupling partners. The ease of manipulation of aldehydes and their orthogonality to other classes of bioorthogonal reactions have inspired the exploration of chemistries, which generate irreversible conjugates. Similarly, nitrones have been shown to be potent 1,3-dipoles in bioorthogonal reactions when paired with strained alkynes. Here, we combine the reactivity of nitrones with the simplicity of aldehydes using an N-allylglyoxylamide, in a cascade reaction with an N-alkylhydroxylamine to produce a bicyclic isoxazolidine. The reaction is found to be catalyzed by 5-methoxyanthranilic acid and proceeds at pH 7 with favorable kinetics. Using the HaloTag7 protein bearing an N-alkylhydroxylamine, we show the reaction to be bioorthogonal in a complex cell lysate and to proceed well at the surface of a HEK293 cell. Furthermore, the reaction is compatible with a typical strain-promoted alkyne-azide click reaction. The characteristics of this reaction suggest it will be a useful addition to the pallet of bioorthogonal reactions that have revolutionized chemical biology.
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Affiliation(s)
- Daniel Lee
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Simon Latour
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E6, Canada
| | - Michael Emblem
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Hunter J Clark
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Jobette T Santos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Jaewan Jang
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Alison P McGuigan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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8
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Matarèse BFE, Rusin A, Seymour C, Mothersill C. Quantum Biology and the Potential Role of Entanglement and Tunneling in Non-Targeted Effects of Ionizing Radiation: A Review and Proposed Model. Int J Mol Sci 2023; 24:16464. [PMID: 38003655 PMCID: PMC10671017 DOI: 10.3390/ijms242216464] [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: 09/20/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
It is well established that cells, tissues, and organisms exposed to low doses of ionizing radiation can induce effects in non-irradiated neighbors (non-targeted effects or NTE), but the mechanisms remain unclear. This is especially true of the initial steps leading to the release of signaling molecules contained in exosomes. Voltage-gated ion channels, photon emissions, and calcium fluxes are all involved but the precise sequence of events is not yet known. We identified what may be a quantum entanglement type of effect and this prompted us to consider whether aspects of quantum biology such as tunneling and entanglement may underlie the initial events leading to NTE. We review the field where it may be relevant to ionizing radiation processes. These include NTE, low-dose hyper-radiosensitivity, hormesis, and the adaptive response. Finally, we present a possible quantum biological-based model for NTE.
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Affiliation(s)
- Bruno F. E. Matarèse
- Department of Haematology, University of Cambridge, Cambridge CB2 1TN, UK;
- Department of Physics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Andrej Rusin
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
| | - Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
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9
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Wang X, Almet AA, Nie Q. The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics. Semin Cancer Biol 2023; 95:42-51. [PMID: 37454878 PMCID: PMC10627116 DOI: 10.1016/j.semcancer.2023.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/02/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Cell-cell interactions instruct cell fate and function. These interactions are hijacked to promote cancer development. Single-cell transcriptomics and spatial transcriptomics have become powerful new tools for researchers to profile the transcriptional landscape of cancer at unparalleled genetic depth. In this review, we discuss the rapidly growing array of computational tools to infer cell-cell interactions from non-spatial single-cell RNA-sequencing and the limited but growing number of methods for spatial transcriptomics data. Downstream analyses of these computational tools and applications to cancer studies are highlighted. We finish by suggesting several directions for further extensions that anticipate the increasing availability of multi-omics cancer data.
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Affiliation(s)
- Xinyi Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States.
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States.
