1
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Bisogni AJ, Armstead BL, Lin DM. Protocol for optimizing surface expression and speed in coaggregation assays using K562 cells and subsequent analysis with a CoAg Index. STAR Protoc 2024; 5:103192. [PMID: 39024095 DOI: 10.1016/j.xpro.2024.103192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/14/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
Coaggregation assays using K562 cells have been extensively employed to study how cell adhesion molecules mediate specificity between different populations. Here we describe how to prepare K562 cells, optimize electroporation conditions, calibrate antibodies used for protein detection, determine the surface expression of desired adhesion molecules, and considerations for the rotational force to be applied during the assay. We also detail procedures for analyzing coaggregates using our established CoAggregation (CoAg) Index. For complete details on the use and execution of this protocol, please refer to Bisogni et al.1.
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Affiliation(s)
- Adam J Bisogni
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA; Inso Biosciences, 237 Tower Road, Ithaca, NY 14850, USA
| | - Benjamin L Armstead
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - David M Lin
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA.
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2
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Dash S, Biswas J, Goswami S, Mukherjee S, Ganguli N, Duraivelan K, Mondal S, Mukhopadhyay R, Samanta D. Molecular Crosstalk Between Adherens Junction Proteins, E-cadherin and Nectin-4. J Mol Biol 2024; 436:168709. [PMID: 39009071 DOI: 10.1016/j.jmb.2024.168709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024]
Abstract
Cell-cell junctions formed by the association of cell adhesion molecules facilitate physiological events necessary for growth and development of multicellular organisms. Among them, cadherins and nectins organize and assemble to form adherens junction, which thereby mechanically couples interacting cells. A detailed understanding of the crosstalk involving these cell adhesion molecules is fundamental to the study of the various developmental processes. Although, cadherins and nectins can recruit each other in the adherens junction through an interplay of cytoplasmic adaptor molecules, here, we report a direct interaction between N-terminal extracellular domains of E-cadherin and nectin-4 as demonstrated by surface plasmon resonance (SPR) and Atomic Force Microscopy (AFM)-based single molecule force spectroscopy (SMFS). Kinetic studies using SPR demonstrate the binding between the ectodomains of E-cadherin and nectin-4 with a KD of 3.7 ± 0.7 µM and KD of 5.4 ± 0.2 µM (reciprocal experiment). AFM-based SMFS experiments also support interaction between the ectodomains of E-cadherin and nectin-4 with the koff value of 31.48 ± 1.53 s-1 and the lifetime of the complex of 0.036 ± 0.0026 s. We thus propose a cell adhesion mechanism mediated by E-cadherin and nectin-4, which can have functional significance in early embryogenesis as evident from the expression pattern of both the proteins during early development.
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Affiliation(s)
- Sagarika Dash
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Jayita Biswas
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra Mallick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Saumyadeep Goswami
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Sarbartha Mukherjee
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Namrata Ganguli
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Kheerthana Duraivelan
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Sourav Mondal
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra Mallick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra Mallick Road, Jadavpur, Kolkata 700032, West Bengal, India.
| | - Dibyendu Samanta
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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3
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Wiseglass G, Rubinstein R. Following the Evolutionary Paths of Dscam1 Proteins toward Highly Specific Homophilic Interactions. Mol Biol Evol 2024; 41:msae141. [PMID: 38989909 PMCID: PMC11272049 DOI: 10.1093/molbev/msae141] [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: 03/20/2024] [Revised: 06/05/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024] Open
Abstract
Many adhesion proteins, evolutionarily related through gene duplication, exhibit distinct and precise interaction preferences and affinities crucial for cell patterning. Yet, the evolutionary paths by which these proteins acquire new specificities and prevent cross-interactions within their family members remain unknown. To bridge this gap, this study focuses on Drosophila Down syndrome cell adhesion molecule-1 (Dscam1) proteins, which are cell adhesion proteins that have undergone extensive gene duplication. Dscam1 evolved under strong selective pressure to achieve strict homophilic recognition, essential for neuronal self-avoidance and patterning. Through a combination of phylogenetic analyses, ancestral sequence reconstruction, and cell aggregation assays, we studied the evolutionary trajectory of Dscam1 exon 4 across various insect lineages. We demonstrated that recent Dscam1 duplications in the mosquito lineage bind with strict homophilic specificities without any cross-interactions. We found that ancestral and intermediate Dscam1 isoforms maintained their homophilic binding capabilities, with some intermediate isoforms also engaging in promiscuous interactions with other paralogs. Our results highlight the robust selective pressure for homophilic specificity integral to the Dscam1 function within the process of neuronal self-avoidance. Importantly, our study suggests that the path to achieving such selective specificity does not introduce disruptive mutations that prevent self-binding but includes evolutionary intermediates that demonstrate promiscuous heterophilic interactions. Overall, these results offer insights into evolutionary strategies that underlie adhesion protein interaction specificities.
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Affiliation(s)
- Gil Wiseglass
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Rubinstein
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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4
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Morano NC, Lopez DH, Meltzer H, Sergeeva AP, Katsamba PS, Rostam KD, Gupta HP, Becker JE, Bornstein B, Cosmanescu F, Schuldiner O, Honig B, Mann RS, Shapiro L. Cis inhibition of co-expressed DIPs and Dprs shapes neural development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583391. [PMID: 38895375 PMCID: PMC11185508 DOI: 10.1101/2024.03.04.583391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
In Drosophila , two interacting adhesion protein families, Dprs and DIPs, coordinate the assembly of neural networks. While intercellular DIP/Dpr interactions have been well characterized, DIPs and Dprs are often co-expressed within the same cells, raising the question as to whether they also interact in cis . We show, in cultured cells and in vivo, that DIP-α and DIP-δ can interact in cis with their ligands, Dpr6/10 and Dpr12, respectively. When co-expressed in cis with their cognate partners, these Dprs regulate the extent of trans binding, presumably through competitive cis interactions. We demonstrate the neurodevelopmental effects of cis inhibition in fly motor neurons and in the mushroom body. We further show that a long disordered region of DIP-α at the C-terminus is required for cis but not trans interactions, likely because it alleviates geometric constraints on cis binding. Thus, the balance between cis and trans interactions plays a role in controlling neural development.
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5
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Su Z, Griffin B, Emmons S, Wu Y. Prediction of interactions between cell surface proteins by machine learning. Proteins 2024; 92:567-580. [PMID: 38050713 DOI: 10.1002/prot.26648] [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: 05/25/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023]
Abstract
Cells detect changes in their external environments or communicate with each other through proteins on their surfaces. These cell surface proteins form a complicated network of interactions in order to fulfill their functions. The interactions between cell surface proteins are highly dynamic and, thus, challenging to detect using traditional experimental techniques. Here, we tackle this challenge using a computational framework. The primary focus of the framework is to develop new tools to identify interactions between domains in the immunoglobulin (Ig) fold, which is the most abundant domain family in cell surface proteins. These interactions could be formed between ligands and receptors from different cells or between proteins on the same cell surface. In practice, we collected all structural data on Ig domain interactions and transformed them into an interface fragment pair library. A high-dimensional profile can then be constructed from the library for a given pair of query protein sequences. Multiple machine learning models were used to read this profile so that the probability of interaction between the query proteins could be predicted. We tested our models on an experimentally derived dataset that contains 564 cell surface proteins in humans. The cross-validation results show that we can achieve higher than 70% accuracy in identifying the PPIs within this dataset. We then applied this method to a group of 46 cell surface proteins in Caenorhabditis elegans. We screened every possible interaction between these proteins. Many interactions recognized by our machine learning classifiers have been experimentally confirmed in the literature. In conclusion, our computational platform serves as a useful tool to help identify potential new interactions between cell surface proteins in addition to current state-of-the-art experimental techniques. The tool is freely accessible for use by the scientific community. Moreover, the general framework of the machine learning classification can also be extended to study the interactions of proteins in other domain superfamilies.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Brian Griffin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Scott Emmons
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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6
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Chao G, Zukin S, Fortuna PRJ, Boettner B, Church GM. Progress and limitations in engineering cellular adhesion for research and therapeutics. Trends Cell Biol 2024; 34:277-287. [PMID: 37580241 DOI: 10.1016/j.tcb.2023.07.007] [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: 05/03/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/16/2023]
Abstract
Intercellular interactions form the cornerstone of multicellular biology. Despite advances in protein engineering, researchers artificially directing physical cell interactions still rely on endogenous cell adhesion molecules (CAMs) alongside off-target interactions and unintended signaling. Recently, methods for directing cellular interactions have been developed utilizing programmable domains such as coiled coils (CCs), nanobody-antigen, and single-stranded DNA (ssDNA). We first discuss desirable molecular- and systems-level properties in engineered CAMs, using the helixCAM platform as a benchmark. Next, we propose applications for engineered CAMs in immunology, developmental biology, tissue engineering, and neuroscience. Biologists in various fields can readily adapt current engineered CAMs to establish control over cell interactions, and their utilization in basic and translational research will incentivize further expansion in engineered CAM capabilities.
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Affiliation(s)
- George Chao
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Stefan Zukin
- Wyss Institute, Harvard Medical School, Boston, MA, USA
| | | | | | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Wyss Institute, Harvard Medical School, Boston, MA, USA.
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7
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Lobb-Rabe M, Nawrocka WI, Zhang R, Ashley J, Carrillo RA, Özkan E. Neuronal Wiring Receptors Dprs and DIPs Are GPI Anchored and This Modification Contributes to Their Cell Surface Organization. eNeuro 2024; 11:ENEURO.0184-23.2023. [PMID: 38233143 PMCID: PMC10863630 DOI: 10.1523/eneuro.0184-23.2023] [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: 05/26/2023] [Revised: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
The Drosophila Dpr and DIP proteins belong to the immunoglobulin superfamily of cell surface proteins (CSPs). Their hetero- and homophilic interactions have been implicated in a variety of neuronal functions, including synaptic connectivity, cell survival, and axon fasciculation. However, the signaling pathways underlying these diverse functions are unknown. To gain insight into Dpr-DIP signaling, we sought to examine how these CSPs are associated with the membrane. Specifically, we asked whether Dprs and DIPs are integral membrane proteins or membrane anchored through the addition of glycosylphosphatidylinositol (GPI) linkage. We demonstrate that most Dprs and DIPs are GPI anchored to the membrane of insect cells and validate these findings for some family members in vivo using Drosophila larvae, where GPI anchor cleavage results in loss of surface labeling. Additionally, we show that GPI cleavage abrogates aggregation of insect cells expressing cognate Dpr-DIP partners. To test if the GPI anchor affects Dpr and DIP localization, we replaced it with a transmembrane domain and observed perturbation of subcellular localization on motor neurons and muscles. These data suggest that membrane anchoring of Dprs and DIPs through GPI linkage is required for localization and that Dpr-DIP intracellular signaling likely requires transmembrane coreceptors.
