CD47 interactions with exportin-1 limit the targeting of m7G-modified RNAs to extracellular vesicles

Sukhbir Kaur; Alejandra Cavazos Saldana; Abdel G Elkahloun; Jennifer D Petersen; Anush Arakelyan; Satya P Singh; Lisa M Jenkins; Bethany Kuo; Bianca Reginauld; David G Jordan; Andy D Tran; Weiwei Wu; Joshua Zimmerberg; Leonid Margolis; David D Roberts

doi:10.1007/s12079-021-00646-y

CD47 interactions with exportin-1 limit the targeting of m⁷G-modified RNAs to extracellular vesicles

J Cell Commun Signal. 2022 Sep;16(3):397-419. doi: 10.1007/s12079-021-00646-y. Epub 2021 Nov 29.

Authors

Affiliations

¹ Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10 Room 2S235, 10 Center Dr, Bethesda, MD, 20892-1500, USA.
² Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA.
³ Section On Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, USA.
⁴ Section On Intercellular Interactions, Division of Basic and Translational Biophysics, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, USA.
⁵ Inflammation Biology Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA.
⁶ Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, USA.
⁷ Confocal Microscopy Core Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, USA.
⁸ Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10 Room 2S235, 10 Center Dr, Bethesda, MD, 20892-1500, USA. droberts@mail.nih.gov.

Abstract

CD47 is a marker of self and a signaling receptor for thrombospondin-1 that is also a component of extracellular vesicles (EVs) released by various cell types. Previous studies identified CD47-dependent functional effects of T cell EVs on target cells, mediated by delivery of their RNA contents, and enrichment of specific subsets of coding and noncoding RNAs in CD47⁺ EVs. Mass spectrometry was employed here to identify potential mechanisms by which CD47 regulates the trafficking of specific RNAs to EVs. Specific interactions of CD47 and its cytoplasmic adapter ubiquilin-1 with components of the exportin-1/Ran nuclear export complex were identified and confirmed by coimmunoprecipitation. Exportin-1 is known to regulate nuclear to cytoplasmic trafficking of 5'-7-methylguanosine (m⁷G)-modified microRNAs and mRNAs that interact with its cargo protein EIF4E. Interaction with CD47 was inhibited following alkylation of exportin-1 at Cys⁵²⁸ by its covalent inhibitor leptomycin B. Leptomycin B increased levels of m⁷G-modified RNAs, and their association with exportin-1 in EVs released from wild type but not CD47-deficient cells. In addition to perturbing nuclear to cytoplasmic transport, transcriptomic analyses of EVs released by wild type and CD47-deficient Jurkat T cells revealed a global CD47-dependent enrichment of m⁷G-modified microRNAs and mRNAs in EVs released by CD47-deficient cells. Correspondingly, decreasing CD47 expression in wild type cells or treatment with thrombospondin-1 enhanced levels of specific m⁷G-modified RNAs released in EVs, and re-expressing CD47 in CD47-deficient T cells decreased their levels. Therefore, CD47 signaling limits the trafficking of m⁷G-modified RNAs to EVs through physical interactions with the exportin-1/Ran transport complex.

Keywords: CD47; Exportin-1; Extracellular vesicles; Micro-RNA; RNA trafficking; Ubiquilin-1.

Abstract

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