1
|
Zhang S, Ma Z. trans-Interacting Plasma Membrane Proteins and Binding Partner Identification. J Proteome Res 2024; 23:3322-3331. [PMID: 38937710 DOI: 10.1021/acs.jproteome.4c00289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Plasma membrane proteins (PMPs) play critical roles in a myriad of physiological and disease conditions. A unique subset of PMPs functions through interacting with each other in trans at the interface between two contacting cells. These trans-interacting PMPs (tiPMPs) include adhesion molecules and ligands/receptors that facilitate cell-cell contact and direct communication between cells. Among the tiPMPs, a significant number have apparent extracellular binding domains but remain orphans with no known binding partners. Identification of their potential binding partners is therefore important for the understanding of processes such as organismal development and immune cell activation. While a number of methods have been developed for the identification of protein binding partners in general, very few are applicable to tiPMPs, which interact in a two-dimensional fashion with low intrinsic binding affinities. In this review, we present the significance of tiPMP interactions, the challenges of identifying binding partners for tiPMPs, and the landscape of method development. We describe current avidity-based screening approaches for identifying novel tiPMP binding partners and discuss their advantages and limitations. We conclude by highlighting the importance of developing novel methods of identifying new tiPMP interactions for deciphering the complex protein interactome and developing targeted therapeutics for diseases.
Collapse
Affiliation(s)
- Shenyu Zhang
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
| | - Zhengyu Ma
- Nemours Children's Hospital, Wilmington, Delaware 19803, United States
| |
Collapse
|
2
|
Shilts J, Severin Y, Galaway F, Müller-Sienerth N, Chong ZS, Pritchard S, Teichmann S, Vento-Tormo R, Snijder B, Wright GJ. A physical wiring diagram for the human immune system. Nature 2022; 608:397-404. [PMID: 35922511 PMCID: PMC9365698 DOI: 10.1038/s41586-022-05028-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/28/2022] [Indexed: 12/14/2022]
Abstract
The human immune system is composed of a distributed network of cells circulating throughout the body, which must dynamically form physical associations and communicate using interactions between their cell-surface proteomes1. Despite their therapeutic potential2, our map of these surface interactions remains incomplete3,4. Here, using a high-throughput surface receptor screening method, we systematically mapped the direct protein interactions across a recombinant library that encompasses most of the surface proteins that are detectable on human leukocytes. We independently validated and determined the biophysical parameters of each novel interaction, resulting in a high-confidence and quantitative view of the receptor wiring that connects human immune cells. By integrating our interactome with expression data, we identified trends in the dynamics of immune interactions and constructed a reductionist mathematical model that predicts cellular connectivity from basic principles. We also developed an interactive multi-tissue single-cell atlas that infers immune interactions throughout the body, revealing potential functional contexts for new interactions and hubs in multicellular networks. Finally, we combined targeted protein stimulation of human leukocytes with multiplex high-content microscopy to link our receptor interactions to functional roles, in terms of both modulating immune responses and maintaining normal patterns of intercellular associations. Together, our work provides a systematic perspective on the intercellular wiring of the human immune system that extends from systems-level principles of immune cell connectivity down to mechanistic characterization of individual receptors, which could offer opportunities for therapeutic intervention.
Collapse
Affiliation(s)
- Jarrod Shilts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
| | - Yannik Severin
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | | | - Zheng-Shan Chong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | - Sophie Pritchard
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Sarah Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Roser Vento-Tormo
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, UK.
| |
Collapse
|
3
|
Anisul M, Shilts J, Schwartzentruber J, Hayhurst J, Buniello A, Shaikho Elhaj Mohammed E, Zheng J, Holmes M, Ochoa D, Carmona M, Maranville J, Gaunt TR, Emilsson V, Gudnason V, McDonagh EM, Wright GJ, Ghoussaini M, Dunham I. A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance. eLife 2021; 10:e69719. [PMID: 34402426 PMCID: PMC8457835 DOI: 10.7554/elife.69719] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/07/2021] [Indexed: 12/16/2022] Open
Abstract
Background The virus SARS-CoV-2 can exploit biological vulnerabilities (e.g. host proteins) in susceptible hosts that predispose to the development of severe COVID-19. Methods To identify host proteins that may contribute to the risk of severe COVID-19, we undertook proteome-wide genetic colocalisation tests, and polygenic (pan) and cis-Mendelian randomisation analyses leveraging publicly available protein and COVID-19 datasets. Results Our analytic approach identified several known targets (e.g. ABO, OAS1), but also nominated new proteins such as soluble Fas (colocalisation probability >0.9, p=1 × 10-4), implicating Fas-mediated apoptosis as a potential target for COVID-19 risk. The polygenic (pan) and cis-Mendelian randomisation analyses showed consistent associations of genetically predicted ABO protein with several COVID-19 phenotypes. The ABO signal is highly pleiotropic, and a look-up of proteins associated with the ABO signal revealed that the strongest association was with soluble CD209. We demonstrated experimentally that CD209 directly interacts with the spike protein of SARS-CoV-2, suggesting a mechanism that could explain the ABO association with COVID-19. Conclusions Our work provides a prioritised list of host targets potentially exploited by SARS-CoV-2 and is a precursor for further research on CD209 and FAS as therapeutically tractable targets for COVID-19. Funding MAK, JSc, JH, AB, DO, MC, EMM, MG, ID were funded by Open Targets. J.Z. and T.R.G were funded by the UK Medical Research Council Integrative Epidemiology Unit (MC_UU_00011/4). JSh and GJW were funded by the Wellcome Trust Grant 206194. This research was funded in part by the Wellcome Trust [Grant 206194]. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.
