1
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Sonnert ND, Rosen CE, Ghazi AR, Franzosa EA, Duncan-Lowey B, González-Hernández JA, Huck JD, Yang Y, Dai Y, Rice TA, Nguyen MT, Song D, Cao Y, Martin AL, Bielecka AA, Fischer S, Guan C, Oh J, Huttenhower C, Ring AM, Palm NW. A host-microbiota interactome reveals extensive transkingdom connectivity. Nature 2024; 628:171-179. [PMID: 38509360 DOI: 10.1038/s41586-024-07162-0] [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: 05/07/2022] [Accepted: 02/05/2024] [Indexed: 03/22/2024]
Abstract
The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown1-3. Classical pathogens often invade host tissues and modulate immune responses through interactions with human extracellular and secreted proteins (the 'exoproteome'). Commensal microorganisms may also facilitate niche colonization and shape host biology by engaging host exoproteins; however, direct exoproteome-microbiota interactions remain largely unexplored. Here we developed and validated a novel technology, BASEHIT, that enables proteome-scale assessment of human exoproteome-microbiome interactions. Using BASEHIT, we interrogated more than 1.7 million potential interactions between 519 human-associated bacterial strains from diverse phylogenies and tissues of origin and 3,324 human exoproteins. The resulting interactome revealed an extensive network of transkingdom connectivity consisting of thousands of previously undescribed host-microorganism interactions involving 383 strains and 651 host proteins. Specific binding patterns within this network implied underlying biological logic; for example, conspecific strains exhibited shared exoprotein-binding patterns, and individual tissue isolates uniquely bound tissue-specific exoproteins. Furthermore, we observed dozens of unique and often strain-specific interactions with potential roles in niche colonization, tissue remodelling and immunomodulation, and found that strains with differing host interaction profiles had divergent interactions with host cells in vitro and effects on the host immune system in vivo. Overall, these studies expose a previously unexplored landscape of molecular-level host-microbiota interactions that may underlie causal effects of indigenous microorganisms on human health and disease.
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Affiliation(s)
- Nicole D Sonnert
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Connor E Rosen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew R Ghazi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - John D Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yi Yang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tyler A Rice
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mytien T Nguyen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Deguang Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yiyun Cao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anjelica L Martin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Agata A Bielecka
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Suzanne Fischer
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron M Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
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2
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Yang L, Sheets TP, Feng Y, Yu G, Bajgain P, Hsu KS, So D, Seaman S, Lee J, Lin L, Evans CN, Guest MR, Chari R, St. Croix B. Uncovering receptor-ligand interactions using a high-avidity CRISPR activation screening platform. SCIENCE ADVANCES 2024; 10:eadj2445. [PMID: 38354234 PMCID: PMC10866537 DOI: 10.1126/sciadv.adj2445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The majority of clinically approved drugs target proteins that are secreted or cell surface bound. However, further advances in this area have been hindered by the challenging nature of receptor deorphanization, as there are still many secreted and cell-bound proteins with unknown binding partners. Here, we developed an advanced screening platform that combines CRISPR-CAS9 guide-mediated gene activation (CRISPRa) and high-avidity bead-based selection. The CRISPRa platform incorporates serial enrichment and flow cytometry-based monitoring, resulting in substantially improved screening sensitivity for well-known yet weak interactions of the checkpoint inhibitor family. Our approach has successfully revealed that siglec-4 exerts regulatory control over T cell activation through a low affinity trans-interaction with the costimulatory receptor 4-1BB. Our highly efficient screening platform holds great promise for identifying extracellular interactions of uncharacterized receptor-ligand partners, which is essential to develop next-generation therapeutics, including additional immune checkpoint inhibitors.
