1
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Xue EY, 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 DOI: 10.1021/jacs.4c04317] [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: 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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2
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Teng F, Cui T, Zhou L, Gao Q, Zhou Q, Li W. Programmable synthetic receptors: the next-generation of cell and gene therapies. Signal Transduct Target Ther 2024; 9:7. [PMID: 38167329 PMCID: PMC10761793 DOI: 10.1038/s41392-023-01680-5] [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: 05/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Cell and gene therapies hold tremendous promise for treating a range of difficult-to-treat diseases. However, concerns over the safety and efficacy require to be further addressed in order to realize their full potential. Synthetic receptors, a synthetic biology tool that can precisely control the function of therapeutic cells and genetic modules, have been rapidly developed and applied as a powerful solution. Delicately designed and engineered, they can be applied to finetune the therapeutic activities, i.e., to regulate production of dosed, bioactive payloads by sensing and processing user-defined signals or biomarkers. This review provides an overview of diverse synthetic receptor systems being used to reprogram therapeutic cells and their wide applications in biomedical research. With a special focus on four synthetic receptor systems at the forefront, including chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors, we address the generalized strategies to design, construct and improve synthetic receptors. Meanwhile, we also highlight the expanding landscape of therapeutic applications of the synthetic receptor systems as well as current challenges in their clinical translation.
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Affiliation(s)
- Fei Teng
- University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingqin Gao
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Wei Li
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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3
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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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4
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Weizman OE, Luyten S, Lu P, Song E, Qin K, Mostaghimi D, Ring AM, Iwasaki A. Developing synthetic tools to decipher the tumor-immune interactome. Proc Natl Acad Sci U S A 2023; 120:e2306632120. [PMID: 37871202 PMCID: PMC10622925 DOI: 10.1073/pnas.2306632120] [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: 04/25/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
The ability of immune cells to directly interact with transformed cells is an essential component of immune surveillance and critical for optimal tissue function. The tumor-immune interactome (the collective cellular interactions between oncogenic cells and immune cells) is distinct and varied based on the tissue location and immunogenicity of tumor subtypes. However, comprehensive landscape and the consequences of tumor-interacting immune cells in the tumor microenvironment are not well understood. Current tools are limited in their ability to identify and record interactors in vivo or be utilized for downstream analysis. Here, we describe the development and validation of a technology leveraging synthetic Notch receptors reporting physical tumor cell-immune cell contact in vivo in order to decipher the tumor-immune interactome. We call this approach, Tumor-Immune Interactome Non-biased Discovery Retroviral Reporter or TIINDRR. Using TIINDRR, we identify the tumor-immune interactomes that define immunological refractory and sensitive tumors and how different immunotherapies alter these interactions. Thus, TIINDRR provides a flexible and versatile tool for studying in-vivo tumor-immune cell interactions, aiding in the identification of biologically relevant information needed for the rational design of immune-based therapies.
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Affiliation(s)
- Orr-El Weizman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Sophia Luyten
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
- Department of Ophthalmology, Yale University School of Medicine, New Haven, CT06520
| | - Kai Qin
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Darius Mostaghimi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Aaron M. Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT06520
- HHMI, Chevy Chase, MD20815
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5
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Luo X, Liu Z, Xu R. Adult tissue-specific stem cell interaction: novel technologies and research advances. Front Cell Dev Biol 2023; 11:1220694. [PMID: 37808078 PMCID: PMC10551553 DOI: 10.3389/fcell.2023.1220694] [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: 05/11/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
Adult tissue-specific stem cells play a dominant role in tissue homeostasis and regeneration. Various in vivo markers of adult tissue-specific stem cells have been increasingly reported by lineage tracing in genetic mouse models, indicating that marked cells differentiation is crucial during homeostasis and regeneration. How adult tissue-specific stem cells with indicated markers contact the adjacent lineage with indicated markers is of significance to be studied. Novel methods bring future findings. Recent advances in lineage tracing, synthetic receptor systems, proximity labeling, and transcriptomics have enabled easier and more accurate cell behavior visualization and qualitative and quantitative analysis of cell-cell interactions than ever before. These technological innovations have prompted researchers to re-evaluate previous experimental results, providing increasingly compelling experimental results for understanding the mechanisms of cell-cell interactions. This review aimed to describe the recent methodological advances of dual enzyme lineage tracing system, the synthetic receptor system, proximity labeling, single-cell RNA sequencing and spatial transcriptomics in the study of adult tissue-specific stem cells interactions. An enhanced understanding of the mechanisms of adult tissue-specific stem cells interaction is important for tissue regeneration and maintenance of homeostasis in organisms.
