Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction
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RESEARCH
Open Access
Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction Norman Huang1†, Xiaochen Fan1†, Kathia Zaleta-Rivera1†, Tri C. Nguyen1, Jiarong Zhou2, Yingjun Luo3, Jie Gao2, Ronnie H. Fang2, Zhangming Yan1, Zhen Bouman Chen3, Liangfang Zhang2 and Sheng Zhong1* * Correspondence: szhong@ucsd. edu † Norman Huang, Xiaochen Fan and Kathia Zaleta-Rivera contributed equally to this work. 1 Department of Bioengineering, University of California San Diego, San Diego, CA 92093, USA Full list of author information is available at the end of the article
Abstract Background: Compared to proteins, glycans, and lipids, much less is known about RNAs on the cell surface. We develop a series of technologies to test for any nuclearencoded RNAs that are stably attached to the cell surface and exposed to the extracellular space, hereafter called membrane-associated extracellular RNAs (maxRNAs). Results: We develop a technique called Surface-seq to selectively sequence maxRNAs and validate two Surface-seq identified maxRNAs by RNA fluorescence in situ hybridization. To test for cell-type specificity of maxRNA, we use antisense oligos to hybridize to single-stranded transcripts exposed on the surface of human peripheral blood mononuclear cells (PBMCs). Combining this strategy with imaging flow cytometry, single-cell RNA sequencing, and maxRNA sequencing, we identify monocytes as the major type of maxRNA+ PBMCs and prioritize 11 candidate maxRNAs for functional tests. Extracellular application of antisense oligos of FNDC3B and CTSS transcripts inhibits monocyte adhesion to vascular endothelial cells. Conclusions: Collectively, these data highlight maxRNAs as functional components of the cell surface, suggesting an expanded role for RNA in cell-cell and cell-environment interactions. Keywords: Cell surface, Extracellular RNA, Cell membrane, Single cell, Cell-environment interaction, Monocyte, Endothelial cells
Introduction The cell surface is the crucial interface between the interior and exterior of the cell. Bioactive molecules, including proteins, glycans, lipids, and their chemically modified variations, are essential for the cell surface functions, e.g., extracellular signal sensing, extracellular matrix anchoring, and antigen presentation. In contrast, the contribution of nucleic acids particularly RNAs to the cell surface functions is largely unknown. Typically, the nuclear genome encoded RNAs (ngRNA) are not expected to be present on the surface of eukaryotic cells with intact cell membranes [1]. There have been a few cases suggesting exceptions. Ribonucleoproteins were shown to be released © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images
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