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Affiliation(s)
- Liping Yang
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Timothy P. Sheets
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Yang Feng
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Guojun Yu
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Pradip Bajgain
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Kuo-Sheng Hsu
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Daeho So
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Steven Seaman
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Jaewon Lee
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Ling Lin
- Proteomic Instability of Cancer Section, MCGP, NCI, NIH, Frederick, MD 21702, USA
| | - Christine N. Evans
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Mary R. Guest
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Brad St. Croix
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
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3
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Cell-based receptor discovery identifies host factors specifically targeted by the SARS CoV-2 spike. Commun Biol 2022; 5:788. [PMID: 35931765 PMCID: PMC9355963 DOI: 10.1038/s42003-022-03695-0] [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: 11/22/2021] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Receptor-ligand interactions on the plasma membrane regulate cellular communication and play a key role in viral infection. Despite representing main targets for drug development, the characterization of these interactions remains challenging in part due to the dearth of optimal technologies. Here, we build a comprehensive library of human proteins engineered for controlled cell surface expression. Coupled to tetramer-based screening for increased binding avidity, we develop a high throughput cell-based platform that enables systematic interrogation of receptor-ligand interactomes. Using this technology, we characterize the cell surface proteins targeted by the receptor binding domain (RBD) of the SARS-CoV spike protein. Host factors that specifically bind to SARS CoV-2 but not SARS CoV RBD are identified, including proteins that are expressed in the nervous system or olfactory epithelium. Remarkably, our results show that Contactin-1, a previously unknown SARS CoV-2 spike-specific receptor that is upregulated in COVID-19 patients, significantly enhances ACE2-dependent pseudotyped virus infection. Starting from a versatile platform to characterize cell surface interactomes, this study uncovers host factors specifically targeted by SARS CoV-2, information that may help design improved therapeutic strategies against COVID-19. A high-throughput cell-based platform is developed for systematic investigation of receptor-ligand interactions and applied to identify cell-surface proteins that bind to SARS CoV-2.
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4
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Identification of lamprey variable lymphocyte receptors that target the brain vasculature. Sci Rep 2022; 12:6044. [PMID: 35411012 PMCID: PMC9001667 DOI: 10.1038/s41598-022-09962-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/28/2022] [Indexed: 12/21/2022] Open
Abstract
AbstractThe blood–brain barrier (BBB) represents a significant bottleneck for the delivery of therapeutics to the central nervous system. In recent years, the promise of coopting BBB receptor-mediated transport systems for brain drug delivery has increased in large part due to the discovery and engineering of BBB-targeting antibodies. Here we describe an innovative screening platform for identification of new BBB targeting molecules from a class of lamprey antigen recognition proteins known as variable lymphocyte receptors (VLRs). Lamprey were immunized with murine brain microvessel plasma membranes, and the resultant repertoire cloned into the yeast surface display system. The library was screened via a unique workflow that identified 16 VLR clones that target extracellular epitopes of in vivo-relevant BBB membrane proteins. Of these, three lead VLR candidates, VLR-Fc-11, VLR-Fc-30, and VLR-Fc-46 selectively target the brain vasculature and traffic within brain microvascular endothelial cells after intravenous administration in mice, with VLR-Fc-30 being confirmed as trafficking into the brain parenchyma. Epitope characterization indicates that the VLRs, in part, recognize sialylated glycostructures. These promising new targeting molecules have the potential for brain targeting and drug delivery with improved brain vascular specificity.