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10
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Maffuid K, Cao Y. Decoding the Complexity of Immune-Cancer Cell Interactions: Empowering the Future of Cancer Immunotherapy. Cancers (Basel) 2023; 15:4188. [PMID: 37627216 PMCID: PMC10453128 DOI: 10.3390/cancers15164188] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The tumor and tumor microenvironment (TME) consist of a complex network of cells, including malignant, immune, fibroblast, and vascular cells, which communicate with each other. Disruptions in cell-cell communication within the TME, caused by a multitude of extrinsic and intrinsic factors, can contribute to tumorigenesis, hinder the host immune system, and enable tumor evasion. Understanding and addressing intercellular miscommunications in the TME are vital for combating these processes. The effectiveness of immunotherapy and the heterogeneous response observed among patients can be attributed to the intricate cellular communication between immune cells and cancer cells. To unravel these interactions, various experimental, statistical, and computational techniques have been developed. These include ligand-receptor analysis, intercellular proximity labeling approaches, and imaging-based methods, which provide insights into the distorted cell-cell interactions within the TME. By characterizing these interactions, we can enhance the design of cancer immunotherapy strategies. In this review, we present recent advancements in the field of mapping intercellular communication, with a particular focus on immune-tumor cellular interactions. By modeling these interactions, we can identify critical factors and develop strategies to improve immunotherapy response and overcome treatment resistance.
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Affiliation(s)
- Kaitlyn Maffuid
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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11
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Xie Z, Li X, Mora A. A Comparison of Cell-Cell Interaction Prediction Tools Based on scRNA-seq Data. Biomolecules 2023; 13:1211. [PMID: 37627276 PMCID: PMC10452151 DOI: 10.3390/biom13081211] [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: 06/18/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Computational prediction of cell-cell interactions (CCIs) is becoming increasingly important for understanding disease development and progression. We present a benchmark study of available CCI prediction tools based on single-cell RNA sequencing (scRNA-seq) data. By comparing prediction outputs with a manually curated gold standard for idiopathic pulmonary fibrosis (IPF), we evaluated prediction performance and processing time of several CCI prediction tools, including CCInx, CellChat, CellPhoneDB, iTALK, NATMI, scMLnet, SingleCellSignalR, and an ensemble of tools. According to our results, CellPhoneDB and NATMI are the best performer CCI prediction tools, among the ones analyzed, when we define a CCI as a source-target-ligand-receptor tetrad. In addition, we recommend specific tools according to different types of research projects and discuss the possible future paths in the field.
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Affiliation(s)
- Zihong Xie
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, China;
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, China;
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12
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Engineering Biomimetic Trogocytosis with Farnesylated Chemically Self-Assembled Nanorings. Biomacromolecules 2022; 23:5018-5035. [PMID: 36416233 PMCID: PMC9869669 DOI: 10.1021/acs.biomac.2c00837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Inspired by the natural intercellular material-transfer process of trans-endocytosis or trogocytosis, we proposed that targeted farnesylated chemically self-assembled nanorings (f-CSANs) could serve as a biomimetic trogocytosis vehicle for engineering directional cargo transfer between cells, thus allowing cell-cell interactions to be monitored and facilitating cell-cell communications. The membranes of sender cells were stably modified by hydrophobic insertion with the targeted f-CSANs, which were efficiently transferred to receiver cells expressing the appropriate receptors by endocytosis. CSAN-assisted cell-cell cargo transfer (C4T) was demonstrated to be receptor specific and dependent on direct cell-cell interactions, the rate of receptor internalization, and the level of receptor expression. In addition, C4T was shown to facilitate cell-to-cell delivery of an apoptosis inducing drug, as wells as antisense oligonucleotides. Taken together, the C4T approach is a potentially versatile biomimetic trogocytosis platform that can be deployed as a macro-chemical biological tool for monitoring cell-cell interactions and engineering cell-cell communications.
