Graphene Oxide-Facilitated Comprehensive Analysis of Cellular Nucleic Acid Binding Proteins for Lung Cancer.

Abstract

Nucleic acid binding proteins (NABPs) mediate a broad range of essential cellular functions. However, it is very challenging to comprehensively extract whole cellular NABPs due to the lack of approaches with high efficiency. To this end, carbon nanomaterials, including graphene oxide (GO), carboxylated graphene (cG), and carboxylated carbon nanotube (cCNT), were utilized to extract cellular NABPs in this study through a new strategy. Our data demonstrated that GO, cG, and cCNT could extract nearly 100% cellular DNA in vitro. Conversely, their RNA extraction efficiencies were 60, 50, and 29%, respectively, partially explaining why GO has the highest NABPs yield compared to cG and cCNT. We further found that ionic bond mediated by cations between RNA and functional groups of nanomaterials facilitated RNA absorption on nanomaterials. About 2400 proteins were successfully identified from GO-enriched NABPs sample, and 88% of annotated NABPs were enriched at least 2 times compared to cell lysate, indicating the high selectivity of our strategy. The developed method was further applied to compare the NABPs in two lung cancer cell lines with different tumor progression abilities. According to label-free quantification results, 118 differentially expressed NABPs were discovered and 6 candidate NABPs, including ACAA2, GTF2I, VIM, SAMHD1, LYAR, and IGF2BP1, were successfully validated by immunoassay. The level of SAMHD1 in the serum of lung cancer patients was measured, which significantly increased upon cancer progression. Our results collectively demonstrated that GO is an ideal nanomaterial for NABPs selective extraction, which could be broadly used in varied physiological and pathophysiological settings.