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 nuclear-encoded 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.

中文翻译：

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细胞表面核编码 RNA 的自然展示及其对细胞相互作用的影响

背景 与蛋白质、聚糖和脂质相比，对细胞表面 RNA 的了解要少得多。我们开发了一系列技术来测试任何稳定附着在细胞表面并暴露于细胞外空间的核编码 RNA，以下称为膜相关细胞外 RNA (maxRNA)。结果我们开发了一种称为 Surface-seq 的技术来选择性地对 maxRNA 进行测序，并通过 RNA 荧光原位杂交验证两个 Surface-seq 鉴定的 maxRNA。为了测试 maxRNA 的细胞类型特异性，我们使用反义寡核苷酸与暴露在人外周血单核细胞 (PBMC) 表面的单链转录本杂交。将此策略与成像流式细胞术、单细胞 RNA 测序和 maxRNA 测序相结合，我们将单核细胞确定为 maxRNA+ PBMC 的主要类型，并优先考虑 11 个候选 maxRNA 进行功能测试。FNDC3B 和 CTSS 转录物的反义寡核苷酸的细胞外应用抑制单核细胞与血管内皮细胞的粘附。结论 总的来说，这些数据突出了 maxRNAs 作为细胞表面的功能成分，表明 RNA 在细胞-细胞和细胞-环境相互作用中的作用扩大。