UC San Diego

RNA has been proved to interact with lipid bilayers and various proteins near the membrane, however; the existence of cell surface RNA was less explored. Using CLICK reaction and fluorescence visualization, preliminary research in Zhong Lab had suggested the existence of cell surface RNAs(csRNA) that attached firmly on the outer membrane of mouse and human cells. For the first step in this study, functionality assay of cytotoxicity, which measured by LDH release of human immune Natural Killer cell line NK92, showed that the global csRNA perturbation could significantly impact NK92’s cell killing activity. To further capture and characterize csRNAs using sequencing data, we have developed a method to pull-down lipid-associated RNAs using lipid-coated beads followed by RNA-sequencing. csRNAs were identified based on differential analysis of RNAs bound to 8 types of membrane-associated lipid against the control bead. Candidate RNAs discovered were validated using two sequencing techniques developed by the Zhong Lab, i.e. SurfaceClick and SurfaceSeq, to further remove background noise. Functional and structural analysis of validated csRNAs showed significant enrichment on immune and cancer-related functions as miRNAs. Furthermore, the analysis result further indicated potential cellular functions such as cell-cell recognition, structural support, and signaling regulation. In a nutshell, this study indicated the existence of RNA on cell’s outer membrane as functional and structural groups for cellular functions such as anti-tumor cytotoxicity and immune response.