Introduction: Traditionally, three criteria have been used for predicting the malignant potential of gastrointestinal stromal tumors (GISTs), tumor size, mitotic rate, and site of disease. Since aberrant promoter methylation of tumor suppressor genes affords selective growth advantages to human neoplasms, the characterization of gene methylation patterns among GISTs may be useful for predicting tumor behavior.

Design: Thirty-eight c-kit-positive gastric stromal tumors were selected randomly and studied as paraffin-embedded tissue blocks. Each tumor was subjected to methylation-specific PCR to detect promoter methylation associated with 10 candidate tumor suppressor genes (p16, APC, MGMT, p73, E-cadherin, RAR-Β, RASSF-1, RB, ER, and DAPK), established to have a role in the tumorigenesis of several solid human organs. Methylation differences among GIST populations, subdivided according to clinicopathological features and recurrence-free outcome, were compared using a Cox regression multivariate analysis.

Results: Aberrant methylation of any of the 10 candidate tumor suppressor genes was detected in 84% of all GISTs. In decreasing order of frequency, the five most commonly methylated genes were: MGMT (47%), p16 (45%), RASSF-1 (40%), E-cadherin (37%), and APC (31%). Methylation of E-cadherin was found more frequently among GISTs larger than 5 cm compared to smaller tumors, (42% v. 28%). E-cadherin methylation was also detected more frequently among GISTs exceeding 5 mitoses per 50 high-power fields (hpf) compared to those with a low mitotic index, (42% v. 31%). The promoter methylation status of the GISTs was reliable in predicting clinical outcomes after surgical resection. Compared to E-cadherin unmethylated GISTs, E-cadherin methylated tumors experienced an increased 2-year recurrence (51% v. 13%, p=0.013) and a poorer tumor-free 5-year survival (55% v. 83%, p=0.028). Among the mitotically-active (> 5/50 hpf), histologically indistinguishable GISTs, E-cadherin methylation was an independent predictor of cancer-related mortality: 5-year disease-free survival was worse for the E-cadherin methylated GISTs (19%) compared to the E-cadherin unmethylated tumors (73%), p=0.010.

Conclusions: Detection of methylation within selected genes may afford a reliable and accurate molecular marker system for predicting neoplastic behavior among GISTs. The methylation status of E-cadherin is a prognostic marker for early GIST recurrence and survival.