Homozygous Deletion of MTAP Gene as a Poor Prognosticator in Gastrointestinal Stromal Tumors

Abstract

Purpose: Chromosome 9 is frequently deleted in high-risk gastrointestinal stromal tumors (GISTs), whereas its specific tumor suppressor genes (TSGs) are less understood. We did an integrative study of MTAP gene at 9p21 to analyze its implication in GISTs. Experimental Design: To search TSGs on chromosome 9, we used ultrahigh-resolution array comparative genomic hybridization to profile DNA copy number alterations of 22 GISTs, with special attention to MTAP gene. MTAP immunoexpression was assessable for 306 independent GISTs on tissue microarrays, with 146 cases analyzed for MTAP homozygous deletion, 181 for mutations of KIT and PDGFRA receptor tyrosine kinase genes, and 7 for MTAP hypermethylation. Results: Array comparative genomic hybridization identified 11 candidate TSGs on 9p and six on 9q. MTAP and/or CDKN2A/CDKN2B at 9p21.3 were deleted in one intermediate-risk (11%) and seven high-risk (70%) GISTs with two cases homozygously codeleted at both loci. MTAP homozygous deletion, present in 25 of 146 cases, was highly associated with larger size and higher mitotic rate, Ki-67 index, and risk level (all P < 0.01) but not with receptor tyrosine kinase genotypes. Whereas MTAP homozygous deletion correlated with MTAP protein loss (P < 0.001), 7 of 30 GISTs without MTAP expression did not show homozygous deletion, including three MTAP-hypermethylated cases. MTAP homozygous deletion was univariately predictive of decreased disease-free survival (P < 0.0001) and remained multivariately independent (P = 0.0369, hazard ratio = 2.166), together with high-risk category (P < 0.0001), Ki-67 index >5% (P = 0.0106), and nongastric location (P = 0.0416). Conclusions: MTAP homozygous deletion, the predominant mechanism to deplete protein expression, is present in 17% of GISTs. It correlates with important prognosticators and independently predicts worse outcomes, highlighting the role in disease progression. (Clin Cancer Res 2009;15(22):6963-72)

Mitotic Checkpoints and Chromosome Instability Are Strong Predictors of Clinical Outcome in Gastrointestinal Stromal Tumors

“…Previous studies on GISTs have linked 9p21 alterations to tumor progression (11)(12)(13)(14)(15)(16)45), but the driver gene was not positively identified (CDKN2A, CDKN2B, or MTAP; refs. 37,39,[46][47][48]. Here, we have shown that homozygous deletions target CDKN2A and more specifically p16 INK4a .…”

Characterization and Prognostic Significance of Methylthioadenosine Phosphorylase Deficiency in Nasopharyngeal Carcinoma

“…Two pathologists (H-LH and C-FL) evaluated the immunostainings of MTAP according to the previous published criteria. 6,20,25,38 No cytoplasmic staining or faint cytoplasmic staining in <10% of tumor cells was defined as MTAP deficiency. Moderate or strong cytoplasmic staining in >10% of tumor cells was defined as intact MTAP expression.…”

“…Following our previous defined criteria for formalin-fixed samples, the MTAP / PIK3R1 gene ratio <0.2 was considered as homozygous deletion. 25,39 Also, a calibration standard curve was plotted using input templates of 100, 20, 8, and 0.4 ng human genomic DNA (Clontech, Mountain View, CA, USA) to ensure the PCR efficiency and precision in the experiment…”

Prognostic implication of MET overexpression in myxofibrosarcomas: an integrative array comparative genomic hybridization, real-time quantitative PCR, immunoblotting, and immunohistochemical analysis

“…The procedures of DNA labeling, hybridization, normalization of oligonucleotide arrays, window averaging of contained probes, and data acquisition were carried out by the facility of manufacturer as earlier reported. 13 Briefly, genomic DNAs of tumor and reference samples were sonicated to a size range of 500-2000 bp before labeling by random priming with fluorescent Cy3 and Cy5, respectively. After combining the data of signal intensity with information of the genomic coordinates, the Cy3 and Cy5 signal intensities are MET overexpression in myxofibrosarcoma J-C Lee et al normalized to one another using Qspline normalization, a robust non-linear normalized method for two-color experiments.…”

“…5,8,13,14 In this series, we applied ultrahigh-resolution tiling-path aCGH to pinpoint breakpoints of DNA copy number alterations (CNAs) in chromosome 7 for 12 myxofibrosarcomas, so as to identify candidate oncogenes implicating its tumorigenesis. Special attention was given to chromosomal segments harboring the established oncogenes, such as hepatocyte growth factor (HGF) at 7q21 and MET at 7q31.…”