Collapse
Affiliation(s)
- Mohd Anisul
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Jarrod Shilts
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Jeremy Schwartzentruber
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
| | - James Hayhurst
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | - Annalisa Buniello
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | | | - Jie Zheng
- Medical Research Council (MRC) Integrative Epidemiology Unit, Department of Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Michael Holmes
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU), Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
| | - David Ochoa
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | - Miguel Carmona
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | | | - Tom R Gaunt
- Medical Research Council (MRC) Integrative Epidemiology Unit, Department of Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Valur Emilsson
- Icelandic Heart AssociationKopavogurIceland
- Faculty of Medicine, University of IcelandReykjavikIceland
| | - Vilmundur Gudnason
- Icelandic Heart AssociationKopavogurIceland
- Faculty of Medicine, University of IcelandReykjavikIceland
| | - Ellen M McDonagh
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | - Gavin J Wright
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Department of Biology, York Biomedical Research Institute, Hull York Medical School, University of YorkYorkUnited Kingdom
| | - Maya Ghoussaini
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| |
Collapse
|
4
|
Khairil Anuar INA, Banerjee A, Keeble AH, Carella A, Nikov GI, Howarth M. Spy&Go purification of SpyTag-proteins using pseudo-SpyCatcher to access an oligomerization toolbox. Nat Commun 2019; 10:1734. [PMID: 30988307 PMCID: PMC6465384 DOI: 10.1038/s41467-019-09678-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Peptide tags are a key resource, introducing minimal change while enabling a consistent process to purify diverse proteins. However, peptide tags often provide minimal benefit post-purification. We previously designed SpyTag, forming an irreversible bond with its protein partner SpyCatcher. SpyTag provides an easy route to anchor, bridge or multimerize proteins. Here we establish Spy&Go, enabling protein purification using SpyTag. Through rational engineering we generated SpyDock, which captures SpyTag-fusions and allows efficient elution. Spy&Go enabled sensitive purification of SpyTag-fusions from Escherichia coli, giving superior purity than His-tag/nickel-nitrilotriacetic acid. Spy&Go allowed purification of mammalian-expressed, N-terminal, C-terminal or internal SpyTag. As an oligomerization toolbox, we established a panel of SpyCatcher-linked coiled coils, so SpyTag-fusions can be dimerized, trimerized, tetramerized, pentamerized, hexamerized or heptamerized. Assembling oligomers for Death Receptor 5 stimulation, we probed multivalency effects on cancer cell death. Spy&Go, combined with simple oligomerization, should have broad application for exploring multivalency in signaling.
Collapse
Affiliation(s)
| | - Anusuya Banerjee
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Alberto Carella
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Georgi I Nikov
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| |
Collapse
|
5
|
Gonzalez-Gil A, Porell RN, Fernandes SM, Wei Y, Yu H, Carroll DJ, McBride R, Paulson JC, Tiemeyer M, Aoki K, Bochner BS, Schnaar RL. Sialylated keratan sulfate proteoglycans are Siglec-8 ligands in human airways. Glycobiology 2019; 28:786-801. [PMID: 29924315 PMCID: PMC6142871 DOI: 10.1093/glycob/cwy057] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/18/2018] [Indexed: 01/02/2023] Open
Abstract
Human siglecs are a family of 14 sialic acid-binding proteins, most of which are expressed on subsets of immune cells where they regulate immune responses. Siglec-8 is expressed selectively on human allergic inflammatory cells—primarily eosinophils and mast cells—where engagement causes eosinophil apoptosis and inhibits mast cell mediator release. Evidence supports a model in which human eosinophils and mast cells bind to Siglec-8 sialoglycan ligands on inflammatory target tissues to resolve allergic inflammation and limit tissue damage. To identify Siglec-8-binding sialoglycans from human airways, proteins extracted from postmortem human trachea were resolved by size-exclusion chromatography and composite agarose–acrylamide gel electrophoresis, blotted and probed by Siglec-8-Fc blot overlay. Three size classes of Siglec-8 ligands were identified: 250 kDa, 600 kDa and 1 MDa, each of which was purified by affinity chromatography using a recombinant pentameric form of Siglec-8. Proteomic mass spectrometry identified all size classes as the proteoglycan aggrecan, a finding validated by immunoblotting. Glycan array studies demonstrated Siglec-8 binding to synthetic glycans with a terminal Neu5Acα2-3(6-sulfo)-Gal determinant, a quantitatively minor terminus on keratan sulfate (KS) chains of aggrecan. Treating human tracheal extracts with sialidase or keratanase eliminated Siglec-8 binding, indicating sialylated KS chains as Siglec-8-binding determinants. Treating human tracheal histological sections with keratanase also completely eliminated the binding of Siglec-8-Fc. Finally, Siglec-8 ligand purified from human trachea extracts induced increased apoptosis of freshly isolated human eosinophils in vitro. We conclude that sialylated KS proteoglycans are endogenous human airway ligands that bind Siglec-8 and may regulate allergic inflammation.
