Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction [surfaceSeq]

Compared to proteins, glycans, and lipids, much less is known about RNAs on the cell surface. We developed 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). We visualized maxRNAs on the cell surface, sequenced selected maxRNAs, and validated two maxRNAs by RNA fluorescence in situ hybridization. To test for cell-type specificity of maxRNA, we used randomized 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 identified monocyte as the major type of maxRNA+ PBMCs and prioritized 11 maxRNAs for functional tests. Extracellular hybridization of antisense oligos to the cell surface-exposed fragments of FNDC3B and CTSS transcripts inhibited monocyte adhesion to vascular endothelial cells. Collectively, these data highlight maxRNAs as a functional component of the cell surface, suggesting an expanded role for RNA in cell-cell interaction and communication. Targeted RNA sequencing using Surface-Seq on EL4 cell line