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5
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Wojtowicz WM, Vielmetter J, Fernandes RA, Siepe DH, Eastman CL, Chisholm GB, Cox S, Klock H, Anderson PW, Rue SM, Miller JJ, Glaser SM, Bragstad ML, Vance J, Lam AW, Lesley SA, Zinn K, Garcia KC. A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions. Cell 2021; 182:1027-1043.e17. [PMID: 32822567 PMCID: PMC7440162 DOI: 10.1016/j.cell.2020.07.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/19/2020] [Accepted: 07/17/2020] [Indexed: 12/17/2022]
Abstract
Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition, and responses. We executed an interactome screen of 564 human cell-surface and secreted proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using a high-throughput, automated ELISA-based screening platform employing a pooled-protein strategy to test all 318,096 PPI combinations. Screen results, augmented by phylogenetic homology analysis, revealed ∼380 previously unreported PPIs. We validated a subset using surface plasmon resonance and cell binding assays. Observed PPIs reveal a large and complex network of interactions both within and across biological systems. We identified new PPIs for receptors with well-characterized ligands and binding partners for “orphan” receptors. New PPIs include proteins expressed on multiple cell types and involved in diverse processes including immune and nervous system development and function, differentiation/proliferation, metabolism, vascularization, and reproduction. These PPIs provide a resource for further biological investigation into their functional relevance and may offer new therapeutic drug targets. Human IgSF interactome reveals complex network of cell-surface protein interactions Phylogenetic homology analysis predicts protein-protein interactions ∼380 previously unknown protein-protein interactions identified Deorphanization of receptors and new binding partners for well-studied receptors
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Affiliation(s)
- Woj M Wojtowicz
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Jost Vielmetter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ricardo A Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dirk H Siepe
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Catharine L Eastman
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gregory B Chisholm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah Cox
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Heath Klock
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Paul W Anderson
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Sarah M Rue
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Jessica J Miller
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Scott M Glaser
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Melisa L Bragstad
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Julie Vance
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Annie W Lam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Scott A Lesley
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Kai Zinn
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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6
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Caicedo A, Zambrano K, Sanon S, Gavilanes AWD. Extracellular mitochondria in the cerebrospinal fluid (CSF): Potential types and key roles in central nervous system (CNS) physiology and pathogenesis. Mitochondrion 2021; 58:255-269. [PMID: 33662579 DOI: 10.1016/j.mito.2021.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
The cerebrospinal fluid (CSF) has an important role in the transport of nutrients and signaling molecules to the central nervous and immune systems through its circulation along the brain and spinal cord tissues. The mitochondrial activity in the central nervous system (CNS) is essential in processes such as neuroplasticity, neural differentiation and production of neurotransmitters. Interestingly, extracellular and active mitochondria have been detected in the CSF where they act as a biomarker for the outcome of pathologies such as subarachnoid hemorrhage and delayed cerebral ischemia. Additionally, cell-free-circulating mitochondrial DNA (ccf-mtDNA) has been detected in both the CSF of healthy donors and in that of patients with neurodegenerative diseases. Key questions arise as there is still much debate regarding if ccf-mtDNA detected in CSF is associated with a diversity of active or inactive extracellular mitochondria coexisting in distinct pathologies. Additionally, it is of great scientific and medical importance to identify the role of extracellular mitochondria (active and inactive) in the CSF and the difference between them being damage associated molecular patterns (DAMPs) or factors that promote homeostasis. This review analyzes the different types of extracellular mitochondria, methods for their identification and their presence in CSF. Extracellular mitochondria in the CSF could have an important implication in health and disease, which may lead to the development of medical approaches that utilize mitochondria as therapeutic agents.
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Affiliation(s)
- Andrés Caicedo
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Sistemas Médicos SIME, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Kevin Zambrano
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands; Instituto de Neurociencias, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Serena Sanon
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Cornell University, Ithaca, United States
| | - Antonio W D Gavilanes
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
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7
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Abid MSR, Mousavi S, Checco JW. Identifying Receptors for Neuropeptides and Peptide Hormones: Challenges and Recent Progress. ACS Chem Biol 2021; 16:251-263. [PMID: 33539706 DOI: 10.1021/acschembio.0c00950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intercellular signaling events mediated by neuropeptides and peptide hormones represent important targets for both basic science and drug discovery. For many bioactive peptides, the protein receptors that transmit information across the receiving cell membrane are not known, severely limiting these signaling pathways as potential therapeutic targets. Identifying the receptor(s) for a given peptide of interest is complicated by several factors. Most notably, cell-cell signaling peptides are generated through dynamic biosynthetic pathways, can act on many different families of receptor proteins, and can participate in complex ligand-receptor interactions that extend beyond a simple one-to-one archetype. Here, we discuss recent methodological advances to identify signaling partners for bioactive peptides. Recent efforts have centered on methods to identify candidate receptors via transcript expression, methods to match peptide-receptor pairs through high throughput screening, and methods to capture direct ligand-receptor interactions using chemical probes. Future applications of the receptor identification approaches discussed here, as well as technical advancements to address their limitations, promise to lead to a greater understanding of how cells communicate to deliver complex physiologies. Importantly, such advancements will likely provide novel targets for the treatment of human diseases within the central nervous and endocrine systems.