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Affiliation(s)
- Meike Lobb-Rabe
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637
- Program in Cell and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
| | - Wioletta I Nawrocka
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637
| | - Ruiling Zhang
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
- Committee on Development, Regeneration, and Stem Cell Biology, The University of Chicago, Chicago, Illinois 60637
| | - James Ashley
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
| | - Robert A Carrillo
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637
- Program in Cell and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
| | - Engin Özkan
- Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637
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8
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Wu Z, Huang D, Wang J, Zhao Y, Sun W, Shen X. Engineering Heterogeneous Tumor Models for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304160. [PMID: 37946674 PMCID: PMC10767453 DOI: 10.1002/advs.202304160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/16/2023] [Indexed: 11/12/2023]
Abstract
Tumor tissue engineering holds great promise for replicating the physiological and behavioral characteristics of tumors in vitro. Advances in this field have led to new opportunities for studying the tumor microenvironment and exploring potential anti-cancer therapeutics. However, the main obstacle to the widespread adoption of tumor models is the poor understanding and insufficient reconstruction of tumor heterogeneity. In this review, the current progress of engineering heterogeneous tumor models is discussed. First, the major components of tumor heterogeneity are summarized, which encompasses various signaling pathways, cell proliferations, and spatial configurations. Then, contemporary approaches are elucidated in tumor engineering that are guided by fundamental principles of tumor biology, and the potential of a bottom-up approach in tumor engineering is highlighted. Additionally, the characterization approaches and biomedical applications of tumor models are discussed, emphasizing the significant role of engineered tumor models in scientific research and clinical trials. Lastly, the challenges of heterogeneous tumor models in promoting oncology research and tumor therapy are described and key directions for future research are provided.
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Affiliation(s)
- Zhuhao Wu
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Danqing Huang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Jinglin Wang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Yuanjin Zhao
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalWenzhou Medical UniversityWenzhou325035China
| | - Weijian Sun
- Department of Gastrointestinal SurgeryThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Xian Shen
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalWenzhou Medical UniversityWenzhou325035China
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9
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Mukherjee S, Goswami S, Dash S, Samanta D. Structural basis of molecular recognition among classical cadherins mediating cell adhesion. Biochem Soc Trans 2023; 51:2103-2115. [PMID: 37970977 DOI: 10.1042/bst20230356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Cadherins are type-I membrane glycoproteins that primarily participate in calcium-dependent cell adhesion and homotypic cell sorting in various stages of embryonic development. Besides their crucial role in cellular and physiological processes, increasing studies highlight their involvement in pathophysiological functions ranging from cancer progression and metastasis to being entry receptors for pathogens. Cadherins mediate these cellular processes through homophilic, as well as heterophilic interactions (within and outside the superfamily) by their membrane distal ectodomains. This review provides an in-depth structural perspective of molecular recognition among type-I and type-II classical cadherins. Furthermore, this review offers structural insights into different dimeric assemblies like the 'strand-swap dimer' and 'X-dimer' as well as mechanisms relating these dimer forms like 'two-step adhesion' and 'encounter complex'. Alongside providing structural details, this review connects structural studies to bond mechanics merging crystallographic and single-molecule force spectroscopic findings. Finally, the review discusses the recent discoveries on dimeric intermediates that uncover prospects of further research beyond two-step adhesion.
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Affiliation(s)
- Sarbartha Mukherjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Saumyadeep Goswami
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Sagarika Dash
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Dibyendu Samanta
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
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10
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Zhang N, Häring M, Wolf F, Großhans J, Kong D. Dynamics and functions of E-cadherin complexes in epithelial cell and tissue morphogenesis. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:585-601. [PMID: 38045551 PMCID: PMC10689684 DOI: 10.1007/s42995-023-00206-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Cell-cell adhesion is at the center of structure and dynamics of epithelial tissue. E-cadherin-catenin complexes mediate Ca2+-dependent trans-homodimerization and constitute the kernel of adherens junctions. Beyond the basic function of cell-cell adhesion, recent progress sheds light the dynamics and interwind interactions of individual E-cadherin-catenin complex with E-cadherin superclusters, contractile actomyosin and mechanics of the cortex and adhesion. The nanoscale architecture of E-cadherin complexes together with cis-interactions and interactions with cortical actomyosin adjust to junctional tension and mechano-transduction by reinforcement or weakening of specific features of the interactions. Although post-translational modifications such as phosphorylation and glycosylation have been implicated, their role for specific aspects of in E-cadherin function has remained unclear. Here, we provide an overview of the E-cadherin complex in epithelial cell and tissue morphogenesis focusing on nanoscale architectures by super-resolution approaches and post-translational modifications from recent, in particular in vivo, studies. Furthermore, we review the computational modelling in E-cadherin complexes and highlight how computational modelling has contributed to a deeper understanding of the E-cadherin complexes.
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Affiliation(s)
- Na Zhang
- Department of Biology, Philipps University, 35043 Marburg, Germany
| | - Matthias Häring
- Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN), Georg August University Göttingen, 37073 Göttingen, Germany
| | - Fred Wolf
- Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN), Georg August University Göttingen, 37073 Göttingen, Germany
| | - Jörg Großhans
- Department of Biology, Philipps University, 35043 Marburg, Germany
- Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN), Georg August University Göttingen, 37073 Göttingen, Germany
| | - Deqing Kong
- Department of Biology, Philipps University, 35043 Marburg, Germany
- Göttingen Campus Institute for Dynamics of Biological Networks (CIDBN), Georg August University Göttingen, 37073 Göttingen, Germany
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11
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Wauford N, Patel A, Tordoff J, Enghuus C, Jin A, Toppen J, Kemp ML, Weiss R. Synthetic symmetry breaking and programmable multicellular structure formation. Cell Syst 2023; 14:806-818.e5. [PMID: 37689062 PMCID: PMC10919224 DOI: 10.1016/j.cels.2023.08.001] [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: 10/17/2022] [Revised: 04/14/2023] [Accepted: 08/02/2023] [Indexed: 09/11/2023]
Abstract
During development, cells undergo symmetry breaking into differentiated subpopulations that self-organize into complex structures.1,2,3,4,5 However, few tools exist to recapitulate these behaviors in a controllable and coupled manner.6,7,8,9 Here, we engineer a stochastic recombinase genetic switch tunable by small molecules to induce programmable symmetry breaking, commitment to downstream cell fates, and morphological self-organization. Inducers determine commitment probabilities, generating tunable subpopulations as a function of inducer dosage. We use this switch to control the cell-cell adhesion properties of cells committed to each fate.10,11 We generate a wide variety of 3D morphologies from a monoclonal population and develop a computational model showing high concordance with experimental results, yielding new quantitative insights into the relationship between cell-cell adhesion strengths and downstream morphologies. We expect that programmable symmetry breaking, generating precise and tunable subpopulation ratios and coupled to structure formation, will serve as an integral component of the toolbox for complex tissue and organoid engineering.
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Affiliation(s)
- Noreen Wauford
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshay Patel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jesse Tordoff
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Casper Enghuus
- Department of Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Jin
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jack Toppen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Melissa L Kemp
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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12
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Su Z, Griffin B, Emmons S, Wu Y. Prediction of Interactions between Cell Surface Proteins by Machine Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557337. [PMID: 37745607 PMCID: PMC10515853 DOI: 10.1101/2023.09.12.557337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Cells detect changes of external environments or communicate with each other through proteins on their surfaces. These cell surface proteins form a complicated network of interactions in order to fulfill their functions. The interactions between cell surface proteins are highly dynamic and thus challenging to detect using traditional experimental techniques. Here we tackle this challenge by a computational framework. The primary focus of the framework is to develop new tools to identify interactions between domains in immunoglobulin (Ig) fold, which is the most abundant domain family in cell surface proteins. These interactions could be formed between ligands and receptors from different cells, or between proteins on the same cell surface. In practice, we collected all structural data of Ig domain interactions and transformed them into an interface fragment pair library. A high dimensional profile can be then constructed from the library for a given pair of query protein sequences. Multiple machine learning models were used to read this profile, so that the probability of interaction between the query proteins can be predicted. We tested our models to an experimentally derived dataset which contains 564 cell surface proteins in human. The cross-validation results show that we can achieve higher than 70% accuracy in identifying the PPIs within this dataset. We then applied this method to a group of 46 cell surface proteins in C elegans. We screened every possible interaction between these proteins. Many interactions recognized by our machine learning classifiers have been experimentally confirmed in the literatures. In conclusion, our computational platform serves a useful tool to help identifying potential new interactions between cell surface proteins in addition to current state-of-the-art experimental techniques. The tool is freely accessible for use by the scientific community. Moreover, the general framework of the machine learning classification can also be extended to study interactions of proteins in other domain superfamilies.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Brian Griffin
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Scott Emmons
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
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13
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Nagendra K, Izzet A, Judd NB, Zakine R, Friedman L, Harrison OJ, Pontani LL, Shapiro L, Honig B, Brujic J. Push-pull mechanics of E-cadherin ectodomains in biomimetic adhesions. Biophys J 2023; 122:3506-3515. [PMID: 37528581 PMCID: PMC10502478 DOI: 10.1016/j.bpj.2023.07.026] [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: 01/18/2023] [Revised: 06/12/2023] [Accepted: 07/27/2023] [Indexed: 08/03/2023] Open
Abstract
E-cadherin plays a central role in cell-cell adhesion. The ectodomains of wild-type cadherins form a crystalline-like two-dimensional lattice in cell-cell interfaces mediated by both trans (apposed cell) and cis (same cell) interactions. In addition to these extracellular forces, adhesive strength is further regulated by cytosolic phenomena involving α and β catenin-mediated interactions between cadherin and the actin cytoskeleton. Cell-cell adhesion can be further strengthened under tension through mechanisms that have not been definitively characterized in molecular detail. Here we quantitatively determine the role of the cadherin ectodomain in mechanosensing. To this end, we devise an E-cadherin-coated emulsion system, in which droplet surface tension is balanced by protein binding strength to give rise to stable areas of adhesion. To reach the honeycomb/cohesive limit, an initial emulsion compression by centrifugation facilitates E-cadherin trans binding, whereas a high protein surface concentration enables the cis-enhanced stabilization of the interface. We observe an abrupt concentration dependence on recruitment into adhesions of constant crystalline density, reminiscent of a first-order phase transition. Removing the lateral cis interaction with a "cis mutant" shifts this transition to higher surface densities leading to denser, yet weaker adhesions. In both proteins, the stabilization of progressively larger areas of deformation is consistent with single-molecule experiments that show a force-dependent lifetime enhancement in the cadherin ectodomain, which may be attributed to the "X-dimer" bond.