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13
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Khamaisi B, Luca VC, Blacklow SC, Sprinzak D. Functional Comparison between Endogenous and Synthetic Notch Systems. ACS Synth Biol 2022; 11:3343-3353. [PMID: 36107643 PMCID: PMC9594772 DOI: 10.1021/acssynbio.2c00247] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The Notch pathway converts receptor-ligand interactions at the cell surface into a transcriptional response in the receiver cell. In recent years, synthetic Notch systems (synNotch) that respond to different inputs and transduce different transcriptional responses have been engineered. One class of synNotch systems uses antibody-antigen interactions at the cell surface to induce the proteolytic cleavage cascade of the endogenous Notch autoregulatory core and the consequent release of a synNotch intracellular domain (ICD), converting surface antigen detection into a cellular response. While the activation of endogenous Notch requires ubiquitylation and subsequent endocytosis of the ligand ICD, these synNotch systems do not seem to have such a requirement because the synNotch ligands completely lack an ICD. This observation raises questions about existing models for the synNotch activation mechanism. Here, we test how different structural and biochemical factors affect the dependence of endogenous and synthetic Notch activation on ligand ICD. We compare the behavior of antibody-antigen synNotch (aa-synNotch) to that of endogenous Notch, and to a synNotch system that uses rapamycin induced dimerization of FK506 binding protein (FKBP) and FKBP rapamycin binding (FRB) domaindimerization domains (ff-synNotch), which still requires a ligand ICD. We found that differences in receptor-ligand affinity, in the identity of the transmembrane domain, or in the presence or absence of extracellular epidermal growth factor repeats cannot explain the differences in ligand ICD requirement that distinguishes aa-synNotch from endogenous Notch or ff-synNotch. We also found that unlike endogenous Notch and ff-synNotch, the aa-synNotch system does not exhibit trans-endocytosis of the receptor extracellular domain into the sender cell. These findings suggest that the aa-synNotch systems bypass the ligand ICD requirement because antigen-antibody pairs are able to promote other adhesive cell-cell interactions that provide the mechanical tension needed for ligand activation.
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Affiliation(s)
- Bassma Khamaisi
- George
S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry,
and Biophysics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vincent C. Luca
- Department
of Drug Discovery, Moffitt Cancer Center
and Research Institute, Tampa, Florida 33612, United States
| | - Stephen C. Blacklow
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - David Sprinzak
- George
S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry,
and Biophysics, Tel Aviv University, Tel Aviv 69978, Israel,
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14
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Yamamoto T, Cockburn K, Greco V, Kawaguchi K. Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks. PLoS Comput Biol 2022; 18:e1010477. [PMID: 36067226 PMCID: PMC9481156 DOI: 10.1371/journal.pcbi.1010477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/16/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Robustness in developing and homeostatic tissues is supported by various types of spatiotemporal cell-to-cell interactions. Although live imaging and cell tracking are powerful in providing direct evidence of cell coordination rules, extracting and comparing these rules across many tissues with potentially different length and timescales of coordination requires a versatile framework of analysis. Here we demonstrate that graph neural network (GNN) models are suited for this purpose, by showing how they can be applied to predict cell fate in tissues and utilized to infer the cell interactions governing the multicellular dynamics. Analyzing the live mammalian epidermis data, where spatiotemporal graphs constructed from cell tracks and cell contacts are given as inputs, GNN discovers distinct neighbor cell fate coordination rules that depend on the region of the body. This approach demonstrates how the GNN framework is powerful in inferring general cell interaction rules from live data without prior knowledge of the signaling involved. During development and homeostasis, cells coordinate with each other to grow, deform, and maintain the tissues. Even with the modern high-throughput cell profiling technologies and high-resolution microscopy, it is still challenging to infer how cell coordination affects the dynamics such as cell fate choice, due to the complexity of the problem and the limited methods to perform perturbation experiments. We here propose a versatile framework of analysis utilizing an interpretable machine learning method based on graph neural network (GNN) which infers the cell-to-cell interaction rules from live images of multicellular dynamics. From the spatiotemporal graphs generated from live images of skin stem cells, we identified previously unaddressed neighbor fate coupling as well as rules consistent with past findings. We further found distinct interaction rules in a different skin region of the body, indicating that our method is useful in probing the diverse mechanism behind the robustness and flexibility in multicellular systems. The GNN framework is applicable for interaction rule discovery for general multicellular dynamics as well as in a wide range of systems where modeling by stochastic interacting agents is effective.