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Affiliation(s)
| | | | - Ruoshi Xu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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6
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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7
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He L, Perrimon N. Synthetic Notch receptors and their applications to study cell-cell contacts in vivo. Dev Cell 2023; 58:171-173. [PMID: 36750017 DOI: 10.1016/j.devcel.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Physical cell-cell interaction is a fundamental mechanism that controls the development and physiology of multicellular organisms. However, methods to study cell contact within complex tissues are limited. In a recent issue of Science, Zhang et al. developed synthetic Notch (synNotch)-based tools that can monitor and trace cell-cell contacts in mammals.
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Affiliation(s)
- Li He
- School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02138, USA.
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8
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Liu J, Lu F. Visualization of in vivo cell-cell contact in the present and in the past. SCIENCE CHINA. LIFE SCIENCES 2023; 66:889-891. [PMID: 36622577 DOI: 10.1007/s11427-022-2262-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 01/10/2023]
Affiliation(s)
- Jingwen Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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9
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Zhang S, Zhao H, Liu Z, Liu K, Zhu H, Pu W, He L, Wang RA, Zhou B. Monitoring of cell-cell communication and contact history in mammals. Science 2022; 378:eabo5503. [PMID: 36454848 DOI: 10.1126/science.abo5503] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Monitoring of cell-cell communication in multicellular organisms is fundamental to understanding diverse biological processes such as embryogenesis and tumorigenesis. To track cell-cell contacts in vivo, we developed an intercellular genetic technology to monitor cell-cell contact and to trace cell contact histories by permanently marking contacts between cells. In mice, we engineered an artificial Notch ligand into one cell (the sender cell) and an artificial receptor into another cell (the receiver cell). Contact between the sender and receiver cells triggered a synthetic Notch signaling that activated downstream transcriptional programs in the receiver cell, thereby transiently or permanently labeling it. In vivo cell-cell contact was observed during development, tissue homeostasis, and tumor growth. This technology may be useful for studying dynamic in vivo cell-cell contacts and cell fate plasticity.
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Affiliation(s)
- Shaohua Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huan Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zixin Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Kuo Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Huan Zhu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenjuan Pu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lingjuan He
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Rong A Wang
- Laboratory for Accelerated Vascular Research, Department of Surgery, Division of Vascular Surgery, University of California, San Francisco, CA 94143, USA
| | - Bin Zhou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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10
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Mukherjee S, Sakpal A, Mehrotra M, Phadte P, Rekhi B, Ray P. Homo and Heterotypic Cellular Cross-Talk in Epithelial Ovarian Cancer Impart Pro-Tumorigenic Properties through Differential Activation of the Notch3 Pathway. Cancers (Basel) 2022; 14:3365. [PMID: 35884426 PMCID: PMC9319742 DOI: 10.3390/cancers14143365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023] Open
Abstract
An active fluidic microenvironment governs peritoneal metastasis in epithelial ovarian cancer (EOC), but its critical functional/molecular cues are not fully understood. Utilizing co-culture models of NIH3T3 cells (differentially overexpressing Jagged1) and SKOV3 cells expressing a Notch3 luciferase reporter-sensor (SNFT), we showed that incremental expression of Jagged1 led to proportional Notch3 activation in SNFT. With no basal luciferase activity, this system efficiently recorded dose-dependent Notch3 activation by rh-Jag1 peptide and the non-appearance of such induction in co-culture with NIH3T3Δjag1 cells indicates its sensitivity and specificity. Similar Notch3 modulation was shown for the first time in co-cultures with HGSOC patients' ascites-derived cancer-associated fibroblasts and Jagged1-expressing EOC cell lines. NIH3T3J1-A and OVCAR3 co-cultured SNFT cells showed maximum proliferation, invasion, and cisplatin resistance among all the heterotypic/homotypic cellular partners. VEGFA and CDKN1A are the two most upregulated genes identified across co-cultures by the gene profiler array. Co-culture induced VEGFA secretion from SNFT cells which also reduced cancer stem cell differentiation in platinum-resistant A2780 cells. rh-Jag1-peptide promoted enhanced nuclear-cytoplasmic p21 expression. Additionally, metastatic HGSOC tumors had higher VEGFA than corresponding primary tumors. This study thus demonstrates the tumoral and non-tumoral cell-mediated differential Notch3 activation imparting its tumorigenic effects through two critical molecular regulators, VEGFA and p21, during EOC progression.
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Affiliation(s)
- Souvik Mukherjee
- Imaging Cell Signaling and Therapeutics Lab, Advanced Centre for Training Research and Education in Cancer, Navi Mumbai 410210, India; (S.M.); (A.S.); (M.M.); (P.P.)
- Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India;
| | - Asmita Sakpal
- Imaging Cell Signaling and Therapeutics Lab, Advanced Centre for Training Research and Education in Cancer, Navi Mumbai 410210, India; (S.M.); (A.S.); (M.M.); (P.P.)
| | - Megha Mehrotra
- Imaging Cell Signaling and Therapeutics Lab, Advanced Centre for Training Research and Education in Cancer, Navi Mumbai 410210, India; (S.M.); (A.S.); (M.M.); (P.P.)
- Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India;
| | - Pratham Phadte
- Imaging Cell Signaling and Therapeutics Lab, Advanced Centre for Training Research and Education in Cancer, Navi Mumbai 410210, India; (S.M.); (A.S.); (M.M.); (P.P.)
- Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India;
| | - Bharat Rekhi
- Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India;
- Tata Memorial Hospital, Dr. E Borges Road, Parel, Mumbai 400012, India
| | - Pritha Ray
- Imaging Cell Signaling and Therapeutics Lab, Advanced Centre for Training Research and Education in Cancer, Navi Mumbai 410210, India; (S.M.); (A.S.); (M.M.); (P.P.)
- Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India;
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11
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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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12
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [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] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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13
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Javdan SB, Deans TL. Design and development of engineered receptors for cell and tissue engineering. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100363. [PMID: 34527831 PMCID: PMC8437148 DOI: 10.1016/j.coisb.2021.100363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Advances in synthetic biology have provided genetic tools to reprogram cells to obtain desired cellular functions that include tools to enable the customization of cells to sense an extracellular signal and respond with a desired output. These include a variety of engineered receptors capable of transmembrane signaling that transmit information from outside of the cell to inside when specific ligands bind to them. Recent advances in synthetic receptor engineering have enabled the reprogramming of cell and tissue behavior, controlling cell fate decisions, and providing new vehicles for therapeutic delivery.
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Affiliation(s)
- Shwan B. Javdan
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT
| | - Tara L. Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT
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14
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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: 1] [Impact Index Per Article: 0.3] [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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15
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Huang H, Zhang X, Lv J, Yang H, Wang X, Ma S, Shao R, Peng X, Lin Y, Rong Z. Cell-cell contact-induced gene editing/activation in mammalian cells using a synNotch-CRISPR/Cas9 system. Protein Cell 2020; 11:299-303. [PMID: 32002793 PMCID: PMC7093359 DOI: 10.1007/s13238-020-00690-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Hongxin Huang
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Xin Zhang
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China
| | - Jie Lv
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China
| | - Hongcheng Yang
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China
| | - Xinlong Wang
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China
| | - Shufeng Ma
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China
| | - Ruoyang Shao
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China
| | - Xin Peng
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China
| | - Ying Lin
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China.
| | - Zhili Rong
- School of Basic Medical Sciences, Cancer Research Institute, Southern Medical University, Guangzhou, 510515, China.
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China.
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16
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Notch Pathway: A Journey from Notching Phenotypes to Cancer Immunotherapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1287:201-222. [PMID: 33034034 DOI: 10.1007/978-3-030-55031-8_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Notch is a key evolutionary conserved pathway, which has fascinated and engaged the work of investigators in an uncountable number of biological fields, from development of metazoans to immunotherapy for cancer. The study of Notch has greatly contributed to the understanding of cancer biology and a substantial effort has been spent in designing Notch-targeting therapies. Due to its broad involvement in cancer, targeting Notch would allow to virtually modulate any aspect of the disease. However, this means that Notch-based therapies must be highly specific to avoid off-target effects. This review will present the newest mechanistic and therapeutic advances in the Notch field and discuss the promises and challenges of this constantly evolving field.
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17
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Abstract
A handful of core intercellular signaling pathways play pivotal roles in a broad variety of developmental processes. It has remained puzzling how so few pathways can provide the precision and specificity of cell-cell communication required for multicellular development. Solving this requires us to quantitatively understand how developmentally relevant signaling information is actively sensed, transformed and spatially distributed by signaling pathways. Recently, single cell analysis and cell-based reconstitution, among other approaches, have begun to reveal the 'communication codes' through which information is represented in the identities, concentrations, combinations and dynamics of extracellular ligands. They have also revealed how signaling pathways decipher these features and control the spatial distribution of signaling in multicellular contexts. Here, we review recent work reporting the discovery and analysis of communication codes and discuss their implications for diverse developmental processes.