Collapse
Affiliation(s)
- Anabel Gonzalez-Gil
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan N Porell
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steve M Fernandes
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yadong Wei
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Huifeng Yu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniela J Carroll
- Department of Medicine, Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ryan McBride
- Departments of Chemical Physiology, Cell and Molecular Biology, and Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - James C Paulson
- Departments of Chemical Physiology, Cell and Molecular Biology, and Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Bruce S Bochner
- Department of Medicine, Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ronald L Schnaar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
6
|
Toledano Furman NE, Prabhakara KS, Bedi S, Cox CS, Olson SD. OMIP-041: Optimized multicolor immunofluorescence panel rat microglial staining protocol. Cytometry A 2017; 93:182-185. [DOI: 10.1002/cyto.a.23267] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 09/14/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Naama E. Toledano Furman
- Department of Pediatric Surgery; McGovern Medical School, The University of Texas Health Science Center; Houston Texas
| | - Karthik S. Prabhakara
- Department of Pediatric Surgery; McGovern Medical School, The University of Texas Health Science Center; Houston Texas
| | - Supinder Bedi
- Department of Pediatric Surgery; McGovern Medical School, The University of Texas Health Science Center; Houston Texas
| | - Charles S. Cox
- Department of Pediatric Surgery; McGovern Medical School, The University of Texas Health Science Center; Houston Texas
| | - Scott D. Olson
- Department of Pediatric Surgery; McGovern Medical School, The University of Texas Health Science Center; Houston Texas
| |
Collapse
|
7
|
Li H, Watson A, Olechwier A, Anaya M, Sorooshyari SK, Harnett DP, Lee HKP, Vielmetter J, Fares MA, Garcia KC, Özkan E, Labrador JP, Zinn K. Deconstruction of the beaten Path-Sidestep interaction network provides insights into neuromuscular system development. eLife 2017; 6:28111. [PMID: 28829740 PMCID: PMC5578738 DOI: 10.7554/elife.28111] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/28/2017] [Indexed: 12/16/2022] Open
Abstract
An ‘interactome’ screen of all Drosophila cell-surface and secreted proteins containing immunoglobulin superfamily (IgSF) domains discovered a network formed by paralogs of Beaten Path (Beat) and Sidestep (Side), a ligand-receptor pair that is central to motor axon guidance. Here we describe a new method for interactome screening, the Bio-Plex Interactome Assay (BPIA), which allows identification of many interactions in a single sample. Using the BPIA, we ‘deorphanized’ four more members of the Beat-Side network. We confirmed interactions using surface plasmon resonance. The expression patterns of beat and side genes suggest that Beats are neuronal receptors for Sides expressed on peripheral tissues. side-VI is expressed in muscle fibers targeted by the ISNb nerve, as well as at growth cone choice points and synaptic targets for the ISN and TN nerves. beat-V genes, encoding Side-VI receptors, are expressed in ISNb and ISN motor neurons. Within every organ of the body, cells must be able to recognise and communicate with one another in order to work together to perform a particular role. Each cell has a specific protein on its surface that acts like a molecular identity card, and which can form weak bonds with a complementary protein on another cell. There are thousands of different cell surface proteins, and the interactions between them – known collectively as the interactome – dictate the how cells interact with one another. Many cell surface proteins are similar across species. Humans and fruit flies, for example, both possess a family of cell surface proteins that contain a region called the Immunoglobulin Superfamily domain. This family can be further divided into subfamilies, two of which are known as “Beats” and “Sides” for short. As the nervous system develops, nerve cells carrying a particular Beat protein interact with nerve or muscle cells carrying a corresponding Side protein. Yet while experiments have matched up many Beats and Sides, the partners of others remain unknown. Li et al. have now developed a new technique called the Bio-Plex Interactome Assay to rapidly screen for interactions between multiple cell surface proteins in a single sample. Applying the technique to cells from fruit flies revealed new binding partners within the Beats and the Sides. After verifying several of these interactions, Li et al. explored the role of various Beats and Sides in the developing nervous system of fruit fly embryos by mapping the cells that display them on their surfaces. This increased knowledge of the Beat-Side binding network should provide further insights into how connections form between nerve cells. The new screening technique could also eventually be used to map the cell surface protein interactome in humans. A number of key drugs, including the breast cancer drug Herceptin, target cell surface proteins. Identifying interactions among cell surface proteins could thus provide additional leads for developing new therapies.
Collapse
Affiliation(s)
- Hanqing Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ash Watson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Institute of Neuroscience, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Agnieszka Olechwier
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Michael Anaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | | | - Dermott P Harnett
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Institute of Neuroscience, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Hyung-Kook Peter Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Jost Vielmetter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Mario A Fares
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Department of Abiotic Stress, Group of Integrative and Systems Biology, Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
| | - Engin Özkan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Juan-Pablo Labrador
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Institute of Neuroscience, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Kai Zinn
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| |
Collapse
|
8
|
Synthesis and evaluation of multivalent M2pep peptides for targeting alternatively activated M2 macrophages. J Control Release 2016; 224:103-111. [PMID: 26772876 DOI: 10.1016/j.jconrel.2015.12.057] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/02/2015] [Accepted: 12/31/2015] [Indexed: 01/09/2023]
Abstract
The tumor microenvironment in the majority of cancers is known to favor polarization of tumor-associated macrophages (TAMs) to alternatively activated M2 phenotype, promoting disease progression and reducing patient survival. Effective therapy targeting this M2 macrophage population is thus a promising adjuvant to approved cancer therapies. One of the challenges in targeting M2-like TAMs is a lack of high affinity targeting ligand with good selectivity over anti-tumor M1-like TAMs. We have previously identified an M2 macrophage-targeting peptide (M2pep) that binds preferentially to murine M2 macrophages and M2-like TAMs. A fusion peptide of M2pep with pro-apoptotic peptide KLA (M2pepKLA) was further used to reduce TAM population in vivo but high concentrations and frequent dosing were required due to low binding affinity of M2pep for M2 macrophage. The goal of this study was to develop more potent TAM depletion constructs by increasing the valency of both the M2pep targeting and KLA drug domains. Divalent and tetravalent displays of M2pep ([M2pep]2-Biotin and [M2pep]4-Biotin) were synthesized and evaluated for improvement in binding avidity to the murine macrophages. High avidity and selective binding of [M2pep]2-Biotin to M2 macrophages were achieved with at least 10-fold lower concentration than required for monovalent M2pep activity. Increasing M2pep valency to four, however, resulted in a reduction in both binding activity and selectivity. Surprisingly, both divalent and tetravalent M2pep, without conjugation of any cytotoxic drug cargo, exhibited M2 macrophage-selective toxicity not observed in monovalent M2pep treatment. We next synthesized divalent M2pep with monovalent and divalent KLA ([M2pep]2-[KLA] and [M2pep]2-[KLA]2) to evaluate its enhanced potency compared to M2pepKLA. While both constructs were significantly more toxic than M2pepKLA to primary, bone marrow-derived M2 macrophage, desired selectivity was retained only with [M2pep]2-[KLA]. Finally, we evaluated all multivalent M2pep and M2pepKLA analogs using a syngeneic CT-26 tumor cell suspension. In this setting, [M2pep]4-Biotin and [M2pep]2-[KLA]2 exhibited selective toxicity to both M2-like TAMs and malignant cells but not to M1-like TAMs. Therefore, these constructs are promising anti-cancer constructs with dual-modality mechanisms: malignant cell killing and TAM-based immunomodulation.