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Affiliation(s)
- Takaki Yamamoto
- Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- * E-mail: (TY); (KK)
| | - Katie Cockburn
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Valentina Greco
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Departments of Cell Biology and Dermatology, Yale Stem Cell Center, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Kyogo Kawaguchi
- Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- RIKEN Cluster for Pioneering Research, Kobe, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
- * E-mail: (TY); (KK)
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15
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Li Z, Seehawer M, Polyak K. Untangling the web of intratumour heterogeneity. Nat Cell Biol 2022; 24:1192-1201. [PMID: 35941364 DOI: 10.1038/s41556-022-00969-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/27/2022] [Indexed: 02/06/2023]
Abstract
Intratumour heterogeneity (ITH) is a hallmark of cancer that drives tumour evolution and disease progression. Technological and computational advances have enabled us to assess ITH at unprecedented depths, yet this accumulating knowledge has not had a substantial clinical impact. This is in part due to a limited understanding of the functional relevance of ITH and the inadequacy of preclinical experimental models to reproduce it. Here, we discuss progress made in these areas and illuminate future directions.
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Affiliation(s)
- Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
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16
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Malaguti M, Portero Migueles R, Annoh J, Sadurska D, Blin G, Lowell S. SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo. Development 2022; 149:275525. [PMID: 35616331 PMCID: PMC9270970 DOI: 10.1242/dev.200226] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/13/2022] [Indexed: 12/11/2022]
Abstract
Cell-cell interactions govern differentiation and cell competition in pluripotent cells during early development, but the investigation of such processes is hindered by a lack of efficient analysis tools. Here, we introduce SyNPL: clonal pluripotent stem cell lines that employ optimised Synthetic Notch (SynNotch) technology to report cell-cell interactions between engineered ‘sender’ and ‘receiver’ cells in cultured pluripotent cells and chimaeric mouse embryos. A modular design makes it straightforward to adapt the system for programming differentiation decisions non-cell-autonomously in receiver cells in response to direct contact with sender cells. We demonstrate the utility of this system by enforcing neuronal differentiation at the boundary between two cell populations. In summary, we provide a new adaptation of SynNotch technology that could be used to identify cell interactions and to profile changes in gene or protein expression that result from direct cell-cell contact with defined cell populations in culture and in early embryos, and that can be customised to generate synthetic patterning of cell fate decisions. Summary: Optimised Synthetic Notch circuitry in mouse pluripotent stem cells provides a modular tool with which to monitor cell-cell interactions and program synthetic patterning of cell fates in culture and in embryos.
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Affiliation(s)
- Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Rosa Portero Migueles
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Jennifer Annoh
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Daina Sadurska
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Guillaume Blin
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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17
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Albers JJ, Pelka K. Listening in on Multicellular Communication in Human Tissue Immunology. Front Immunol 2022; 13:884185. [PMID: 35634333 PMCID: PMC9136009 DOI: 10.3389/fimmu.2022.884185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/14/2022] [Indexed: 11/23/2022] Open
Abstract
Immune responses in human tissues rely on the concerted action of different cell types. Inter-cellular communication shapes both the function of the multicellular interaction networks and the fate of the individual cells that comprise them. With the advent of new methods to profile and experimentally perturb primary human tissues, we are now in a position to systematically identify and mechanistically dissect these cell-cell interactions and their modulators. Here, we introduce the concept of multicellular hubs, functional modules of immune responses in tissues. We outline a roadmap to discover multicellular hubs in human tissues and discuss how emerging technologies may further accelerate progress in this field.
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Affiliation(s)
- Julian J. Albers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Karin Pelka
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- Gladstone-University of California San Francisco (UCSF) Institute of Genomic Immunology, Gladstone Institutes, San Francisco, CA, United States
- *Correspondence: Karin Pelka,
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18
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Cho KF, Gillespie SM, Kalogriopoulos NA, Quezada MA, Jacko M, Monje M, Ting AY. A light-gated transcriptional recorder for detecting cell-cell contacts. eLife 2022; 11:e70881. [PMID: 35311648 PMCID: PMC8937215 DOI: 10.7554/elife.70881] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 02/25/2022] [Indexed: 01/21/2023] Open
Abstract
Technologies for detecting cell-cell contacts are powerful tools for studying a wide range of biological processes, from neuronal signaling to cancer-immune interactions within the tumor microenvironment. Here, we report TRACC (Transcriptional Readout Activated by Cell-cell Contacts), a GPCR-based transcriptional recorder of cellular contacts, which converts contact events into stable transgene expression. TRACC is derived from our previous protein-protein interaction recorders, SPARK (Kim et al., 2017) and SPARK2 (Kim et al., 2019), reported in this journal. TRACC incorporates light gating via the light-oxygen-voltage-sensing (LOV) domain, which provides user-defined temporal control of tool activation and reduces background. We show that TRACC detects cell-cell contacts with high specificity and sensitivity in mammalian cell culture and that it can be used to interrogate interactions between neurons and glioma, a form of brain cancer.