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Affiliation(s)
- Kartikeya Nagendra
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York; Molecular Biophysics and Biochemistry Training Program, NYU Grossman School of Medicine, New York, New York
| | - Adrien Izzet
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Nicolas B Judd
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Ruben Zakine
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Leah Friedman
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York; Département de Physique, École Normale Supérieure, PSL University, Paris, France
| | - Oliver J Harrison
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
| | - Léa-Laetitia Pontani
- Laboratoire Jean Perrin, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York; Department of Medicine, Division of Nephrology, Columbia University, New York, New York; Department of Systems Biology, Columbia University, New York, New York
| | - Jasna Brujic
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York; Laboratoire de Physique et Mécanique de Milieux Hétérogènes, UMR 7636, CNRS, ESPCI Paris-PSL, Sorbonne Université, Université Paris Cité, Paris, France.
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14
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Senoo A, Nagatoishi S, Kuroda D, Ito S, Ueno G, Caaveiro JMM, Tsumoto K. Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion. Protein Sci 2023; 32:e4744. [PMID: 37531208 PMCID: PMC10443342 DOI: 10.1002/pro.4744] [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: 04/19/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
Small molecules that regulate protein-protein interactions can be valuable drugs; however, the development of such small molecules is challenging as the molecule must interfere with an interaction that often involves a large surface area. Herein, we propose that modulating the conformational ensemble of the proteins participating in a given interaction, rather than blocking the interaction by directly binding to the interface, is a relevant strategy for interfering with a protein-protein interaction. In this study, we applied this concept to P-cadherin, a cell surface protein forming homodimers that are essential for cell-cell adhesion in various biological contexts. We first determined the crystal structure of P-cadherin with a small molecule inhibitor whose inhibitory mechanism was unknown. Molecular dynamics simulations suggest that the inhibition of cell adhesion by this small molecule results from modulation of the conformational ensemble of P-cadherin. Our study demonstrates the potential of small molecules altering the conformation ensemble of a protein as inhibitors of biological relevant protein-protein interactions.
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Affiliation(s)
- Akinobu Senoo
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Department of Global Healthcare, Graduate School of Pharmaceutical SciencesKyushu UniversityFukuokaJapan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Research Center for Drug and Vaccine DevelopmentNational Institute of Infectious DiseasesTokyoJapan
| | - Sho Ito
- DIC Central Research LaboratoriesChibaJapan
| | - Go Ueno
- RIKEN SPring‐8 CenterSayo‐gunHyogoJapan
| | - Jose M. M. Caaveiro
- Department of Global Healthcare, Graduate School of Pharmaceutical SciencesKyushu UniversityFukuokaJapan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
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15
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Sivasankar S, Xie B. Engineering the Interactions of Classical Cadherin Cell-Cell Adhesion Proteins. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:343-349. [PMID: 37459190 PMCID: PMC10361579 DOI: 10.4049/jimmunol.2300098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/30/2023] [Indexed: 07/20/2023]
Abstract
Classical cadherins are calcium-dependent cell-cell adhesion proteins that play key roles in the formation and maintenance of tissues. Deficiencies in cadherin adhesion are hallmarks of numerous cancers. In this article, we review recent biophysical studies on the regulation of cadherin structure and adhesion. We begin by reviewing distinct cadherin binding conformations, their biophysical properties, and their response to mechanical stimuli. We then describe biophysical guidelines for engineering Abs that can regulate adhesion by either stabilizing or destabilizing cadherin interactions. Finally, we review molecular mechanisms by which cytoplasmic proteins regulate the conformation of cadherin extracellular regions from the inside out.
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Affiliation(s)
- Sanjeevi Sivasankar
- Department of Biomedical Engineering, University of California, Davis, Davis, CA
- Biophysics Graduate Group, University of California, Davis, Davis, CA
| | - Bin Xie
- Biophysics Graduate Group, University of California, Davis, Davis, CA
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16
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Structure of the planar cell polarity cadherins Fat4 and Dachsous1. Nat Commun 2023; 14:891. [PMID: 36797229 PMCID: PMC9935876 DOI: 10.1038/s41467-023-36435-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
The atypical cadherins Fat and Dachsous are key regulators of cell growth and animal development. In contrast to classical cadherins, which form homophilic interactions to segregate cells, Fat and Dachsous cadherins form heterophilic interactions to induce cell polarity within tissues. Here, we determine the co-crystal structure of the human homologs Fat4 and Dachsous1 (Dchs1) to establish the molecular basis for Fat-Dachsous interactions. The binding domains of Fat4 and Dchs1 form an extended interface along extracellular cadherin (EC) domains 1-4 of each protein. Biophysical measurements indicate that Fat4-Dchs1 affinity is among the highest reported for cadherin superfamily members, which is attributed to an extensive network of salt bridges not present in structurally similar protocadherin homodimers. Furthermore, modeling suggests that unusual extracellular phosphorylation modifications directly modulate Fat-Dachsous binding by introducing charged contacts across the interface. Collectively, our analyses reveal how the molecular architecture of Fat4-Dchs1 enables them to form long-range, high-affinity interactions to maintain planar cell polarity.
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17
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Robust and accurate prediction of self-interacting proteins from protein sequence information by exploiting weighted sparse representation based classifier. BMC Bioinformatics 2022; 23:518. [PMID: 36457083 PMCID: PMC9713954 DOI: 10.1186/s12859-022-04880-y] [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: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Self-interacting proteins (SIPs), two or more copies of the protein that can interact with each other expressed by one gene, play a central role in the regulation of most living cells and cellular functions. Although numerous SIPs data can be provided by using high-throughput experimental techniques, there are still several shortcomings such as in time-consuming, costly, inefficient, and inherently high in false-positive rates, for the experimental identification of SIPs even nowadays. Therefore, it is more and more significant how to develop efficient and accurate automatic approaches as a supplement of experimental methods for assisting and accelerating the study of predicting SIPs from protein sequence information. RESULTS In this paper, we present a novel framework, termed GLCM-WSRC (gray level co-occurrence matrix-weighted sparse representation based classification), for predicting SIPs automatically based on protein evolutionary information from protein primary sequences. More specifically, we firstly convert the protein sequence into Position Specific Scoring Matrix (PSSM) containing protein sequence evolutionary information, exploiting the Position Specific Iterated BLAST (PSI-BLAST) tool. Secondly, using an efficient feature extraction approach, i.e., GLCM, we extract abstract salient and invariant feature vectors from the PSSM, and then perform a pre-processing operation, the adaptive synthetic (ADASYN) technique, to balance the SIPs dataset to generate new feature vectors for classification. Finally, we employ an efficient and reliable WSRC model to identify SIPs according to the known information of self-interacting and non-interacting proteins. CONCLUSIONS Extensive experimental results show that the proposed approach exhibits high prediction performance with 98.10% accuracy on the yeast dataset, and 91.51% accuracy on the human dataset, which further reveals that the proposed model could be a useful tool for large-scale self-interacting protein prediction and other bioinformatics tasks detection in the future.
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18
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Chataigner LMP, Gogou C, den Boer MA, Frias CP, Thies-Weesie DME, Granneman JCM, Heck AJR, Meijer DH, Janssen BJC. Structural insights into the contactin 1 - neurofascin 155 adhesion complex. Nat Commun 2022; 13:6607. [PMID: 36329006 PMCID: PMC9633819 DOI: 10.1038/s41467-022-34302-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Cell-surface expressed contactin 1 and neurofascin 155 control wiring of the nervous system and interact across cells to form and maintain paranodal myelin-axon junctions. The molecular mechanism of contactin 1 - neurofascin 155 adhesion complex formation is unresolved. Crystallographic structures of complexed and individual contactin 1 and neurofascin 155 binding regions presented here, provide a rich picture of how competing and complementary interfaces, post-translational glycosylation, splice differences and structural plasticity enable formation of diverse adhesion sites. Structural, biophysical, and cell-clustering analysis reveal how conserved Ig1-2 interfaces form competing heterophilic contactin 1 - neurofascin 155 and homophilic neurofascin 155 complexes whereas contactin 1 forms low-affinity clusters through interfaces on Ig3-6. The structures explain how the heterophilic Ig1-Ig4 horseshoe's in the contactin 1 - neurofascin 155 complex define the 7.4 nm paranodal spacing and how the remaining six domains enable bridging of distinct intercellular distances.
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Affiliation(s)
- Lucas M. P. Chataigner
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Christos Gogou
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maurits A. den Boer
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cátia P. Frias
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dominique M. E. Thies-Weesie
- grid.5477.10000000120346234Van’t Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute of Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joke C. M. Granneman
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Albert J. R. Heck
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dimphna H. Meijer
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Bert J. C. Janssen
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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19
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Takeichi M. Cell sorting in vitro and in vivo: How are cadherins involved? Semin Cell Dev Biol 2022; 147:2-11. [PMID: 36376196 DOI: 10.1016/j.semcdb.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Animal tissues are composed of heterogenous cells, and their sorting into different compartments of the tissue is a pivotal process for organogenesis. Cells accomplish sorting by themselves-it is well known that singly dispersed cells can self-organize into tissue-like structures in vitro. Cell sorting is regulated by both biochemical and physical mechanisms. Adhesive proteins connect cells together, selecting particular partners through their specific binding properties, while physical forces, such as cell-cortical tension, control the cohesiveness between cells and in turn cell assembly patterns in mechanical ways. These processes cooperate in determining the overall cell sorting behavior. This article focuses on the 'cadherin' family of adhesion molecules as a biochemical component of cell-cell interactions, addressing how they regulate cell sorting by themselves or by cooperating with other factors. New ideas beyond the classical models of cell sorting are also discussed.