Collapse
|
9
|
Wright GJ, Bianchi E. The challenges involved in elucidating the molecular basis of sperm-egg recognition in mammals and approaches to overcome them. Cell Tissue Res 2015. [PMID: 26224538 PMCID: PMC4700105 DOI: 10.1007/s00441-015-2243-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Sexual reproduction is used by many different organisms to create a new generation of genetically distinct progeny. Cells originating from separate sexes or mating types segregate their genetic material into haploid gametes which must then recognize and fuse with each other in a process known as fertilization to form a diploid zygote. Despite the central importance of fertilization, we know remarkably little about the molecular mechanisms that are involved in how gametes recognize each other, particularly in mammals, although the proteins that are displayed on their surfaces are almost certainly involved. This paucity of knowledge is largely due to both the unique biological properties of mammalian gametes (sperm and egg) which make them experimentally difficult to manipulate, and the technical challenges of identifying interactions between membrane-embedded cell surface receptor proteins. In this review, we will discuss our current knowledge of animal gamete recognition, highlighting where important contributions to our understanding were made, why particular model systems were helpful, and why progress in mammals has been particularly challenging. We discuss how the development of mammalian in vitro fertilization and targeted gene disruption in mice were important technological advances that triggered progress. We argue that approaches employed to discover novel interactions between cell surface gamete recognition proteins should account for the unusual biochemical properties of membrane proteins and the typically highly transient nature of their interactions. Finally, we describe how these principles were applied to identify Juno as the egg receptor for sperm Izumo1, an interaction that is essential for mammalian fertilization.
Collapse
Affiliation(s)
- Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Enrica Bianchi
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
| |
Collapse
|
10
|
Tom I, Estevez A, Bowman K, Gonzalez LC. Baculovirus display for discovery of low-affinity extracellular receptor-ligand interactions using protein microarrays. Anal Biochem 2015; 479:1-5. [PMID: 25797350 DOI: 10.1016/j.ab.2015.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/02/2015] [Accepted: 03/12/2015] [Indexed: 12/16/2022]
Abstract
When used in conjunction with multivalent protein probes, protein microarrays offer a robust technology for discovery of low-affinity extracellular protein-protein interactions. Probes for receptor-matching screens generally consist of purified extracellular domains fused to affinity tags. Given that approximately two-thirds of extracellular proteins are transmembrane domain-containing proteins, it would be desirable to develop a system to express and display probe receptors in a native-like membrane environment. Toward this end, we evaluated baculovirus display as a platform for generating multivalent probes for protein microarray screens. Virion particles were generated displaying single-transmembrane domain receptors BTLA, CD200, and EFNB2, representing a range of affinities for their interacting partners. Virions directly labeled with Cy5 fluorophore were screened against a microarray containing more than 600 extracellular proteins, and the results were compared with data derived from soluble Fc protein or probe-coated protein A microbeads. An optimized protocol employing a blocking step with a nonrelated probe-expressing control baculovirus allowed identification of the expected interactions with a signal-to-noise ratio similar to or higher than those obtained with the other formats. Our results demonstrate that baculovirus display is suitable for detection of high- and low-affinity extracellular protein-protein interactions on protein microarrays. This platform eliminates the need for protein purification and provides a native-like lipid environment for membrane-associated receptors.
Collapse
Affiliation(s)
- Irene Tom
- Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Alberto Estevez
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - Krista Bowman
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - Lino C Gonzalez
- Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA.
| |
Collapse
|
11
|
Tom I, Lewin-Koh N, Ramani SR, Gonzalez LC. Protein microarrays for identification of novel extracellular protein-protein interactions. ACTA ACUST UNITED AC 2013; Chapter 27:Unit 27.3. [PMID: 23546621 DOI: 10.1002/0471140864.ps2703s72] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Functional protein microarrays offer the capability for high-throughput protein interaction analysis and have long promised to be a powerful tool for understanding protein interactions at the proteome scale. Although popular techniques for protein-protein interaction mapping like yeast-two-hybrid and affinity-purification mass spectrometry have performed well for identifying intracellular protein-protein interactions, the study of interactions between extracellular proteins has remained challenging for these methods. Instead, the use of protein microarrays appears to be a robust and efficient method for the identification of interactions among the members of this class of protein. This unit describes methods for extracellular protein microarray production, screening, and analysis. A protocol is described for enhanced detection of low-affinity interactions by generating multivalent complexes using Fc-fusion bait proteins and protein A microbeads, along with a statistical method for hit scoring and identification of nonspecific interactions.
Collapse
Affiliation(s)
- Irene Tom
- Department of Protein Chemistry, Genentech, South San Francisco, California, USA
| | | | | | | |
Collapse
|
12
|
Vincent TL, Woolfson DN, Adams JC. Prediction and analysis of higher-order coiled-coils: insights from proteins of the extracellular matrix, tenascins and thrombospondins. Int J Biochem Cell Biol 2013; 45:2392-401. [PMID: 23891848 DOI: 10.1016/j.biocel.2013.07.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/14/2013] [Accepted: 07/09/2013] [Indexed: 12/27/2022]
Abstract
α-Helical coiled-coil domains (CCDs) direct protein oligomerisation in many biological processes and are of great interest as tools in protein engineering. Although CCDs are recognizable from protein sequences, prediction of oligomer state remains challenging especially for trimeric states and above. Here we evaluate LOGICOIL, a new multi-state predictor for CCDs, with regard to families of extracellular matrix proteins. Tenascins, which are known to assemble as trimers, were the first test case. LOGICOIL out-performed other algorithms in predicting trimerisation of these proteins and sequence analyses identified features associated with many other trimerising CCDs. The thrombospondins are a larger and more ancient family that includes sub-groups that assemble as trimers or pentamers. LOGICOIL predicted the pentamerising CCDs accurately. However, prediction of TSP trimerisation was relatively poor, although accuracy was improved by analyzing only the central regions of the CCDs. Sequence clustering and phylogenetic analyses grouped the TSP CCDs into three clades comprising trimers and pentamers from vertebrates, and TSPs from invertebrates. Sequence analyses revealed distinctive, conserved features that distinguish trimerising and pentamerising CCDs. Together, these analyses provide insight into the specification of higher-order CCDs that should direct improved CCD predictions and future experimental investigations of sequence-to-structure functional relationships.