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Affiliation(s)
- Kelvin F Cho
- Cancer Biology Program, Stanford UniversityStanfordUnited States
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Shawn M Gillespie
- Cancer Biology Program, Stanford UniversityStanfordUnited States
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
| | | | - Michael A Quezada
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
| | | | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
- Department of Pathology, Stanford UniversityStanfordUnited States
- Department of Pediatrics, Stanford UniversityStanfordUnited States
- Department of Neurosurgery, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Alice Y Ting
- Department of Genetics, Stanford UniversityStanfordUnited States
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Chemistry, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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19
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Weiss JM, Lumaquin-Yin D, Montal E, Suresh S, Leonhardt CS, White RM. Shifting the focus of zebrafish toward a model of the tumor microenvironment. eLife 2022; 11:69703. [PMID: 36538362 PMCID: PMC9767465 DOI: 10.7554/elife.69703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 11/21/2022] [Indexed: 12/29/2022] Open
Abstract
Cancer cells exist in a complex ecosystem with numerous other cell types in the tumor microenvironment (TME). The composition of this tumor/TME ecosystem will vary at each anatomic site and affects phenotypes such as initiation, metastasis, and drug resistance. A mechanistic understanding of the large number of cell-cell interactions between tumor and TME requires models that allow us to both characterize as well as genetically perturb this complexity. Zebrafish are a model system optimized for this problem, because of the large number of existing cell-type-specific drivers that can label nearly any cell in the TME. These include stromal cells, immune cells, and tissue resident normal cells. These cell-type-specific promoters/enhancers can be used to drive fluorophores to facilitate imaging and also CRISPR cassettes to facilitate perturbations. A major advantage of the zebrafish is the ease by which large numbers of TME cell types can be studied at once, within the same animal. While these features make the zebrafish well suited to investigate the TME, the model has important limitations, which we also discuss. In this review, we describe the existing toolset for studying the TME using zebrafish models of cancer and highlight unique biological insights that can be gained by leveraging this powerful resource.
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Affiliation(s)
- Joshua M Weiss
- Weill-Cornel Medical College, Tri-Institutional M.D./Ph.D. ProgramNew YorkUnited States
| | - Dianne Lumaquin-Yin
- Weill-Cornel Medical College, Tri-Institutional M.D./Ph.D. ProgramNew YorkUnited States
| | - Emily Montal
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Shruthy Suresh
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Carl S Leonhardt
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Richard M White
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States,Department of Medicine, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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20
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Gardiner JC, Cukierman E. Meaningful connections: Interrogating the role of physical fibroblast cell-cell communication in cancer. Adv Cancer Res 2022; 154:141-168. [PMID: 35459467 PMCID: PMC9483832 DOI: 10.1016/bs.acr.2022.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
As part of the connective tissue, activated fibroblasts play an important role in development and disease pathogenesis, while quiescent resident fibroblasts are responsible for sustaining tissue homeostasis. Fibroblastic activation is particularly evident in the tumor microenvironment where fibroblasts transition into tumor-supporting cancer-associated fibroblasts (CAFs), with some CAFs maintaining tumor-suppressive functions. While the tumor-supporting features of CAFs and their fibroblast-like precursors predominantly function through paracrine chemical communication (e.g., secretion of cytokine, chemokine, and more), the direct cell-cell communication that occurs between fibroblasts and other cells, and the effect that the remodeled CAF-generated interstitial extracellular matrix has in these types of cellular communications, remain poorly understood. Here, we explore the reported roles fibroblastic cell-cell communication play within the cancer stroma context and highlight insights we can gain from other disciplines.
