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.

Multifaceted roles of SAMHD1 in cancer

“…One study found that SAMHD1 is down regulated in lung cancer by methylation and inhibits tumour cell proliferation . The other study reported that SAMHD1 levels increase in the serum of lung cancer patients upon progression [Shang et al, 2018]. Our analysis of SAMHD1 data found significantly higher 5-year survival rates in patients with tumours displaying high SAMHD1 expression levels (Supplementary Table 1) supporting the first study.…”

“…Among the 35 articles that reported on an association between SAMHD1 and cancer, four did not (entirely) support the ‘SAMHD1 is a tumour suppressor’ narrative [Yang et al, 2017; Kodigepalli et al, 2018; Shang et al, 2018; Xagoraris et al, 2021]. One study correlated high SAMHD1 levels with metastasis formation in colorectal cancer [Yang et al, 2017].…”

“…Notably, the title of this study exclusively focused on the inhibitory effects of SAMHD1 on leukaemia cell proliferation and did not mention its role in tumourigenesis [Kodigepalli et al, 2018]. One study detected a SAMHD1 increase upon lung cancer progression [Shang et al, 2018], and the most recent study, correlated the presence of SAMHD1 in Hodgkin lymphoma cells with unfavourable outcome [Xagoraris et al, 2021]. Notably, this study [Xagoraris et al, 2021] even referred to SAMHD1 as "novel tumour suppressor" in the title, although the study rather indicated an oncogenic role of SAMHD1.…”

Comparative proteomics analysis of microvesicles in human serum for the evaluation of osteoporosis

“…Filter‐aided sample preparation digestion was carried out for protein digestion as previously described . Obtained peptides for LC‐MS/MS analysis was performed using an automated platform consisting of an EASY‐nLC 1000 LC system (Thermo Fisher Scientific) coupled to LTQ‐Orbitrap XL Hybrid mass spectrometer (Thermo Fisher Scientific) equipped with a nano‐ESI ion source setup.…”

Involvement of SAMHD1 in dNTP homeostasis and the maintenance of genomic integrity and oncotherapy (Review)

“…Widely expressed in several tissues, SAMHD1 mutations have also been detected in breast cancer, myeloma, pancreatic cancer and others. The mutation and modification sites of SAMHD1 in different types of cancer are presented in Tables I (99)(100)(101)(102)(103)(104) and II, respectively.…”