Collapse
Affiliation(s)
- Thomas L Vincent
- Bristol Centre for Complexity Sciences, University of Bristol, Queen's Building, University Walk, Bristol BS8 1TR, UK; School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | | | | |
Collapse
|
13
|
Özkan E, Carrillo RA, Eastman CL, Weiszmann R, Waghray D, Johnson KG, Zinn K, Celniker SE, Garcia KC. An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell 2013; 154:228-39. [PMID: 23827685 PMCID: PMC3756661 DOI: 10.1016/j.cell.2013.06.006] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 04/02/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022]
Abstract
Extracellular domains of cell surface receptors and ligands mediate cell-cell communication, adhesion, and initiation of signaling events, but most existing protein-protein "interactome" data sets lack information for extracellular interactions. We probed interactions between receptor extracellular domains, focusing on a set of 202 proteins composed of the Drosophila melanogaster immunoglobulin superfamily (IgSF), fibronectin type III (FnIII), and leucine-rich repeat (LRR) families, which are known to be important in neuronal and developmental functions. Out of 20,503 candidate protein pairs tested, we observed 106 interactions, 83 of which were previously unknown. We "deorphanized" the 20 member subfamily of defective-in-proboscis-response IgSF proteins, showing that they selectively interact with an 11 member subfamily of previously uncharacterized IgSF proteins. Both subfamilies interact with a single common "orphan" LRR protein. We also observed interactions between Hedgehog and EGFR pathway components. Several of these interactions could be visualized in live-dissected embryos, demonstrating that this approach can identify physiologically relevant receptor-ligand pairs.
Collapse
Affiliation(s)
- Engin Özkan
- Department of Molecular and Cellular Physiology, and Structural Biology, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert A. Carrillo
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Catharine L. Eastman
- Department of Molecular and Cellular Physiology, and Structural Biology, Stanford, CA 94305, USA
| | - Richard Weiszmann
- Department of Genome Dynamics, Berkeley Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, and Structural Biology, Stanford, CA 94305, USA
| | - Karl G. Johnson
- Department of Biology, and Neuroscience, Pomona College, Claremont, CA 91711, USA
| | - Kai Zinn
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susan E. Celniker
- Department of Genome Dynamics, Berkeley Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, and Structural Biology, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
14
|
Multivalent ligand: design principle for targeted therapeutic delivery approach. Ther Deliv 2012; 3:1171-87. [DOI: 10.4155/tde.12.99] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Multivalent interactions of biological molecules play an important role in many biochemical events. A multivalent ligand comprises of multiple copies of ligands conjugated to scaffolds, allowing the simultaneous binding of multivalent ligands to multiple binding sites or receptors. Many research groups have successfully designed and synthesized multivalent ligands to increase the binding affinity, avidity and specificity of the ligand to the receptor. A multimeric ligand is a promising option for the specific treatment of diseases. In this review, the factors affecting multivalent interactions, including the size and shape of the ligand, geometry and an arrangement of ligands on the scaffold, linker length, thermodynamic, and kinetics of the interactions are discussed. Examples of the multivalent ligand applications for therapeutic delivery are also summarized.
Collapse
|
15
|
Ammann JU, Jahnke M, Dyson MR, Kaufman J, Trowsdale J. Detection of weak receptor-ligand interactions using IgM and J-chain-based fusion proteins. Eur J Immunol 2012; 42:1354-6. [PMID: 22539303 PMCID: PMC3437510 DOI: 10.1002/eji.201142151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Johannes U Ammann
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | |
Collapse
|
16
|
Gonzalez LC. Protein microarrays, biosensors, and cell-based methods for secretome-wide extracellular protein-protein interaction mapping. Methods 2012; 57:448-58. [PMID: 22728035 DOI: 10.1016/j.ymeth.2012.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/02/2012] [Accepted: 06/08/2012] [Indexed: 12/15/2022] Open
Abstract
Approximately one quarter of all human genes encode proteins that function in the extracellular space or serve to bridge the extracellular and intracellular environments. Physical associations between these secretome proteins serve to regulate a wide range of biological activities and consequently represent important therapeutic targets. Moreover, some extracellular proteins are targeted by pathogens to allow host access or immune evasion. Despite the importance of extracellular protein-protein interactions, our knowledge in this area has remained sparse. Weak affinities and low abundance have often hindered efforts to identify these interactions using traditional methods such as biochemical purification and cDNA library expression cloning. Moreover, current large-scale protein-protein interaction mapping techniques largely under represent extracellular protein-protein interactions. This review highlights emerging biosensor and protein microarray technology, along with more traditional cell-based techniques, that are compatible with secretome-wide screens for extracellular protein-protein interaction discovery. A combination of these approaches will serve to rapidly expand our knowledge of the extracellular protein-protein interactome.