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Affiliation(s)
| | - Edna Cukierman
- Cancer Signaling and Epigenetics Program, Marvin and Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Temple Health, Philadelphia, PA, United States.
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21
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An L, Yu R, Han Y, Zhou Z. Decoding the intercellular communication network during tumorigenesis. Cancer Biol Med 2021; 19:j.issn.2095-3941.2021.0558. [PMID: 34783465 PMCID: PMC8958884 DOI: 10.20892/j.issn.2095-3941.2021.0558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/26/2021] [Indexed: 11/15/2022] Open
Affiliation(s)
- Liwei An
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital, School of Life Sciences, Fudan University, Shanghai 200438, China
- Department of Medical Ultrasound, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai Engineering Research Centre of Ultrasound Diagnosis and Treatment, Shanghai 200072, China
| | - Ruixian Yu
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yi Han
- Department of Medical Ultrasound, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai Engineering Research Centre of Ultrasound Diagnosis and Treatment, Shanghai 200072, China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital, School of Life Sciences, Fudan University, Shanghai 200438, China
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22
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Giri AK, Ianevski A. High-throughput screening for drug discovery targeting the cancer cell-microenvironment interactions in hematological cancers. Expert Opin Drug Discov 2021; 17:181-190. [PMID: 34743621 DOI: 10.1080/17460441.2022.1991306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION The interactions between leukemic blasts and cells within the bone marrow environment affect oncogenesis, cancer stem cell survival, as well as drug resistance in hematological cancers. The importance of this interaction is increasingly being recognized as a potentially important target for future drug discoveries and developments. Recent innovations in the high throughput drug screening-related technologies, novel ex-vivo disease-models, and freely available machine-learning algorithms are advancing the drug discovery process by targeting earlier undruggable proteins, complex pathways, as well as physical interactions (e.g. leukemic cell-bone microenvironment interaction). AREA COVERED In this review, the authors discuss the recent methodological advancements and existing challenges to target specialized hematopoietic niches within the bone marrow during leukemia and suggest how such methods can be used to identify drugs targeting leukemic cell-bone microenvironment interactions. EXPERT OPINION The recent development in cell-cell communication scoring technology and culture conditions can speed up the drug discovery by targeting the cell-microenvironment interaction. However, to accelerate this process, collecting clinical-relevant patient tissues, developing culture model systems, and implementing computational algorithms, especially trained to predict drugs and their combination targeting the cancer cell-bone microenvironment interaction are needed.
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Affiliation(s)
- Anil K Giri
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aleksander Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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23
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Zhang X, Lei T, Du H. Prospect of cell penetrating peptides in stem cell tracking. Stem Cell Res Ther 2021; 12:457. [PMID: 34391472 PMCID: PMC8364034 DOI: 10.1186/s13287-021-02522-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/12/2021] [Indexed: 01/19/2023] Open
Abstract
Stem cell therapy has shown great efficacy in many diseases. However, the treatment mechanism is still unclear, which is a big obstacle for promoting clinical research. Therefore, it is particularly important to track transplanted stem cells in vivo, find out the distribution and condition of the stem cells, and furthermore reveal the treatment mechanism. Many tracking methods have been developed, including magnetic resonance imaging (MRI), fluorescence imaging, and ultrasound imaging (UI). Among them, MRI and UI techniques have been used in clinical. In stem cell tracking, a major drawback of these technologies is that the imaging signal is not strong enough, mainly due to the low cell penetration efficiency of imaging particles. Cell penetrating peptides (CPPs) have been widely used for cargo delivery due to its high efficacy, good safety properties, and wide delivery of various cargoes. However, there are few reports on the application of CPPs in current stem cell tracking methods. In this review, we systematically introduced the mechanism of CPPs into cell membranes and their advantages in stem cell tracking, discussed the clinical applications and limitations of CPPs, and finally we summarized several commonly used CPPs and their specific applications in stem cell tracking. Although it is not an innovation of tracer materials, CPPs as a powerful tool have broad prospects in stem cell tracking. ![]()
