Epigenetic analysis on RUNX3 mislocalization and its association with tumor microenvironment alteration in non-small cell lung cancer

Abstract To investigate the epigenetic characteristics and tumor microenvironment status that might probably underlie RUNX3 mislocalization in NSCLC. Epigenetic markers, PD-L1 and CD3/8 were assessed in TMA and TCGA datasets. Methylation level at RUNX3 promoter was assessed via pyrosequencing. RNA-seq assays were performed. NSCLC patients’ survival with different patterns of RUNX3 expression was determined. Among NSCLC with RUNX3 negative, nuclear, cytoplastic and whole-cell expression, epigenetic markers differed significantly (all P <0.05). No difference on PD-L1 expression level or CD8/CD3 ratio existed in 4 or 2 RUNX3 distribution patterns (both P >0.05), as was verified in TCGA database. Pyrosequencing indicated higher methylation level on CpG1/2 would result in low RUNX3 expression, as was also associated with higher probability of local relapse (both P <0.05). RNA-Sq showed that the DEGs were primarily enriched in biological processes associated with tumor metastasis, like MMP11. Survival analysis demonstrated no survival discrepancy in various RUNX3 expression patterns of any stages (all P >0.05). No difference in TME markers were determined, either. Various RUNX3 expression patterns might in part result from different status of epigenetic alteration. RNA-Sq revealed that its expression might connect to genes associated with EMT or distant metastasis, and higher RUNX3 promoter methylation was correlated with local relapse.