The prevalence of lymph node involvement, tumor size (T1–T2 vs T3–T4) and histological grade was significantly greater in RUNX3-negative cases (RUNX3 unmethylated groups) than in RUNX3-positive cases (OR = 0.25, CI = 0.14–0.43, P<0.00001). Here, RUNX3 is linked to neoplasm.