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Affiliation(s)
- Md Shadman Ridwan Abid
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Somayeh Mousavi
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - James W. Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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8
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Zhang Y, Liu T, Wang J, Zou B, Li L, Yao L, Chen K, Ning L, Wu B, Zhao X, Wang D. Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis. Bioinformatics 2021; 37:btab036. [PMID: 33471060 PMCID: PMC7929259 DOI: 10.1093/bioinformatics/btab036] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
MOTIVATION Ligand-receptor (L-R) interactions mediate cell adhesion, recognition and communication and play essential roles in physiological and pathological signaling. With the rapid development of single-cell RNA sequencing (scRNA-seq) technologies, systematically decoding the intercellular communication network involving L-R interactions has become a focus of research. Therefore, construction of a comprehensive, high-confidence and well-organized resource to retrieve L-R interactions in order to study the functional effects of cell-cell communications would be of great value. RESULTS In this study, we developed Cellinker, a manually curated resource of literature-supported L-R interactions that play roles in cell-cell communication. We aimed to provide a useful platform for studies on cell-cell communication mediated by L-R interactions. The current version of Cellinker documents over 3,700 human and 3,200 mouse L-R protein-protein interactions (PPIs) and embeds a practical and convenient webserver with which researchers can decode intercellular communications based on scRNA-seq data. And over 400 endogenous small molecule (sMOL) related L-R interactions were collected as well. Moreover, to help with research on coronavirus (CoV) infection, Cellinker collects information on 16 L-R PPIs involved in CoV-human interactions (including 12 L-R PPIs involved in SARS-CoV-2 infection). In summary, Cellinker provides a user-friendly interface for querying, browsing and visualizing L-R interactions as well as a practical and convenient web tool for inferring intercellular communications based on scRNA-seq data. We believe this platform could promote intercellular communication research and accelerate the development of related algorithms for scRNA-seq studies. AVAILABILITY Cellinker is available at http://www.rna-society.org/cellinker/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Zhang
- Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan 528308, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jing Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bohao Zou
- Department of Statistics, University of California Davis, Davis, CA 95616, USA
| | - Le Li
- Department of Pathology, Harbin Medical University, Harbin 150081, China
| | - Linhui Yao
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kechen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Bingyi Wu
- Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan 528308, China
| | - Xiaoyang Zhao
- Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan 528308, China
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dong Wang
- Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan 528308, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
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9
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Shilts J, Crozier TWM, Greenwood EJD, Lehner PJ, Wright GJ. No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor. Sci Rep 2021; 11:413. [PMID: 33432067 PMCID: PMC7801465 DOI: 10.1038/s41598-020-80464-1] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/20/2020] [Indexed: 02/08/2023] Open
Abstract
The spike protein of SARS-CoV-2 is known to enable viral invasion into human cells through direct binding to host receptors including ACE2. An alternate entry receptor for the virus was recently proposed to be basigin/CD147. These early studies have already prompted a clinical trial and multiple published hypotheses speculating on the role of this host receptor in viral infection and pathogenesis. Here, we report that we are unable to find evidence supporting the role of basigin as a putative spike binding receptor. Recombinant forms of the SARS-CoV-2 spike do not interact with basigin expressed on the surface of human cells, and by using specialized assays tailored to detect receptor interactions as weak or weaker than the proposed basigin-spike binding, we report no evidence for a direct interaction between the viral spike protein to either of the two common isoforms of basigin. Finally, removing basigin from the surface of human lung epithelial cells by CRISPR/Cas9 results in no change in their susceptibility to SARS-CoV-2 infection. Given the pressing need for clarity on which viral targets may lead to promising therapeutics, we present these findings to allow more informed decisions about the translational relevance of this putative mechanism in the race to understand and treat COVID-19.
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Affiliation(s)
- Jarrod Shilts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
| | - Thomas W M Crozier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Edward J D Greenwood
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
- Department of Biology, York Biomedical Research Institute, Hull York Medical School, University of York, Wentworth Way, York, UK.