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Affiliation(s)
- Xiaoshuang Zhang
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, 100083, China.,School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tong Lei
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, 100083, China.,School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hongwu Du
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, 100083, China. .,School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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24
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Love AC, Tran SH, Prescher JA. Caged Cumate Enables Proximity-Dependent Control Over Gene Expression. Chembiochem 2021; 22:2440-2448. [PMID: 34031982 PMCID: PMC9870035 DOI: 10.1002/cbic.202100158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/17/2021] [Indexed: 01/26/2023]
Abstract
Cell-cell interactions underlie diverse physiological processes yet remain challenging to examine with conventional imaging tools. Here we report a novel strategy to illuminate cell proximity using transcriptional activators. We repurposed cumate, a small molecule inducer of gene expression, by caging its key carboxylate group with a nitrile. Nitrilase-expressing activator cells released the cage, liberating cumate for consumption by reporter cells. Reporter cells comprising a cumate-responsive switch expressed a target gene when in close proximity to the activator cells. Overall, this strategy provides a versatile platform to image and potentially manipulate cellular interactions over time.
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Affiliation(s)
- Anna C Love
- Department of Chemistry, University of California, Irvine, 1120 Natural Sciences II, Irvine, CA 92697, USA
| | - Sabrina H Tran
- Department of Biological Sciences, University of California, Irvine, 5120 Natural Sciences II, Irvine, CA, 92627, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, 1120 Natural Sciences II, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 3205 McGaugh Hall, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, 101 Theory, Ste. 101, Irvine, CA 92697, USA
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25
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Giampetraglia M, Weigelin B. Recent advances in intravital microscopy for preclinical research. Curr Opin Chem Biol 2021; 63:200-208. [PMID: 34274700 DOI: 10.1016/j.cbpa.2021.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/08/2021] [Accepted: 05/14/2021] [Indexed: 12/14/2022]
Abstract
Intravital microscopy (IVM) has revolutionized our understanding of single-cell behavior in complex tissues by enabling real-time observation of molecular and cellular processes in their natural environment. In preclinical research, IVM has emerged as a standard tool for mechanistic studies of therapy response and the rational design of new treatment strategies. Technological developments keep expanding the imaging depth and quality that can be achieved in living tissue, and the maturation of imaging modalities such as fluorescence and phosphorescence lifetime imaging facilitates co-registration of individual cell dynamics with metabolic tissue states. Correlation of IVM with mesoscopic and macroscopic imaging modalities further promotes the translation of mechanistic insights gained by IVM into clinically relevant information. This review highlights some of the recent advances in IVM that have made the transition from experimental optical techniques to practical applications in basic and preclinical research.
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Affiliation(s)
- Martina Giampetraglia
- David H. Koch Center for Applied Research of Genitourinary Cancers, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Bettina Weigelin
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Germany.
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26
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Strategies for monitoring cell-cell interactions. Nat Chem Biol 2021; 17:641-652. [PMID: 34035514 DOI: 10.1038/s41589-021-00790-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023]
Abstract
Multicellular organisms depend on physical cell-cell interactions to control physiological processes such as tissue formation, neurotransmission and immune response. These intercellular binding events can be both highly dynamic in their duration and complex in their composition, involving the participation of many different surface and intracellular biomolecules. Untangling the intricacy of these interactions and the signaling pathways they modulate has greatly improved insight into the biological processes that ensue upon cell-cell engagement and has led to the development of protein- and cell-based therapeutics. The importance of monitoring physical cell-cell interactions has inspired the development of several emerging approaches that effectively interrogate cell-cell interfaces with molecular-level detail. Specifically, the merging of chemistry- and biology-based technologies to deconstruct the complexity of cell-cell interactions has provided new avenues for understanding cell-cell interaction biology and opened opportunities for therapeutic development.
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