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20
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Kanadome T, Hayashi K, Seto Y, Eiraku M, Nakajima K, Nagai T, Matsuda T. Development of intensiometric indicators for visualizing N-cadherin interaction across cells. Commun Biol 2022; 5:1065. [PMID: 36207396 PMCID: PMC9546846 DOI: 10.1038/s42003-022-04023-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
N-cadherin (NCad) is a classical cadherin that mediates cell–cell interactions in a Ca2+-dependent manner. NCad participates in various biological processes, from ontogenesis to higher brain functions, though the visualization of NCad interactions in living cells remains limited. Here, we present intensiometric NCad interaction indicators, named INCIDERs, that utilize dimerization-dependent fluorescent proteins. INCIDERs successfully visualize reversible NCad interactions across cells. Compared to FRET-based indicators, INCIDERs have a ~70-fold higher signal contrast, enabling clear identification of NCad interactions. In primary neuronal cells, NCad interactions are visualized between closely apposed processes. Furthermore, visualization of NCad interaction at cell adhesion sites in dense cell populations is achieved by two-photon microscopy. INCIDERs are useful tools in the spatiotemporal investigation of NCad interactions across cells; future research should evaluate the potential of INCIDERs in mapping complex three-dimensional architectures in multi-cellular systems. Intensiometric N-cadherin (NCad) interaction indicators, named INCIDERs, visualize reversible NCad-mediated cell-cell interactions.
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Affiliation(s)
- Takashi Kanadome
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, 332-0012, Japan.,Department of Biomolecular Science and Engineering, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan
| | - Kanehiro Hayashi
- Department of Anatomy, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yusuke Seto
- Laboratory of Developmental Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Mototsugu Eiraku
- Laboratory of Developmental Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8507, Japan
| | - Kazunori Nakajima
- Department of Anatomy, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Takeharu Nagai
- Department of Biomolecular Science and Engineering, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan
| | - Tomoki Matsuda
- Department of Biomolecular Science and Engineering, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan.
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21
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Abstract
Since the proposal of the differential adhesion hypothesis, scientists have been fascinated by how cell adhesion mediates cellular self-organization to form spatial patterns during development. The search for molecular tool kits with homophilic binding specificity resulted in a diverse repertoire of adhesion molecules. Recent understanding of the dominant role of cortical tension over adhesion binding redirects the focus of differential adhesion studies to the signaling function of adhesion proteins to regulate actomyosin contractility. The broader framework of differential interfacial tension encompasses both adhesion and nonadhesion molecules, sharing the common function of modulating interfacial tension during cell sorting to generate diverse tissue patterns. Robust adhesion-based patterning requires close coordination between morphogen signaling, cell fate decisions, and changes in adhesion. Current advances in bridging theoretical and experimental approaches present exciting opportunities to understand molecular, cellular, and tissue dynamics during adhesion-based tissue patterning across multiple time and length scales.
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Affiliation(s)
- Tony Y-C Tsai
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Rikki M Garner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA;
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA;
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22
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Boni N, Shapiro L, Honig B, Wu Y, Rubinstein R. On the formation of ordered protein assemblies in cell-cell interfaces. Proc Natl Acad Sci U S A 2022; 119:e2206175119. [PMID: 35969779 PMCID: PMC9407605 DOI: 10.1073/pnas.2206175119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Crystal structures of many cell-cell adhesion receptors reveal the formation of linear "molecular zippers" comprising an ordered one-dimensional array of proteins that form both intercellular (trans) and intracellular (cis) interactions. The clustered protocadherins (cPcdhs) provide an exemplar of this phenomenon and use it as a basis of barcoding of vertebrate neurons. Here, we report both Metropolis and kinetic Monte Carlo simulations of cPcdh zipper formation using simplified models of cPcdhs that nevertheless capture essential features of their three-dimensional structure. The simulations reveal that the formation of long zippers is an implicit feature of cPcdh structure and is driven by their cis and trans interactions that have been quantitatively characterized in previous work. Moreover, in agreement with cryo-electron tomography studies, the zippers are found to organize into two-dimensional arrays even in the absence of attractive interactions between individual zippers. Our results suggest that the formation of ordered two-dimensional arrays of linear zippers of adhesion proteins is a common feature of cell-cell interfaces. From the perspective of simulations, they demonstrate the importance of a realistic depiction of adhesion protein structure and interactions if important biological phenomena are to be properly captured.
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Affiliation(s)
- Nadir Boni
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Lawrence Shapiro
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032
| | - Barry Honig
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY 10032
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Rotem Rubinstein
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv-Yafo, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv-Yafo, Israel
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23
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Multiple dimeric structures and strand-swap dimerization of E-cadherin in solution visualized by high-speed atomic force microscopy. Proc Natl Acad Sci U S A 2022; 119:e2208067119. [PMID: 35867820 PMCID: PMC9335211 DOI: 10.1073/pnas.2208067119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Classical cadherins play key roles in cell-cell adhesion. The adhesion process is thought to comprise mainly two steps: X-dimer and strand-swap (SS-) dimer formation of the extracellular domains (ectodomains) of cadherins. The dimerization mechanism of this two-step process has been investigated for type I cadherins, including E-cadherin, of classical cadherins, whereas other binding states also have been proposed, raising the possibility of additional binding processes required for the cadherin dimerization. However, technical limitations in observing single-molecule structures and their dynamics have precluded the investigation of the dynamic binding process of cadherin. Here, we used high-speed atomic force microscopy (HS-AFM) to observe full-length ectodomains of E-cadherin in solution and identified multiple dimeric structures that had not been reported previously. HS-AFM revealed that almost half of the cadherin dimers showed S- (or reverse S-) shaped conformations, which had more dynamic properties than the SS- and X-like dimers. The combined HS-AFM, mutational, and molecular modeling analyses showed that the S-shaped dimer was formed by membrane-distal ectodomains, while the binding interface was different from that of SS- and X-dimers. Furthermore, the formation of the SS-dimer from the S-shaped and X-like dimers was directly visualized, suggesting the processes of SS-dimer formation from S-shaped and X-dimers during cadherin dimerization.
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24
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Halmi CA, Wu CY, Taneyhill LA. Neural crest cell-placodal neuron interactions are mediated by Cadherin-7 and N-cadherin during early chick trigeminal ganglion assembly. F1000Res 2022; 11:741. [PMID: 36128560 PMCID: PMC9475207 DOI: 10.12688/f1000research.122686.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Background: Arising at distinct positions in the head, the cranial ganglia are crucial for integrating various sensory inputs. The largest of these ganglia is the trigeminal ganglion, which relays pain, touch and temperature information through its three primary nerve branches to the central nervous system. The trigeminal ganglion and its nerves are composed of derivatives of two critical embryonic cell types, neural crest cells and placode cells, that migrate from different anatomical locations, coalesce together, and differentiate to form trigeminal sensory neurons and supporting glia. While the dual cellular origin of the trigeminal ganglion has been known for over 60 years, molecules expressed by neural crest cells and placode cells that regulate initial ganglion assembly remain obscure. Prior studies revealed the importance of cell surface cadherin proteins during early trigeminal gangliogenesis, with Cadherin-7 and neural cadherin (N-cadherin) expressed in neural crest cells and placode cells, respectively. Although cadherins typically interact in a homophilic ( i.e., like) fashion, the presence of different cadherins expressed in neural crest cells and placode cells raises the question as to whether heterophilic cadherin interactions may also be occurring. Given this, the aim of the study was to understand whether Cadherin-7 and N-cadherin were interacting during initial trigeminal ganglion formation. Methods: To assess potential interactions between Cadherin-7 and N-cadherin, we used biochemistry and innovative imaging assays conducted in vitro and in vivo, including in the forming chick trigeminal ganglion. Results: Our data revealed a physical interaction between Cadherin-7 and N-cadherin. Conclusions: These studies identify a new molecular basis by which neural crest cells and placode cells can aggregate in vivo to build the trigeminal ganglion during embryogenesis.
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Affiliation(s)
- Caroline A. Halmi
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, 20742, USA
| | - Chyong-Yi Wu
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, 20742, USA
- U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Lisa A. Taneyhill
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, 20742, USA
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25
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Han W, He M, Zhang Y, Zhou J, Li Z, Liu X, Sun X, Yin X, Yao D, Liang H. Cadherin-dependent adhesion modulated 3D cell-assembly. J Mater Chem B 2022; 10:4959-4966. [PMID: 35730726 DOI: 10.1039/d2tb01006b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of synthetic biology has opened new avenues in constructing cell-assembly biosystems with specific gene expression and function. The phenomena of cell spreading and detachment during tissue development and cancer metastasis are caused by surface tension, which in turn results from differences in cell-cell adhesion mediated by the dimerization of cadherin expressed on the cell surface. In this study, E- and P-cadherin plasmids were first constructed based on the differential adhesion hypothesis, then they were electroporated into K562 cells and HEK293T cells, respectively, to explore the process of cell migration and assembly regulated by cadherins. Using this approach, some special 3D cell functional components with a phase separation structure were fabricated successfully. Our work will be of potential application in the construction of self-assembling synthetic tissues and organoids.
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Affiliation(s)
- Wenjie Han
- Hefei National Research Center for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Miao He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Yunhan Zhang
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Junxiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhigang Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Xiaoyu Liu
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Xiaoyun Sun
- Hefei National Research Center for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Xue Yin
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Dongbao Yao
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China. .,School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China.
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Live imaging-based assay for visualising species-specific interactions in gamete adhesion molecules. Sci Rep 2022; 12:9609. [PMID: 35688940 PMCID: PMC9187738 DOI: 10.1038/s41598-022-13547-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/25/2022] [Indexed: 11/08/2022] Open
Abstract
Successful gamete fusion requires species-specific membrane adhesion. However, the interaction of adhesion molecules in gametes is difficult to study in real time through low-throughput microscopic observation. Therefore, we developed a live imaging-based adhesion molecule (LIAM) assay to study gamete adhesion molecule interactions in cultured cells. First, we modified a fusion assay previously established for fusogens introduced into cultured cells, and confirmed that our live imaging technique could visualise cell-cell fusion in the modified fusion assay. Next, instead of fusogen, we introduced adhesion molecules including a mammalian gamete adhesion molecule pair, IZUMO1 and JUNO, and detected their temporal accumulation at the contact interfaces of adjacent cells. Accumulated IZUMO1 or JUNO was partly translocated to the opposite cells as discrete spots; the mutation in amino acids required for their interaction impaired accumulation and translocation. By using the LIAM assay, we investigated the species specificity of IZUMO1 and JUNO of mouse, human, hamster, and pig in all combinations. IZUMO1 and JUNO accumulation and translocation were observed in conspecific, and some interspecific, combinations, suggesting potentially interchangeable combinations of IZUMO1 and JUNO from different species.