Collapse
Affiliation(s)
- Lino C Gonzalez
- Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, United States.
| |
Collapse
|
17
|
Kerr JS, Wright GJ. Avidity-based extracellular interaction screening (AVEXIS) for the scalable detection of low-affinity extracellular receptor-ligand interactions. J Vis Exp 2012:e3881. [PMID: 22414956 PMCID: PMC3460577 DOI: 10.3791/3881] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Extracellular protein:protein interactions between secreted or membrane-tethered proteins are critical for both initiating intercellular communication and ensuring cohesion within multicellular organisms. Proteins predicted to form extracellular interactions are encoded by approximately a quarter of human genes, but despite their importance and abundance, the majority of these proteins have no documented binding partner. Primarily, this is due to their biochemical intractability: membrane-embedded proteins are difficult to solubilise in their native conformation and contain structurally-important posttranslational modifications. Also, the interaction affinities between receptor proteins are often characterised by extremely low interaction strengths (half-lives < 1 second) precluding their detection with many commonly-used high throughput methods. Here, we describe an assay, AVEXIS (AVidity-based EXtracellular Interaction Screen) that overcomes these technical challenges enabling the detection of very weak protein interactions (t(1/2) ≤ 0.1 sec) with a low false positive rate. The assay is usually implemented in a high throughput format to enable the systematic screening of many thousands of interactions in a convenient microtitre plate format (Fig. 1). It relies on the production of soluble recombinant protein libraries that contain the ectodomain fragments of cell surface receptors or secreted proteins within which to screen for interactions; therefore, this approach is suitable for type I, type II, GPI-linked cell surface receptors and secreted proteins but not for multipass membrane proteins such as ion channels or transporters. The recombinant protein libraries are produced using a convenient and high-level mammalian expression system, to ensure that important posttranslational modifications such as glycosylation and disulphide bonds are added. Expressed recombinant proteins are secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (β-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA (Fig. 1). The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, we have shown that interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates.
Collapse
Affiliation(s)
- Jason S Kerr
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute
| | | |
Collapse
|
18
|
A benchmarked protein microarray-based platform for the identification of novel low-affinity extracellular protein interactions. Anal Biochem 2012; 424:45-53. [PMID: 22342946 PMCID: PMC3325482 DOI: 10.1016/j.ab.2012.01.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/04/2011] [Accepted: 01/13/2012] [Indexed: 12/13/2022]
Abstract
Low-affinity extracellular protein interactions are critical for cellular recognition processes, but existing methods to detect them are limited in scale, making genome-wide interaction screens technically challenging. To address this, we report here the miniaturization of the AVEXIS (avidity-based extracellular interaction screen) assay by using protein microarray technology. To achieve this, we have developed protein tags and sample preparation methods that enable the parallel purification of hundreds of recombinant proteins expressed in mammalian cells. We benchmarked the protein microarray-based assay against a set of known quantified receptor–ligand pairs and show that it is sensitive enough to detect even very weak interactions that are typical of this class of interactions. The increase in scale enables interaction screening against a dilution series of immobilized proteins on the microarray enabling the observation of saturation binding behaviors to show interaction specificity and also the estimation of interaction affinities directly from the primary screen. These methodological improvements now permit screening for novel extracellular receptor–ligand interactions on a genome-wide scale.
Collapse
|
19
|
Ramani SR, Tom I, Lewin-Koh N, Wranik B, Depalatis L, Zhang J, Eaton D, Gonzalez LC. A secreted protein microarray platform for extracellular protein interaction discovery. Anal Biochem 2011; 420:127-38. [PMID: 21982860 DOI: 10.1016/j.ab.2011.09.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 09/10/2011] [Accepted: 09/16/2011] [Indexed: 12/01/2022]
Abstract
Characterization of the extracellular protein interactome has lagged far behind that of intracellular proteins, where mass spectrometry and yeast two-hybrid technologies have excelled. Improved methods for identifying receptor-ligand and extracellular matrix protein interactions will greatly accelerate biological discovery in cell signaling and cellular communication. These technologies must be able to identify low-affinity binding events that are often observed between membrane-bound coreceptor molecules during cell-cell or cell-extracellular matrix contact. Here we demonstrate that functional protein microarrays are particularly well-suited for high-throughput screening of extracellular protein interactions. To evaluate the performance of the platform, we screened a set of 89 immunoglobulin (Ig)-type receptors against a highly diverse extracellular protein microarray with 686 genes represented. To enhance detection of low-affinity interactions, we developed a rapid method to assemble bait Fc fusion proteins into multivalent complexes using protein A microbeads. Based on these screens, we developed a statistical methodology for hit calling and identification of nonspecific interactions on protein microarrays. We found that the Ig receptor interactions identified using our methodology are highly specific and display minimal off-target binding, resulting in a 70% true-positive to false-positive hit ratio. We anticipate that these methods will be useful for a wide variety of functional protein microarray users.
Collapse
Affiliation(s)
- Sree R Ramani
- Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Chittasupho C, Siahaan TJ, Vines CM, Berkland C. Autoimmune therapies targeting costimulation and emerging trends in multivalent therapeutics. Ther Deliv 2011; 2:873-89. [PMID: 21984960 PMCID: PMC3186944 DOI: 10.4155/tde.11.60] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Proteins participating in immunological signaling have emerged as important targets for controlling the immune response. A multitude of receptor-ligand pairs that regulate signaling pathways of the immune response have been identified. In the complex milieu of immune signaling, therapeutic agents targeting mediators of cellular signaling often either activate an inflammatory immune response or induce tolerance. This review is primarily focused on therapeutics that inhibit the inflammatory immune response by targeting membrane-bound proteins regulating costimulation or mediating immune-cell adhesion. Many of these signals participate in larger, organized structures such as the immunological synapse. Receptor clustering and arrangement into organized structures is also reviewed and emerging trends implicating a potential role for multivalent therapeutics is posited.