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10
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Chong ZS, Wright GJ, Sharma S. Investigating Cellular Recognition Using CRISPR/Cas9 Genetic Screening. Trends Cell Biol 2020; 30:619-627. [DOI: 10.1016/j.tcb.2020.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
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11
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Galaway F, Wright GJ. Rapid and sensitive large-scale screening of low affinity extracellular receptor protein interactions by using reaction induced inhibition of Gaussia luciferase. Sci Rep 2020; 10:10522. [PMID: 32601498 PMCID: PMC7324543 DOI: 10.1038/s41598-020-67468-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Extracellular protein interactions mediated by cell surface receptors are essential for intercellular communication in multicellular organisms. Assays to detect extracellular interactions must account for their often weak binding affinities and also the biochemical challenges in solubilising membrane-embedded receptors in an active form. Methods based on detecting direct binding of soluble recombinant receptor ectodomains have been successful, but genome-scale screening is limited by the usual requirement of producing sufficient amounts of each protein in two different forms, usually a "bait" and "prey". Here, we show that oligomeric receptor ectodomains coupled to concatenated units of the light-generating Gaussia luciferase enzyme robustly detected low affinity interactions and reduced the amount of protein required by several orders of magnitude compared to other reporter enzymes. Importantly, we discovered that this flash-type luciferase exhibited a reaction-induced inhibition that permitted the use of a single protein preparation as both bait and prey thereby halving the number of expression plasmids and recombinant proteins required for screening. This approach was tested against a benchmarked set of quantified extracellular interactions and shown to detect extremely weak interactions (KDs ≥ μM). This method will facilitate large-scale receptor interaction screening and contribute to the goal of mapping networks of cellular communication.
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Affiliation(s)
- Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
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Swietlik JJ, Sinha A, Meissner F. Dissecting intercellular signaling with mass spectrometry-based proteomics. Curr Opin Cell Biol 2020; 63:20-30. [PMID: 31927463 DOI: 10.1016/j.ceb.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Physiological functions depend on a coordinated interplay of numerous different cell types. Proteins serve as major signaling molecules between cells; however, their comprehensive investigation in physiologically relevant settings has remained challenging. Mass spectrometry (MS)-based shotgun proteomics is emerging as a powerful technology for the systematic analysis of protein-mediated intercellular signaling and regulated post-translational modifications. Here, we discuss recent advancements in cell biological, chemical, and biochemical MS-based approaches for the profiling of cellular messengers released by sending cells, receptors expressed on the cell surface, and their interactions. We highlight methods tailored toward the mapping of dynamic signal transduction mechanisms at cellular interfaces and approaches to dissect communication cell specifically in heterocellular systems. Thereby, MS-based proteomics contributes a unique systems biology perspective for the identification of intercellular signaling pathways deregulated in disease.
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Affiliation(s)
- Jonathan J Swietlik
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany; Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum Rechts der Isar, TU München, Munich, Germany
| | - Felix Meissner
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Germany.
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Wood L, Wright GJ. High-Content Imaging for Large-Scale Detection of Low-Affinity Extracellular Protein Interactions. SLAS DISCOVERY 2019; 24:987-999. [PMID: 31578119 PMCID: PMC6873222 DOI: 10.1177/2472555219879053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Extracellular protein interactions coordinate cellular responses with their local
environment and have important roles in pathogen invasion and disease. Due to
technical challenges associated with studying binding events at the cell
surface, the systematic and reliable identification of novel ligand–receptor
pairs remains difficult. Here, we describe the development of a cell-based assay
using large-scale transient transfections and high-content imaging (HCI) to
detect extracellular binding events. We optimized the parameters for efficient
transfection of human cells with cDNA plasmids encoding full-length cell surface
receptors in 384-well plates. Using a range of well-characterized structurally
diverse low-affinity cell surface interactions, we show that transfected cells
probed with highly avid ligands can be used to successfully identify
ligand–receptor pairs using an HCI platform and automated image analysis
software. To establish the high-throughput potential of this approach, we also
screened a pool of ligands against a collection of 2455 cell surface expression
clones and found that known ligand–receptor interactions could be robustly and
consistently detected across the library using this technology.
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Affiliation(s)
- Laura Wood
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge, UK
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