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Neel BL, Nisler CR, Walujkar S, Araya-Secchi R, Sotomayor M. Elastic versus brittle mechanical responses predicted for dimeric cadherin complexes. Biophys J 2022; 121:1013-1028. [PMID: 35151631 PMCID: PMC8943749 DOI: 10.1016/j.bpj.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/02/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Cadherins are a superfamily of adhesion proteins involved in a variety of biological processes that include the formation of intercellular contacts, the maintenance of tissue integrity, and the development of neuronal circuits. These transmembrane proteins are characterized by ectodomains composed of a variable number of extracellular cadherin (EC) repeats that are similar but not identical in sequence and fold. E-cadherin, along with desmoglein and desmocollin proteins, are three classical-type cadherins that have slightly curved ectodomains and engage in homophilic and heterophilic interactions through an exchange of conserved tryptophan residues in their N-terminal EC1 repeat. In contrast, clustered protocadherins are straighter than classical cadherins and interact through an antiparallel homophilic binding interface that involves overlapped EC1 to EC4 repeats. Here we present molecular dynamics simulations that model the adhesive domains of these cadherins using available crystal structures, with systems encompassing up to 2.8 million atoms. Simulations of complete classical cadherin ectodomain dimers predict a two-phased elastic response to force in which these complexes first softly unbend and then stiffen to unbind without unfolding. Simulated α, β, and γ clustered protocadherin homodimers lack a two-phased elastic response, are brittle and stiffer than classical cadherins and exhibit complex unbinding pathways that in some cases involve transient intermediates. We propose that these distinct mechanical responses are important for function, with classical cadherin ectodomains acting as molecular shock absorbers and with stiffer clustered protocadherin ectodomains facilitating overlap that favors binding specificity over mechanical resilience. Overall, our simulations provide insights into the molecular mechanics of single cadherin dimers relevant in the formation of cellular junctions essential for tissue function.
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Affiliation(s)
- Brandon L Neel
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio
| | - Collin R Nisler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Sanket Walujkar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Raul Araya-Secchi
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Santiago, Chile
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio; Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio.
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28
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Neel BL, Nisler CR, Walujkar S, Araya-Secchi R, Sotomayor M. Collective mechanical responses of cadherin-based adhesive junctions as predicted by simulations. Biophys J 2022; 121:991-1012. [PMID: 35150618 PMCID: PMC8943820 DOI: 10.1016/j.bpj.2022.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/02/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Cadherin-based adherens junctions and desmosomes help stabilize cell-cell contacts with additional function in mechano-signaling, while clustered protocadherin junctions are responsible for directing neuronal circuits assembly. Structural models for adherens junctions formed by epithelial cadherin (CDH1) proteins indicate that their long, curved ectodomains arrange to form a periodic, two-dimensional lattice stabilized by tip-to-tip trans interactions (across junction) and lateral cis contacts. Less is known about the exact architecture of desmosomes, but desmoglein (DSG) and desmocollin (DSC) cadherin proteins are also thought to form ordered junctions. In contrast, clustered protocadherin (PCDH)-based cell-cell contacts in neuronal tissues are thought to be responsible for self-recognition and avoidance, and structural models for clustered PCDH junctions show a linear arrangement in which their long and straight ectodomains form antiparallel overlapped trans complexes. Here, we report all-atom molecular dynamics simulations testing the mechanics of minimalistic adhesive junctions formed by CDH1, DSG2 coupled to DSC1, and PCDHγB4, with systems encompassing up to 3.7 million atoms. Simulations generally predict a favored shearing pathway for the adherens junction model and a two-phased elastic response to tensile forces for the adhesive adherens junction and the desmosome models. Complexes within these junctions first unbend at low tensile force and then become stiff to unbind without unfolding. However, cis interactions in both the CDH1 and DSG2-DSC1 systems dictate varied mechanical responses of individual dimers within the junctions. Conversely, the clustered protocadherin PCDHγB4 junction lacks a distinct two-phased elastic response. Instead, applied tensile force strains trans interactions directly, as there is little unbending of monomers within the junction. Transient intermediates, influenced by new cis interactions, are observed after the main rupture event. We suggest that these collective, complex mechanical responses mediated by cis contacts facilitate distinct functions in robust cell-cell adhesion for classical cadherins and in self-avoidance signaling for clustered PCDHs.
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Affiliation(s)
- Brandon L Neel
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio
| | - Collin R Nisler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Sanket Walujkar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Raul Araya-Secchi
- Facultad de Ingenieria y Tecnologia, Universidad San Sebastian, Santiago, Chile
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio; Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio.
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29
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Goodman KM, Katsamba PS, Rubinstein R, Ahlsén G, Bahna F, Mannepalli S, Dan H, Sampogna RV, Shapiro L, Honig B. How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition. eLife 2022; 11:e72416. [PMID: 35253643 PMCID: PMC8901172 DOI: 10.7554/elife.72416] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/26/2022] [Indexed: 12/30/2022] Open
Abstract
The stochastic expression of fewer than 60 clustered protocadherin (cPcdh) isoforms provides diverse identities to individual vertebrate neurons and a molecular basis for self-/nonself-discrimination. cPcdhs form chains mediated by alternating cis and trans interactions between apposed membranes, which has been suggested to signal self-recognition. Such a mechanism requires that cPcdh cis dimers form promiscuously to generate diverse recognition units, and that trans interactions have precise specificity so that isoform mismatches terminate chain growth. However, the extent to which cPcdh interactions fulfill these requirements has not been definitively demonstrated. Here, we report biophysical experiments showing that cPcdh cis interactions are promiscuous, but with preferences favoring formation of heterologous cis dimers. Trans homophilic interactions are remarkably precise, with no evidence for heterophilic interactions between different isoforms. A new C-type cPcdh crystal structure and mutagenesis data help to explain these observations. Overall, the interaction characteristics we report for cPcdhs help explain their function in neuronal self-/nonself-discrimination.
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Affiliation(s)
- Kerry Marie Goodman
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Phinikoula S Katsamba
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Rotem Rubinstein
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv UniversityTel AvivIsrael
- Sagol School of Neuroscience, Tel Aviv UniversityTel AvivIsrael
| | - Göran Ahlsén
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Fabiana Bahna
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Seetha Mannepalli
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Hanbin Dan
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
| | - Rosemary V Sampogna
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
| | - Lawrence Shapiro
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
| | - Barry Honig
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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Huene AL, Nicotra ML. Cell Aggregation Assays for Homophilic Interactions Between Cell Surface Proteins. Methods Mol Biol 2022; 2421:91-102. [PMID: 34870813 DOI: 10.1007/978-1-0716-1944-5_6] [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: 06/13/2023]
Abstract
Many proteins expressed on the cellular surface provide signaling and cell adhesion properties required for vital cellular functions. These binding interactions can occur between different but complementary proteins such as a ligand and receptor, or between the same protein acting as both ligand and receptor. The cell aggregation assay is a straightforward technique to identify homophilic interactions from such proteins. Here we describe the procedure for testing proteins via cell aggregation assays in HEK293T cells.
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Affiliation(s)
- Aidan L Huene
- Department of Surgery and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew L Nicotra
- Departments of Surgery and Immunology, Thomas E. Starzl Transplantation Institute, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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31
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Cadherin-13 is a critical regulator of GABAergic modulation in human stem-cell-derived neuronal networks. Mol Psychiatry 2022; 27:1-18. [PMID: 33972691 PMCID: PMC8960401 DOI: 10.1038/s41380-021-01117-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023]
Abstract
Activity in the healthy brain relies on a concerted interplay of excitation (E) and inhibition (I) via balanced synaptic communication between glutamatergic and GABAergic neurons. A growing number of studies imply that disruption of this E/I balance is a commonality in many brain disorders; however, obtaining mechanistic insight into these disruptions, with translational value for the patient, has typically been hampered by methodological limitations. Cadherin-13 (CDH13) has been associated with autism and attention-deficit/hyperactivity disorder. CDH13 localizes at inhibitory presynapses, specifically of parvalbumin (PV) and somatostatin (SST) expressing GABAergic neurons. However, the mechanism by which CDH13 regulates the function of inhibitory synapses in human neurons remains unknown. Starting from human-induced pluripotent stem cells, we established a robust method to generate a homogenous population of SST and MEF2C (PV-precursor marker protein) expressing GABAergic neurons (iGABA) in vitro, and co-cultured these with glutamatergic neurons at defined E/I ratios on micro-electrode arrays. We identified functional network parameters that are most reliably affected by GABAergic modulation as such, and through alterations of E/I balance by reduced expression of CDH13 in iGABAs. We found that CDH13 deficiency in iGABAs decreased E/I balance by means of increased inhibition. Moreover, CDH13 interacts with Integrin-β1 and Integrin-β3, which play opposite roles in the regulation of inhibitory synaptic strength via this interaction. Taken together, this model allows for standardized investigation of the E/I balance in a human neuronal background and can be deployed to dissect the cell-type-specific contribution of disease genes to the E/I balance.
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32
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The Autophagic Route of E-Cadherin and Cell Adhesion Molecules in Cancer Progression. Cancers (Basel) 2021; 13:cancers13246328. [PMID: 34944948 PMCID: PMC8699259 DOI: 10.3390/cancers13246328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary A hallmark of carcinoma progression is the loss of epithelial integrity. In this context, the deregulation of adhesion molecules, such as E-cadherin, affects epithelial structures and associates with epithelial to mesenchymal transition (EMT). This, in turn, fosters cancer progression. Autophagy endows cancer cells with the ability to overcome intracellular and environmental stress stimuli, such as anoikis, nutrient deprivation, hypoxia, and drugs. Furthermore, it plays an important role in the degradation of cell adhesion proteins and in EMT. This review focuses on the interplay between the turnover of adhesion molecules, primarily E-cadherin, and autophagy in cancer progression. Abstract Cell-to-cell adhesion is a key element in epithelial tissue integrity and homeostasis during embryogenesis, response to damage, and differentiation. Loss of cell adhesion and gain of mesenchymal features, a phenomenon known as epithelial to mesenchymal transition (EMT), are essential steps in cancer progression. Interestingly, downregulation or degradation by endocytosis of epithelial adhesion molecules (e.g., E-cadherin) associates with EMT and promotes cell migration. Autophagy is a physiological intracellular degradation and recycling process. In cancer, it is thought to exert a tumor suppressive role in the early phases of cell transformation but, once cells have gained a fully transformed phenotype, autophagy may fuel malignant progression by promoting EMT and conferring drug resistance. In this review, we discuss the crosstalk between autophagy, EMT, and turnover of epithelial cell adhesion molecules, with particular attention to E-cadherin.
