P16 DNA Methylation Coupled with Somatic Copy Number Variations in the Development of Gastric Carcinomas

Background/Objectives: Tumor suppressor genes are often inactivated by genetic and epigenetic mechanisms. However, whether genetic alterations of these genes, including CDKN2A/P16, are coupled with epigenetic changes in cancer development and progression is unknown. Methods: Freshly frozen gastric carcinoma (GC) samples, paired noncancer surgical margin (SM) samples, white blood cell (WBC) samples, and clinicopathological information were collected from 200 patients. The copy number (CN) of the CDKN2A/P16 gene in these samples was determined by a P16-Light assay and normalized to that in white blood cells (WBCs). The DNA methylation level of the P16 promoter in GC and SM samples was determined by a 115 bp P16-specific MethyLight assay. Results: Both the P16 copy number and the DNA methylation level were significantly lower in GC samples than in SM samples (median, 1.94 vs. 2.14, p < 0.001 for P16 CN; 0.0004 vs. 0.0013, p = 0.002 for P16 methylation) and were associated with GC metastasis. The normalized P16 copy number was significantly lower in GCs without vs. with P16 methylation (p = 0.007). Similarly, more P16 somatic copy number deletions (SCNdel) were detected in GCs without vs. with P16 methylation (38.6% vs. 24.1%, p = 0.027). Conclusions: Somatic P16 copy number variations are closely coupled with P16 promoter DNA methylation during GC development. SCNdel and promoter DNA methylation complementarily inactivate P16 in GC development and promote GC metastasis.