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Affiliation(s)
- Pulin Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA .,Howard Hughes Medical Institute, Pasadena, CA 91125, USA
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18
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Petruccelli E, Kaun KR. Insights from intoxicated Drosophila. Alcohol 2019; 74:21-27. [PMID: 29980341 DOI: 10.1016/j.alcohol.2018.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 01/31/2023]
Abstract
Our understanding of alcohol use disorder (AUD), particularly alcohol's effects on the nervous system, has unquestionably benefited from the use of model systems such as Drosophila melanogaster. Here, we briefly introduce the use of flies in alcohol research, and highlight the genetic accessibility and neurobiological contribution that flies have made to our understanding of AUD. Future fly research offers unique opportunities for addressing unresolved questions in the alcohol field, such as the neuromolecular and circuit basis for cravings and alcohol-induced neuroimmune dysfunction. This review strongly advocates for interdisciplinary approaches and translational collaborations with the united goal of confronting the major health problems associated with alcohol abuse and addiction.
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19
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Microfluidic dielectrophoretic cell manipulation towards stable cell contact assemblies. Biomed Microdevices 2018; 20:95. [DOI: 10.1007/s10544-018-0341-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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20
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Harmansa S, Affolter M. Protein binders and their applications in developmental biology. Development 2018; 145:145/2/dev148874. [PMID: 29374062 DOI: 10.1242/dev.148874] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Developmental biology research would benefit greatly from tools that enable protein function to be regulated, both systematically and in a precise spatial and temporal manner, in vivo In recent years, functionalized protein binders have emerged as versatile tools that can be used to target and manipulate proteins. Such protein binders can be based on various scaffolds, such as nanobodies, designed ankyrin repeat proteins (DARPins) and monobodies, and can be used to block or perturb protein function in living cells. In this Primer, we provide an overview of the protein binders that are currently available and highlight recent progress made in applying protein binder-based tools in developmental and synthetic biology.
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Affiliation(s)
- Stefan Harmansa
- Growth and Development, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, 4056 Basel, Switzerland
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21
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Huang TH, Niesman P, Arasu D, Lee D, De La Cruz AL, Callejas A, Hong EJ, Lois C. Tracing neuronal circuits in transgenic animals by transneuronal control of transcription ( TRACT). eLife 2017; 6:32027. [PMID: 29231171 PMCID: PMC5777821 DOI: 10.7554/elife.32027] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/02/2017] [Indexed: 12/20/2022] Open
Abstract
Understanding the computations that take place in brain circuits requires identifying how neurons in those circuits are connected to one another. We describe a technique called TRACT (TRAnsneuronal Control of Transcription) based on ligand-induced intramembrane proteolysis to reveal monosynaptic connections arising from genetically labeled neurons of interest. In this strategy, neurons expressing an artificial ligand (‘donor’ neurons) bind to and activate a genetically-engineered artificial receptor on their synaptic partners (‘receiver’ neurons). Upon ligand-receptor binding at synapses the receptor is cleaved in its transmembrane domain and releases a protein fragment that activates transcription in the synaptic partners. Using TRACT in Drosophila we have confirmed the connectivity between olfactory receptor neurons and their postsynaptic targets, and have discovered potential new connections between neurons in the circadian circuit. Our results demonstrate that the TRACT method can be used to investigate the connectivity of neuronal circuits in the brain. One of the main obstacles to understanding how the brain works is that we know relatively little about how its nerve cells or neurons are connected to one another. These connections make up the brain’s wiring diagram. Current methods for revealing this wiring all have limitations. The most popular method – serial electron microscopy – can reveal the connections in a small region of the brain in great detail, but it cannot show connections between neurons that are far apart. Huang et al. have now created a genetic system for visualizing these connections. For neurons to communicate, one neuron must produce a signal called a ligand. This ligand can then bind to and activate its partner neuron. Huang et al. modified the DNA of neurons so that every time those cells produced a specific ligand, they also produced a red fluorescent protein. Similar modifications ensured that every time the ligand activated a partner neuron, the activated neuron produced a green fluorescent protein. Viewing the red and green neurons under a microscope enabled Huang et al. to see which cells were communicating with which others. While these experiments took place in fruit flies, the same approach should also work in other laboratory animals, including fish, mice and rats. Once we know the wiring diagram of the brain, the next step is to investigate the role of the various connections. To understand how a computer works, for example, we might change the connections between its circuit components and look at how this affects the computer’s output. With this new method, we can change how neurons communicate with one another in the brain, and then look at the effects on behavior. This should provide insights into the workings of the human brain, and clues to what goes wrong in disorders like schizophrenia and autism.
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Affiliation(s)
- Ting-Hao Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Peter Niesman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Deepshika Arasu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Donghyung Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Aubrie L De La Cruz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Antuca Callejas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Department of Cell Biology, School of Science, University of Extremadura, Badajoz, Spain
| | - Elizabeth J Hong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
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22
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Crocker J, Ilsley GR. Using synthetic biology to study gene regulatory evolution. Curr Opin Genet Dev 2017; 47:91-101. [DOI: 10.1016/j.gde.2017.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 12/21/2022]
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