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Gray ME, Johnson ZR, Modak D, Tamilselvan E, Tyska MJ, Sotomayor M. Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent. PLoS Biol 2021; 19:e3001463. [PMID: 34871294 PMCID: PMC8691648 DOI: 10.1371/journal.pbio.3001463] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/21/2021] [Accepted: 10/30/2021] [Indexed: 11/19/2022] Open
Abstract
Enterocytes are specialized epithelial cells lining the luminal surface of the small intestine that build densely packed arrays of microvilli known as brush borders. These microvilli drive nutrient absorption and are arranged in a hexagonal pattern maintained by intermicrovillar links formed by 2 nonclassical members of the cadherin superfamily of calcium-dependent cell adhesion proteins: protocadherin-24 (PCDH24, also known as CDHR2) and the mucin-like protocadherin (CDHR5). The extracellular domains of these proteins are involved in heterophilic and homophilic interactions important for intermicrovillar function, yet the structural determinants of these interactions remain unresolved. Here, we present X-ray crystal structures of the PCDH24 and CDHR5 extracellular tips and analyze their species-specific features relevant for adhesive interactions. In parallel, we use binding assays to identify the PCDH24 and CDHR5 domains involved in both heterophilic and homophilic adhesion for human and mouse proteins. Our results suggest that homophilic and heterophilic interactions involving PCDH24 and CDHR5 are species dependent with unique and distinct minimal adhesive units.
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Affiliation(s)
- Michelle E. Gray
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Zachary R. Johnson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Debadrita Modak
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Elakkiya Tamilselvan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
- Biophysics Program, The Ohio State University, Columbus, Ohio, United States of America
| | - Matthew J. Tyska
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Marcos Sotomayor
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
- Biophysics Program, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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34
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Chen Y, Brasch J, Harrison OJ, Bidone TC. Computational model of E-cadherin clustering under force. Biophys J 2021; 120:4944-4954. [PMID: 34687721 DOI: 10.1016/j.bpj.2021.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/02/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
E-cadherins play a critical role in the formation of cell-cell adhesions for several physiological functions, including tissue development, repair, and homeostasis. The formation of clusters of E-cadherins involves extracellular adhesive (trans-) and lateral (cis-) associations between E-cadherin ectodomains and stabilization through intracellular binding to the actomyosin cytoskeleton. This binding provides force to the adhesion and is required for mechanotransduction. However, the exact role of cytoskeletal force on the clustering of E-cadherins is not well understood. To gain insights into this mechanism, we developed a computational model based on Brownian dynamics. In the model, E-cadherins transit between structural and functional states; they are able to bind and unbind other E-cadherins on the same and/or opposite cell(s) through trans- and cis-interactions while also creating dynamic links with the actomyosin cytoskeleton. Our results show that actomyosin force governs the fraction of E-cadherins in clusters and the size and number of clusters. For low forces (below 10 pN), a large number of small E-cadherin clusters form with less than five E-cadherins each. At higher forces, the probability of forming fewer but larger clusters increases. These findings support the idea that force reinforces cell-cell adhesions, which is consistent with differences in cluster size previously observed between apical and lateral junctions of epithelial tissues.
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Affiliation(s)
- Yang Chen
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | - Julia Brasch
- Department of Biochemistry, University of Utah, Salt Lake City, Utah
| | - Oliver J Harrison
- Department of Biochemistry, University of Utah, Salt Lake City, Utah
| | - Tamara C Bidone
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah.
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35
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Passanha FR, Geuens T, LaPointe VLS. Sticking together: Harnessing cadherin biology for tissue engineering. Acta Biomater 2021; 134:107-115. [PMID: 34358698 DOI: 10.1016/j.actbio.2021.07.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/13/2021] [Accepted: 07/29/2021] [Indexed: 12/30/2022]
Abstract
Directing cell behavior and building a tissue for therapeutic impact is the main goal of regenerative medicine, for which scientists need to modulate the interaction of cells with biomaterials. The focus of the field thus far has been on the incorporation of cues from the extracellular matrix but we propose that scientists take lessons from cell-cell adhesion proteins, more specifically cadherin biology, as these proteins make multicellularity possible. In this perspective, we re-examine cadherins through the lens of a tissue engineer for the purpose of advancing regenerative medicine. Furthermore, we summarize exciting developments in biomaterials inspired by cadherins and discuss some challenges and opportunities for the future. STATEMENT OF SIGNIFICANCE: Tissue engineers need tools to direct cell behavior. To date, tissue engineers have designed many sophisticated materials to positively influence cell behavior but are faced with the challenge where these materials sometimes work and sometimes fail. This uncertainty is a big unanswered question that challenges the community. We propose that tissue engineering could be more successful if they would take lessons from cell-cell adhesion proteins, more specifically cadherin biology. In the article, we discuss key structural and functional characteristics that make cadherins ideal for tissue engineering approaches. Furthermore, by providing a state-of-the-art overview of exemplary studies that have used cadherins to influence cell behavior, we show tissue engineers that they already have the tools necessary to incorporate this knowledge.
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Affiliation(s)
- Fiona R Passanha
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands.
| | - Thomas Geuens
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands
| | - Vanessa L S LaPointe
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands.
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36
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Siva Sankar D, Dengjel J. Protein complexes and neighborhoods driving autophagy. Autophagy 2021; 17:2689-2705. [PMID: 33183148 PMCID: PMC8526019 DOI: 10.1080/15548627.2020.1847461] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/16/2020] [Accepted: 11/02/2020] [Indexed: 01/02/2023] Open
Abstract
Autophagy summarizes evolutionarily conserved, intracellular degradation processes targeting cytoplasmic material for lysosomal degradation. These encompass constitutive processes as well as stress responses, which are often found dysregulated in diseases. Autophagy pathways help in the clearance of damaged organelles, protein aggregates and macromolecules, mediating their recycling and maintaining cellular homeostasis. Protein-protein interaction networks contribute to autophagosome biogenesis, substrate loading, vesicular trafficking and fusion, protein translocations across membranes and degradation in lysosomes. Hypothesis-free proteomic approaches tremendously helped in the functional characterization of protein-protein interactions to uncover molecular mechanisms regulating autophagy. In this review, we elaborate on the importance of understanding protein-protein-interactions of varying affinities and on the strengths of mass spectrometry-based proteomic approaches to study these, generating new mechanistic insights into autophagy regulation. We discuss in detail affinity purification approaches and recent developments in proximity labeling coupled to mass spectrometry, which uncovered molecular principles of autophagy mechanisms.Abbreviations: AMPK: AMP-activated protein kinase; AP-MS: affinity purification-mass spectrometry; APEX2: ascorbate peroxidase-2; ATG: autophagy related; BioID: proximity-dependent biotin identification; ER: endoplasmic reticulum; GFP: green fluorescent protein; iTRAQ: isobaric tag for relative and absolute quantification; MS: mass spectrometry; PCA: protein-fragment complementation assay; PL-MS: proximity labeling-mass spectrometry; PtdIns3P: phosphatidylinositol-3-phosphate; PTM: posttranslational modification; PUP-IT: pupylation-based interaction tagging; RFP: red fluorescent protein; SILAC: stable isotope labeling by amino acids in cell culture; TAP: tandem affinity purification; TMT: tandem mass tag.
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Affiliation(s)
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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37
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Simon F, Konstantinides N. Single-cell transcriptomics in the Drosophila visual system: Advances and perspectives on cell identity regulation, connectivity, and neuronal diversity evolution. Dev Biol 2021; 479:107-122. [PMID: 34375653 DOI: 10.1016/j.ydbio.2021.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/10/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022]
Abstract
The Drosophila visual system supports complex behaviors and shares many of its anatomical and molecular features with the vertebrate brain. Yet, it contains a much more manageable number of neurons and neuronal types. In addition to the extensive Drosophila genetic toolbox, this relative simplicity has allowed decades of work to yield a detailed account of its neuronal type diversity, morphology, connectivity and specification mechanisms. In the past three years, numerous studies have applied large scale single-cell transcriptomic approaches to the Drosophila visual system and have provided access to the complete gene expression profile of most neuronal types throughout development. This makes the fly visual system particularly well suited to perform detailed studies of the genetic mechanisms underlying the evolution and development of neuronal systems. Here, we highlight how these transcriptomic resources allow exploring long-standing biological questions under a new light. We first present the efforts made to characterize neuronal diversity in the Drosophila visual system and suggest ways to further improve this description. We then discuss current advances allowed by the single-cell datasets, and envisage how these datasets can be further leveraged to address fundamental questions regarding the regulation of neuronal identity, neuronal circuit development and the evolution of neuronal diversity.
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Affiliation(s)
- Félix Simon
- Department of Biology, New York University, New York, NY, 10003, USA.
| | - Nikolaos Konstantinides
- Department of Biology, New York University, New York, NY, 10003, USA; Institut Jacques Monod, Centre National de la Recherche Scientifique-UMR 7592, Université Paris Diderot, Paris, France.
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38
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Torres-Sánchez A, Winter MK, Salbreux G. Tissue hydraulics: Physics of lumen formation and interaction. Cells Dev 2021; 168:203724. [PMID: 34339904 DOI: 10.1016/j.cdev.2021.203724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/08/2021] [Accepted: 07/20/2021] [Indexed: 11/29/2022]
Abstract
Lumen formation plays an essential role in the morphogenesis of tissues during development. Here we review the physical principles that play a role in the growth and coarsening of lumens. Solute pumping by the cell, hydraulic flows driven by differences of osmotic and hydrostatic pressures, balance of forces between extracellular fluids and cell-generated cytoskeletal forces, and electro-osmotic effects have been implicated in determining the dynamics and steady-state of lumens. We use the framework of linear irreversible thermodynamics to discuss the relevant force, time and length scales involved in these processes. We focus on order of magnitude estimates of physical parameters controlling lumen formation and coarsening.
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Affiliation(s)
| | - Max Kerr Winter
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, United Kingdom
| | - Guillaume Salbreux
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, United Kingdom; University of Geneva, Quai Ernest Ansermet 30, 1205 Genève, Switzerland.
