Cell-Surface RNA Forms Ternary Complex with RNA-Binding Proteins and Heparan Sulfate to Recruit Immune Receptors
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
Abstract Recent discoveries have shown the presence of RNA molecules on the cell surface, defying the traditional view that RNA only functions intracellularly. However, it is not well understood how cell-surface RNA (csRNA) is stably present on the plasma membrane and what functions it performs. We answer the pressing questions in the emerging field by taking integrated omic-wide approaches and multiple orthogonal validatory methods. Firstly, we exploited the RNA-sensing ability of TLR7 as a specific recombinant probe to detect csRNA. Coupling it with a genome-wide CRISPR-Cas9-knockout screening, we identified heparan sulfate (HS) as a crucial factor for RNA presentation on cells. Using the TLR7 probe, cell surface proximity labelling revealed that these HS-associated csRNAs (hepRNAs) are in vicinity with a plethora of RNA-binding proteins. The compelling observation led us to a molecular model where HS, RNA and RBP form ternary complexes at cell surface. A photochemical RNA-protein crosslinking technology termed SCOOPS were then established to validate the termolecular model in a TLR7-orthogonal manner. Moreover, enabled by SCOOPS, we unveiled identities of hepRNA using next-generation sequencing, and identified traits in RNA primary structures that facilitate HS association. We further show that hepRNA binds to killer cell immunoglobulin-like receptor 2DL5 (KIR2DL5), recruiting the protein to cell surface and potentially enhancing receptor-ligand interactions. Our findings provide a foundation for exploring how cell-surface ribonucleoproteins contribute to immune modulation.
Authors 11
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Leiden University · Utrecht University · Leiden University Medical Center · Delft University of Technology
Affiliation as printed
Department of BioNanoScience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ, Delft, The Netherlands
Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
Human Genetics department, Leiden University Medical Centre, 2333ZC Leiden, The Netherlands
Department of BioNanoScience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 69 HZ, Delft, The Netherlands
Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 584 CG Utrecht, The Netherlands
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Delft University of Technology
Affiliation as printed
Department of BioNanoScience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ, Delft, The Netherlands
Department of BioNanoScience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 69 HZ, Delft, The Netherlands
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Radboud University Nijmegen · Leiden University Medical Center · Radboud Institute for Molecular Life Sciences · Oncode Institute · Vrije Universiteit Amsterdam · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2333 ZA Leiden, Zuid-Holland, the Netherlands
Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Medical Center, 1007 MB Amsterdam, Noord-Holland, the Netherlands
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
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Radboud University Nijmegen · Utrecht University · Radboud Institute for Molecular Life Sciences · Oncode Institute
Affiliation as printed
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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Leiden University · Leiden University Medical Center
Affiliation as printed
Human Genetics department, Leiden University Medical Centre, 2333ZC Leiden, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
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Utrecht University · University Medical Center Utrecht · Oncode Institute · Hubrecht Institute for Developmental Biology and Stem Cell Research · Delft University of Technology
Affiliation as printed
Department of BioNanoScience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ, Delft, The Netherlands
Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
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Affiliation as printed
School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
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Radboud University Nijmegen · The Netherlands Cancer Institute · Radboud Institute for Molecular Life Sciences · Oncode Institute
Affiliation as printed
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Leiden University · Leiden University Medical Center
Affiliation as printed
Human Genetics department, Leiden University Medical Centre, 2333ZC Leiden, The Netherlands
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Leiden University · Ewha Womans University · Leiden University Medical Center
Affiliation as printed
Department of Physics, Ewha Womans University, Seoul 03760, Republic of Korea
Human Genetics department, Leiden University Medical Centre, 2333ZC Leiden, The Netherlands
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