Collapse
Affiliation(s)
- Chuda Chittasupho
- Department of Pharmaceutical Chemistry, University of Kansas, KS, USA
- Department of Pharmaceutical Technology, Srinakharinwirot University, Nakhonnayok, Thailand
| | - Teruna J Siahaan
- Department of Pharmaceutical Chemistry, University of Kansas, KS, USA
| | - Charlotte M Vines
- Department of Microbiology, Molecular Genetics & Immunology, University of Kansas Medical Center, KS, USA
| | - Cory Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, KS, USA
- Department of Pharmaceutical Chemistry, Department of Chemical & Petroleum Engineering, 2030 Becker Drive, Lawrence, KS 66047, USA
| |
Collapse
|
21
|
Mihrshahi R, Brown MH. Downstream of tyrosine kinase 1 and 2 play opposing roles in CD200 receptor signaling. THE JOURNAL OF IMMUNOLOGY 2010; 185:7216-22. [PMID: 21078907 DOI: 10.4049/jimmunol.1002858] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The CD200 receptor (CD200R) negatively regulates myeloid cells by interacting with its widely expressed ligand CD200. CD200R signals through a unique inhibitory pathway involving a direct interaction with the adaptor protein downstream of tyrosine kinase 2 (Dok2) and the subsequent recruitment and activation of Ras GTPase-activating protein (RasGAP). Ligand engagement of CD200R also results in tyrosine phosphorylation of Dok1, but this protein is not essential for inhibitory CD200R signaling in human myeloid cells. In this paper, we show that CD200R-induced phosphorylation of Dok2 precedes phosphorylation of Dok1, and that Dok2 and Dok1 recruit different downstream proteins. Compared with Dok2, Dok1 recruits substantially less RasGAP. In addition to binding RasGAP, Dok2 recruits the adaptor molecule Nck in response to ligand engagement of CD200R. CD200R-induced phosphorylation of Dok1 results in the recruitment of CT10 sarcoma oncogene cellular homologue-like (CrkL), whereas the closely related CT10 sarcoma oncogene cellular homologue interacts constitutively with Dok1. Knockdown of Dok1 or CrkL expression in U937 cells resulted in increased Dok2 phosphorylation and RasGAP recruitment to Dok2. These data are consistent with a model in which Dok1 negatively regulates Dok2-mediated CD200R signaling through the recruitment of CrkL.
Collapse
Affiliation(s)
- Robin Mihrshahi
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | | |
Collapse
|
22
|
Martin S, Söllner C, Charoensawan V, Adryan B, Thisse B, Thisse C, Teichmann S, Wright GJ. Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling. Mol Cell Proteomics 2010; 9:2654-65. [PMID: 20802085 PMCID: PMC3101854 DOI: 10.1074/mcp.m110.004119] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Extracellular interactions involving both secreted and membrane-tethered receptor proteins are essential to initiate signaling pathways that orchestrate cellular behaviors within biological systems. Because of the biochemical properties of these proteins and their interactions, identifying novel extracellular interactions remains experimentally challenging. To address this, we have recently developed an assay, AVEXIS (avidity-based extracellular interaction screen) to detect low affinity extracellular interactions on a large scale and have begun to construct interaction networks between zebrafish receptors belonging to the immunoglobulin and leucine-rich repeat protein families to identify novel signaling pathways important for early development. Here, we expanded our zebrafish protein library to include other domain families and many more secreted proteins and performed our largest screen to date totaling 16,544 potential unique interactions. We report 111 interactions of which 96 are novel and include the first documented extracellular ligands for 15 proteins. By including 77 interactions from previous screens, we assembled an expanded network of 188 extracellular interactions between 92 proteins and used it to show that secreted proteins have twice as many interaction partners as membrane-tethered receptors and that the connectivity of the extracellular network behaves as a power law. To try to understand the functional role of these interactions, we determined new expression patterns for 164 genes within our clone library by using whole embryo in situ hybridization at five key stages of zebrafish embryonic development. These expression data were integrated with the binding network to reveal where each interaction was likely to function within the embryo and were used to resolve the static interaction network into dynamic tissue- and stage-specific subnetworks within the developing zebrafish embryo. All these data were organized into a freely accessible on-line database called ARNIE (AVEXIS Receptor Network with Integrated Expression; www.sanger.ac.uk/arnie) and provide a valuable resource of new extracellular signaling interactions for developmental biology.
Collapse
Affiliation(s)
- Stephen Martin
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB101HH, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
23
|
High-throughput identification of transient extracellular protein interactions. Biochem Soc Trans 2010; 38:919-22. [DOI: 10.1042/bst0380919] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Protein interactions are highly diverse in their biochemical nature, varying in affinity and are often dependent on the surrounding biochemical environment. Given this heterogeneity, it seems unlikely that any one method, and particularly those capable of screening for many protein interactions in parallel, will be able to detect all functionally relevant interactions that occur within a living cell. One major class of interactions that are not detected by current popular high-throughput methods are those that occur in the extracellular environment, especially those made by membrane-embedded receptor proteins. In the present article, we discuss some of our recent research in the development of a scalable assay to identify this class of protein interaction and some of the findings from its application in the construction of extracellular protein interaction networks.
Collapse
|
24
|
Wright GJ. Signal initiation in biological systems: the properties and detection of transient extracellular protein interactions. MOLECULAR BIOSYSTEMS 2010; 5:1405-12. [PMID: 19593473 PMCID: PMC2898632 DOI: 10.1039/b903580j] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extracellular glycoprotein interactions are not detected by most high throughput assays creating “blind-spots” in protein interaction maps. This review examines this problem and discusses recent advances that have begun to address it.
Individual cells within biological systems frequently coordinate their functions through signals initiated by specific extracellular protein interactions involving receptors that bridge the cellular membrane. Due to their biochemical nature, these membrane-embedded receptor proteins are difficult to manipulate and their interactions are characterised by very weak binding strengths that cannot be detected using popular high throughput assays. This review will provide a general outline of the biochemical attributes of receptor proteins focussing in particular on the biophysical properties of their transient interactions. Methods that are able to detect these weak extracellular binding events and especially those that can be used for identifying novel interactions will be compared. Finally, I discuss the feasibility of constructing a complete and accurate extracellular protein interaction map, and the methods that are likely to be useful in achieving this goal.
Collapse
Affiliation(s)
- Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
| |
Collapse
|
25
|
Jiang L, Barclay AN. Identification of leucocyte surface protein interactions by high-throughput screening with multivalent reagents. Immunology 2010; 129:55-61. [PMID: 20050330 DOI: 10.1111/j.1365-2567.2009.03153.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We describe a high-throughput screening system to detect interactions between leucocyte surface proteins, taking into account that these interactions are usually of very low affinity. The method involves producing the extracellular regions of leucocyte proteins with tags so that they can be bound to nanoparticles to provide an avid reagent to screen over an array of 36 similar proteins immobilized using the Proteon XPR36 with detection by surface plasmon resonance. The system was tested using established interactions that could be detected without spurious binding. The ability to detect new interactions was shown by identifying a new interaction between carcinoembryonic antigen-related cell adhesion molecule 1 and carcinoembryonic antigen-related cell adhesion molecule 8.