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39
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Huene AL, Chen T, Nicotra ML. New binding specificities evolve via point mutation in an invertebrate allorecognition gene. iScience 2021; 24:102811. [PMID: 34296075 PMCID: PMC8282982 DOI: 10.1016/j.isci.2021.102811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 01/04/2023] Open
Abstract
Many organisms use genetic self-recognition systems to distinguish themselves from conspecifics. In the cnidarian, Hydractinia symbiolongicarpus, self-recognition is partially controlled by allorecognition 2 (Alr2). Alr2 encodes a highly polymorphic transmembrane protein that discriminates self from nonself by binding in trans to other Alr2 proteins with identical or similar sequences. Here, we focused on the N-terminal domain of Alr2, which can determine its binding specificity. We pair ancestral sequence reconstruction and experimental assays to show that amino acid substitutions can create sequences with novel binding specificities either directly (via one mutation) or via sequential mutations and intermediates with relaxed specificities. We also show that one side of the domain has experienced positive selection and likely forms the binding interface. Our results provide direct evidence that point mutations can generate Alr2 proteins with novel binding specificities. This provides a plausible mechanism for the generation and maintenance of functional variation in nature.
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Affiliation(s)
- Aidan L. Huene
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Traci Chen
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA
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40
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Golovkova I, Montel L, Pan F, Wandersman E, Prevost AM, Bertrand T, Pontani LL. Adhesion as a trigger of droplet polarization in flowing emulsions. SOFT MATTER 2021; 17:3820-3828. [PMID: 33725054 DOI: 10.1039/d1sm00097g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tissues are subjected to large external forces and undergo global deformations during morphogenesis. We use synthetic analogues of tissues to study the impact of cell-cell adhesion on the response of cohesive cellular assemblies under such stresses. In particular, we use biomimetic emulsions in which the droplets are functionalized in order to exhibit specific droplet-droplet adhesion. We flow these emulsions in microfluidic constrictions and study their response to this forced deformation via confocal microscopy. We find that the distributions of avalanche sizes are conserved between repulsive and adhesive droplets. However, adhesion locally impairs the rupture of droplet-droplet contacts, which in turn pulls on the rearranging droplets. As a result, adhesive droplets are a lot more deformed along the axis of elongation in the constriction. This finding could shed light on the origin of polarization processes during morphogenesis.
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Affiliation(s)
- Iaroslava Golovkova
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris, France.
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41
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Mendoza C, Nagidi SH, Mizrachi D. Molecular Characterization of the Extracellular Domain of Human Junctional Adhesion Proteins. Int J Mol Sci 2021; 22:ijms22073482. [PMID: 33801758 PMCID: PMC8037251 DOI: 10.3390/ijms22073482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/22/2022] Open
Abstract
The junction adhesion molecule (JAM) family of proteins play central roles in the tight junction (TJ) structure and function. In contrast to claudins (CLDN) and occludin (OCLN), the other membrane proteins of the TJ, whose structure is that of a 4α-helix bundle, JAMs are members of the immunoglobulin superfamily. The JAM family is composed of four members: A, B, C and 4. The crystal structure of the extracellular domain of JAM-A continues to be used as a template to model the secondary and tertiary structure of the other members of the family. In this article, we have expressed the extracellular domains of JAMs fused with maltose-binding protein (MBP). This strategy enabled the work presented here, since JAM-B, JAM-C and JAM4 are more difficult targets due to their more hydrophobic nature. Our results indicate that each member of the JAM family has a unique tertiary structure in spite of having similar secondary structures. Surface plasmon resonance (SPR) revealed that heterotypic interactions among JAM family members can be greatly favored compared to homotypic interactions. We employ the well characterized epithelial cadherin (E-CAD) as a means to evaluate the adhesive properties of JAMs. We present strong evidence that suggests that homotypic or heterotypic interactions among JAMs are stronger than that of E-CADs.
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Affiliation(s)
- Christopher Mendoza
- Department of Physiology and Developmental Biology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA;
| | - Sai Harsha Nagidi
- Department of Molecular Microbiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA;
| | - Dario Mizrachi
- Department of Physiology and Developmental Biology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA;
- Correspondence:
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42
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Polanco J, Reyes-Vigil F, Weisberg SD, Dhimitruka I, Brusés JL. Differential Spatiotemporal Expression of Type I and Type II Cadherins Associated With the Segmentation of the Central Nervous System and Formation of Brain Nuclei in the Developing Mouse. Front Mol Neurosci 2021; 14:633719. [PMID: 33833667 PMCID: PMC8021962 DOI: 10.3389/fnmol.2021.633719] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
Type I and type II classical cadherins comprise a family of cell adhesion molecules that regulate cell sorting and tissue separation by forming specific homo and heterophilic bonds. Factors that affect cadherin-mediated cell-cell adhesion include cadherin binding affinity and expression level. This study examines the expression pattern of type I cadherins (Cdh1, Cdh2, Cdh3, and Cdh4), type II cadherins (Cdh6, Cdh7, Cdh8, Cdh9, Cdh10, Cdh11, Cdh12, Cdh18, Cdh20, and Cdh24), and the atypical cadherin 13 (Cdh13) during distinct morphogenetic events in the developing mouse central nervous system from embryonic day 11.5 to postnatal day 56. Cadherin mRNA expression levels obtained from in situ hybridization experiments carried out at the Allen Institute for Brain Science (https://alleninstitute.org/) were retrieved from the Allen Developing Mouse Brain Atlas. Cdh2 is the most abundantly expressed type I cadherin throughout development, while Cdh1, Cdh3, and Cdh4 are expressed at low levels. Type II cadherins show a dynamic pattern of expression that varies between neuroanatomical structures and developmental ages. Atypical Cdh13 expression pattern correlates with Cdh2 in abundancy and localization. Analyses of cadherin-mediated relative adhesion estimated from their expression level and binding affinity show substantial differences in adhesive properties between regions of the neural tube associated with the segmentation along the anterior–posterior axis. Differences in relative adhesion were also observed between brain nuclei in the developing subpallium (basal ganglia), suggesting that differential cell adhesion contributes to the segregation of neuronal pools. In the adult cerebral cortex, type II cadherins Cdh6, Cdh8, Cdh10, and Cdh12 are abundant in intermediate layers, while Cdh11 shows a gradated expression from the deeper layer 6 to the superficial layer 1, and Cdh9, Cdh18, and Cdh24 are more abundant in the deeper layers. Person’s correlation analyses of cadherins mRNA expression patterns between areas and layers of the cerebral cortex and the nuclei of the subpallium show significant correlations between certain cortical areas and the basal ganglia. The study shows that differential cadherin expression and cadherin-mediated adhesion are associated with a wide range of morphogenetic events in the developing central nervous system including the organization of neurons into layers, the segregation of neurons into nuclei, and the formation of neuronal circuits.
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Affiliation(s)
- Julie Polanco
- Department of Natural Sciences, Mercy College, Dobbs Ferry, NY, United States
| | - Fredy Reyes-Vigil
- Department of Natural Sciences, Mercy College, Dobbs Ferry, NY, United States
| | - Sarah D Weisberg
- Department of Natural Sciences, Mercy College, Dobbs Ferry, NY, United States
| | - Ilirian Dhimitruka
- Department of Natural Sciences, Mercy College, Dobbs Ferry, NY, United States
| | - Juan L Brusés
- Department of Natural Sciences, Mercy College, Dobbs Ferry, NY, United States
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43
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Honig B, Shapiro L. Adhesion Protein Structure, Molecular Affinities, and Principles of Cell-Cell Recognition. Cell 2021; 181:520-535. [PMID: 32359436 DOI: 10.1016/j.cell.2020.04.010] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The ability of cells to organize into multicellular structures in precise patterns requires that they "recognize" one another with high specificity. We discuss recent progress in understanding the molecular basis of cell-cell recognition, including unique phenomena associated with neuronal interactions. We describe structures of select adhesion receptor complexes and their assembly into larger intercellular junction structures and discuss emerging principles that relate cell-cell organization to the binding specificities and energetics of adhesion receptors. Armed with these insights, advances in protein design and gene editing should pave the way for breakthroughs toward understanding the molecular basis of cell patterning in vivo.
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Affiliation(s)
- Barry Honig
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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44
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Ikuta R, Myoenzono K, Wasano J, Hamaguchi-Hamada K, Hamada S, Kurumata-Shigeto M. N-cadherin localization in taste buds of mouse circumvallate papillae. J Comp Neurol 2020; 529:2227-2242. [PMID: 33319419 DOI: 10.1002/cne.25090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/03/2023]
Abstract
Taste buds, the receptor organs for taste, contain 50-100 taste bud cells. Although these cells undergo continuous turnover, the structural and functional integrity of taste buds is maintained. The molecular mechanisms by which synaptic connectivity between taste buds and afferent fibers is formed and maintained remain ambiguous. In the present study, we examined the localization of N-cadherin in the taste buds of the mouse circumvallate papillae because N-cadherin, one of the classical cadherins, is important for the formation and maintenance of synapses. At the light microscopic level, N-cadherin was predominantly detected in type II cells and nerve fibers in the connective tissues in and around the vallate papillae. At the ultrastructural level, N-cadherin immunoreactivity appears along the cell membrane and in the intracellular vesicles of type II cells. N-cadherin immunoreactivity also is evident in the membranes of afferent terminals at the contact sites to N-cadherin-positive type II cells. At channel type synapses between type II cells and nerve fibers, N-cadherin is present surrounding, but not within, the presumed neurotransmitter release zone, identified by large mitochondria apposed to the taste cells. The present results suggest that N-cadherin is important for the formation or maintenance of type II cell afferent synapses in taste buds.
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Affiliation(s)
- Rio Ikuta
- International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Japan
| | - Kanae Myoenzono
- International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Japan.,Humanome Lab., Inc., Tokyo, Japan
| | - Jun Wasano
- International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Japan
| | | | - Shun Hamada
- International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Japan
| | - Mami Kurumata-Shigeto
- International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Japan
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45
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Shafraz O, Xie B, Yamada S, Sivasankar S. Mapping transmembrane binding partners for E-cadherin ectodomains. Proc Natl Acad Sci U S A 2020; 117:31157-31165. [PMID: 33229577 PMCID: PMC7733791 DOI: 10.1073/pnas.2010209117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We combine proximity labeling and single molecule binding assays to discover transmembrane protein interactions in cells. We first screen for candidate binding partners by tagging the extracellular and cytoplasmic regions of a "bait" protein with BioID biotin ligase and identify proximal proteins that are biotin tagged on both their extracellular and intracellular regions. We then test direct binding interactions between proximal proteins and the bait, using single molecule atomic force microscope binding assays. Using this approach, we identify binding partners for the extracellular region of E-cadherin, an essential cell-cell adhesion protein. We show that the desmosomal proteins desmoglein-2 and desmocollin-3, the focal adhesion protein integrin-α2β1, the receptor tyrosine kinase ligand ephrin-B1, and the classical cadherin P-cadherin, all directly interact with E-cadherin ectodomains. Our data shows that combining extracellular and cytoplasmic proximal tagging with a biophysical binding assay increases the precision with which transmembrane ectodomain interactors can be identified.
