Aberrant m5C hypermethylation mediates intrinsic resistance to gefitinib through NSUN2/YBX1/QSOX1 axis in EGFR-mutant non-small-cell lung cancer

Abstract Background RNA 5-methylcytosine (m 5 C) modification plays critical roles in the pathogenesis of various tumors. However, the function and molecular mechanism of RNA m 5 C modification in tumor drug resistance remain unclear. Methods The correlation between RNA m 5 C methylation, m 5 C writer NOP2/Sun RNA methyltransferase family member 2 (NSUN2) and EGFR-TKIs resistance was determined in non-small-cell lung cancer (NSCLC) cell lines and patient samples. The effects of NSUN2 on EGFR-TKIs resistance were investigated by gain- and loss-of-function assays in vitro and in vivo . RNA-sequencing (RNA-seq), RNA bisulfite sequencing (RNA-BisSeq) and m 5 C methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) were performed to identify the target gene of NSUN2 involved in EGFR-TKIs resistance. Furthermore, the regulatory mechanism of NSUN2 modulating the target gene expression was investigated by functional rescue and puromycin incorporation assays. Results RNA m 5 C hypermethylation and NSUN2 were significantly correlated with intrinsic resistance to EGFR-TKIs. Overexpression of NSUN2 resulted in gefitinib resistance and tumor recurrence, while genetic inhibition of NSUN2 led to tumor regression and overcame intrinsic resistance to gefitinib in vitro and in vivo . Integrated RNA-seq and m 5 C-BisSeq analyses identified quiescin sulfhydryl oxidase 1 (QSOX1) as a potential target of aberrant m 5 C modification. NSUN2 methylated QSOX1 coding sequence region, leading to enhanced QSOX1 translation through m 5 C reader Y-box binding protein 1 (YBX1). Conclusions Our study reveals a critical function of aberrant RNA m 5 C modification via the NSUN2-YBX1-QSOX1 axis in mediating intrinsic resistance to gefitinib in EGFR-mutant NSCLC.