Collapse
Affiliation(s)
- Lei Jiang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | |
Collapse
|
26
|
Mihrshahi R, Barclay AN, Brown MH. Essential roles for Dok2 and RasGAP in CD200 receptor-mediated regulation of human myeloid cells. THE JOURNAL OF IMMUNOLOGY 2009; 183:4879-86. [PMID: 19786546 DOI: 10.4049/jimmunol.0901531] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The CD200 receptor (CD200R) acts as a negative regulator of myeloid cells by interacting with its widely expressed ligand CD200. Using mutants expressed in U937 cells, we show that inhibition is mediated by the PTB domain binding motif (NPLY) in the receptor's cytoplasmic region. The adaptor protein downstream of tyrosine kinase 2 (Dok2) bound directly to the phosphorylated NPLY motif with a 10-fold higher affinity (K(D) of approximately 1 microM at 37 degrees C) than the closely related Dok1. Both of these proteins have been suggested to play a role in CD200R signaling in murine cells. Dok2 was phosphorylated in response to CD200R engagement and recruited RAS p21 protein activator 1 (RasGAP). Knockdown of Dok2 and RasGAP by RNA interference revealed that these proteins are required for CD200R signaling, while knockdown of Dok1 and the inositol 5-phosphatase SHIP did not affect CD200R-mediated inhibition. We conclude that CD200R inhibits the activation of human myeloid cells through direct recruitment of Dok2 and subsequent activation of RasGAP, which distinguishes this receptor from the majority of inhibitory receptors that utilize ITIMs and recruit phosphatases.
Collapse
Affiliation(s)
- Robin Mihrshahi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | | |
Collapse
|
27
|
Jiang L, Barclay AN. New assay to detect low-affinity interactions and characterization of leukocyte receptors for collagen including leukocyte-associated Ig-like receptor-1 (LAIR-1). Eur J Immunol 2009; 39:1167-75. [PMID: 19283782 DOI: 10.1002/eji.200839188] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Leukocyte activity is controlled by numerous interactions between membrane receptors and ligands on the cell surface. These interactions are of low affinity making detection difficult. We developed a sensitive assay that could readily detect extremely weak interactions such as that between CD200 and the activating receptor CD200RLa (K(d)>500 microM) at the protein level. We used the new technology to screen for interactions of inhibitory receptors for collagens. We confirmed that both human and mouse leukocyte-associated Ig-like receptor-1, and in addition the related inhibitory leukocyte Ig-like receptor subfamily B member 4 (CD85K, Gp49B), bound collagen specifically, whereas other cell surface proteins gave no binding. The monomeric affinities of the interactions were then determined to allow comparison with other leukocyte interactions and indicate conditions when these interactions might lead to inhibitory signals.
Collapse
Affiliation(s)
- Lei Jiang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | |
Collapse
|
28
|
Sanderson CM. The Cartographers toolbox: building bigger and better human protein interaction networks. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 8:1-11. [DOI: 10.1093/bfgp/elp003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
29
|
Abstract
Eukaryotic genomes encode large numbers of proteins that are either secreted or have exposed extracellular domains. It is highly likely that these proteins facilitate many important biological processes: however, as yet, most remain uncharacterized. Progress in this area of research has been impaired by the lack of a robust screening system that can be used to investigate interactions between large numbers of different extracellular proteins. In this issue, Bushell et al. introduce AVEXIS (avidity-based extracellular interaction screen), a high-throughput screening procedure, which can be used to identify even weak extracellular protein interactions with extremely high confidence. This assay represents an important development in the field of network biology. By combining data from the AVEXIS system with data produced by classical or variant yeast two-hybrid methods, it will be possible to assemble binary protein interaction networks that connect extracellular and intracellular processes. This information will dramatically increase our ability to understand a wide range of physiological processes and facilitate the development of better therapeutic strategies.
Collapse
Affiliation(s)
- Christopher M Sanderson
- Department of Physiology, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, United Kingdom.
| |
Collapse
|
30
|
Bushell KM, Söllner C, Schuster-Boeckler B, Bateman A, Wright GJ. Large-scale screening for novel low-affinity extracellular protein interactions. Genome Res 2008; 18:622-30. [PMID: 18296487 DOI: 10.1101/gr.7187808] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Extracellular protein-protein interactions are essential for both intercellular communication and cohesion within multicellular organisms. Approximately a fifth of human genes encode membrane-tethered or secreted proteins, but they are largely absent from recent large-scale protein interaction datasets, making current interaction networks biased and incomplete. This discrepancy is due to the unsuitability of popular high-throughput methods to detect extracellular interactions because of the biochemical intractability of membrane proteins and their interactions. For example, cell surface proteins contain insoluble hydrophobic transmembrane regions, and their extracellular interactions are often highly transient, having half-lives of less than a second. To detect transient extracellular interactions on a large scale, we developed AVEXIS (avidity-based extracellular interaction screen), a high-throughput assay that overcomes these technical issues and can detect very transient interactions (half-lives <or= 0.1 sec) with a low false-positive rate. We used it to systematically screen for receptor-ligand pairs within the zebrafish immunoglobulin superfamily and identified novel ligands for both well-known and orphan receptors. Genes encoding receptor-ligand pairs were often clustered phylogenetically and expressed in the same or adjacent tissues, immediately implying their involvement in similar biological processes. Using AVEXIS, we have determined the first systematic low-affinity extracellular protein interaction network, supported by independent biological data. This technique will now allow large-scale extracellular protein interaction mapping in a broad range of experimental contexts.
Collapse
Affiliation(s)
- K Mark Bushell
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, United Kingdom
| | | | | | | | | |
Collapse
|