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Affiliation(s)
- Omer Shafraz
- Department of Biomedical Engineering, University of California, Davis, CA 95616
| | - Bin Xie
- Biophysics Graduate Group, University of California, Davis, CA 95616
| | - Soichiro Yamada
- Department of Biomedical Engineering, University of California, Davis, CA 95616
| | - Sanjeevi Sivasankar
- Department of Biomedical Engineering, University of California, Davis, CA 95616;
- Biophysics Graduate Group, University of California, Davis, CA 95616
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46
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Hiraga K, Inoue YU, Asami J, Hotta M, Morimoto Y, Tatsumoto S, Hoshino M, Go Y, Inoue T. Redundant type II cadherins define neuroepithelial cell states for cytoarchitectonic robustness. Commun Biol 2020; 3:574. [PMID: 33060832 PMCID: PMC7567090 DOI: 10.1038/s42003-020-01297-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 09/15/2020] [Indexed: 02/07/2023] Open
Abstract
Individual cell shape and integrity must precisely be orchestrated during morphogenesis. Here, we determine function of type II cadherins, Cdh6, Cdh8, and Cdh11, whose expression combinatorially demarcates the mouse neural plate/tube. While CRISPR/Cas9-based single type II cadherin mutants show no obvious phenotype, Cdh6/8 double knockout (DKO) mice develop intermingled forebrain/midbrain compartments as these two cadherins' expression opposes at the nascent boundary. Cdh6/8/11 triple, Cdh6/8 or Cdh8/11 DKO mice further cause exencephaly just within the cranial region where mutated cadherins' expression merges. In the Cdh8/11 DKO midbrain, we observe less-constricted apical actin meshwork, ventrally-directed spreading, and occasional hyperproliferation among dorsal neuroepithelial cells as origins for exencephaly. These results provide rigid evidence that, by conferring distinct adhesive codes to each cell, redundant type II cadherins serve essential and shared roles in compartmentalization and neurulation, both of which proceed under the robust control of the number, positioning, constriction, and fluidity of neuroepithelial cells.
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Affiliation(s)
- Kou Hiraga
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Junko Asami
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Mayuko Hotta
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
- Graduate School of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Koganei, Tokyo, 184-8588, Japan
| | - Yuki Morimoto
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Shoji Tatsumoto
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Saigo-naka 38, Myoudaiji, Okazaki, Aichi, 444-8585, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan
| | - Yasuhiro Go
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Saigo-naka 38, Myoudaiji, Okazaki, Aichi, 444-8585, Japan
- Department of System Neuroscience, National Institute for Physiological Sciences, Saigo-naka 38, Myoudaiji, Okazaki, Aichi, 444-8585, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Saigo-naka 38, Myoudaiji, Okazaki, Aichi, 444-8585, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo, 187-8502, Japan.
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47
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Rasoulinejad S, Mueller M, Nzigou Mombo B, Wegner SV. Orthogonal Blue and Red Light Controlled Cell-Cell Adhesions Enable Sorting-out in Multicellular Structures. ACS Synth Biol 2020; 9:2076-2086. [PMID: 32610009 PMCID: PMC7757848 DOI: 10.1021/acssynbio.0c00150] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
The self-assembly of different cell
types into multicellular structures
and their organization into spatiotemporally controlled patterns are
both challenging and extremely powerful to understand how cells function
within tissues and for bottom-up tissue engineering. Here, we not
only independently control the self-assembly of two cell types into
multicellular architectures with blue and red light, but also achieve
their self-sorting into distinct assemblies. This required developing
two cell types that form selective and homophilic cell–cell
interactions either under blue or red light using photoswitchable
proteins as artificial adhesion molecules. The interactions were individually
triggerable with different colors of light, reversible in the dark,
and provide noninvasive and temporal control over the cell–cell
adhesions. In mixtures of the two cells, each cell type self-assembled
independently upon orthogonal photoactivation, and cells sorted out
into separate assemblies based on specific self-recognition. These
self-sorted multicellular architectures provide us with a powerful
tool for producing tissue-like structures from multiple cell types
and investigate principles that govern them.
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Affiliation(s)
- Samaneh Rasoulinejad
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Marc Mueller
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Brice Nzigou Mombo
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster Waldeyerstrasse 15, Münster, 48149, Germany
| | - Seraphine V. Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster Waldeyerstrasse 15, Münster, 48149, Germany
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48
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Zhao B, Li N, Xie T, Bagheri Y, Liang C, Keshri P, Sun Y, You M. Quantifying tensile forces at cell-cell junctions with a DNA-based fluorescent probe. Chem Sci 2020; 11:8558-8566. [PMID: 34123115 PMCID: PMC8163409 DOI: 10.1039/d0sc01455a] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Cells are physically contacting with each other. Direct and precise quantification of forces at cell–cell junctions is still challenging. Herein, we have developed a DNA-based ratiometric fluorescent probe, termed DNAMeter, to quantify intercellular tensile forces. These lipid-modified DNAMeters can spontaneously anchor onto live cell membranes. The DNAMeter consists of two self-assembled DNA hairpins of different force tolerance. Once the intercellular tension exceeds the force tolerance to unfold a DNA hairpin, a specific fluorescence signal will be activated, which enables the real-time imaging and quantification of tensile forces. Using E-cadherin-modified DNAMeter as an example, we have demonstrated an approach to quantify, at the molecular level, the magnitude and distribution of E-cadherin tension among epithelial cells. Compatible with readily accessible fluorescence microscopes, these easy-to-use DNA tension probes can be broadly used to quantify mechanotransduction in collective cell behaviors. A DNA-based fluorescent probe to quantify the magnitude and distribution of tensile forces at cell–cell junctions.![]()
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Affiliation(s)
- Bin Zhao
- Department of Chemistry, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Ningwei Li
- Department of Mechanical & Industrial Engineering, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Tianfa Xie
- Department of Mechanical & Industrial Engineering, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Yousef Bagheri
- Department of Chemistry, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Chungwen Liang
- Computational and Modeling Core, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst Massachusetts 01003 USA
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Yubing Sun
- Department of Mechanical & Industrial Engineering, University of Massachusetts Amherst Massachusetts 01003 USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts Amherst Massachusetts 01003 USA
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49
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An JY, Zhou Y, Yan ZJ, Zhao YJ. Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information. Evol Bioinform Online 2020; 16:1176934320924674. [PMID: 32550764 PMCID: PMC7278102 DOI: 10.1177/1176934320924674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/16/2020] [Indexed: 11/15/2022] Open
Abstract
Self-interacting proteins (SIPs) play crucial roles in biological activities of organisms. Many high-throughput methods can be used to identify SIPs. However, these methods are both time-consuming and expensive. How to develop effective computational approaches for identifying SIPs is a challenging task. In the article, we present a novel computational method called RRN-SIFT, which combines the recurrent neural network (RNN) with scale invariant feature transform (SIFT) to predict SIPs based on protein evolutionary information. The main advantage of the proposed RNN-SIFT model is that it uses SIFT for extracting key feature by exploring the evolutionary information embedded in Position-Specific Iterated BLAST-constructed position-specific scoring matrix and employs an RNN classifier to perform classification based on extracted features. Extensive experiments show that the RRN-SIFT obtained average accuracy of 94.34% and 97.12% on the yeast and human dataset, respectively. We also compared our performance with the back propagation neural network (BPNN), the state-of-the-art support vector machine (SVM), and other existing methods. By comparing with experimental results, the performance of RNN-SIFT is significantly better than that of the BPNN, SVM, and other previous methods in the domain. Therefore, we conclude that the proposed RNN-SIFT model is a useful tool for predicting SIPs, as well to solve other bioinformatics tasks. To facilitate widely studies and encourage future proteomics research, a freely available web server called RNN-SIFT-SIPs was developed at http://219.219.62.123:8888/RNNSIFT/ including the source code and the SIP datasets.
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Affiliation(s)
- Ji-Yong An
- School of Computer Science and Technology, China
University of Mining and Technology, Xuzhou, China
| | - Yong Zhou
- School of Computer Science and Technology, China
University of Mining and Technology, Xuzhou, China
| | - Zi-Ji Yan
- School of Computer Science and Technology, China
University of Mining and Technology, Xuzhou, China
| | - Yu-Jun Zhao
- School of Computer Science and Technology, China
University of Mining and Technology, Xuzhou, China
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50
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Terzoli S, Tiana G. Molecular Recognition between Cadherins Studied by a Coarse-Grained Model Interacting with a Coevolutionary Potential. J Phys Chem B 2020; 124:4079-4088. [PMID: 32336092 PMCID: PMC8007105 DOI: 10.1021/acs.jpcb.0c01671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Studying the conformations
involved in the dimerization of cadherins
is highly relevant to understand the development of tissues and its
failure, which is associated with tumors and metastases. Experimental
techniques, like X-ray crystallography, can usually report only the
most stable conformations, missing minority states that could nonetheless
be important for the recognition mechanism. Computer simulations could
be a valid complement to the experimental approach. However, standard
all-atom protein models in explicit solvent are computationally too
demanding to search thoroughly the conformational space of multiple
chains composed of several hundreds of amino acids. To reach this
goal, we resorted to a coarse-grained model in implicit solvent. The
standard problem with this kind of model is to find a realistic potential
to describe its interactions. We used coevolutionary information from
cadherin alignments, corrected by a statistical potential, to build
an interaction potential, which is agnostic about the experimental
conformations of the protein. Using this model, we explored the conformational
space of multichain systems and validated the results comparing with
experimental data. We identified dimeric conformations that are sequence
specific and that can be useful to rationalize the mechanism of recognition
between cadherins.
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Affiliation(s)
- Sara Terzoli
- Department of Physics and Center for Complexity and Biosystems, Universitá degli Studi di Milano and INFN, via Celoria 16, Milano 20133, Italy
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, Universitá degli Studi di Milano and INFN, via Celoria 16, Milano 20133, Italy
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