Abstract
Non-random gains of chromosome 5p have been observed in clinically aggressive gastrointestinal stromal tumors, whereas the driving oncogenes on 5p remain to be characterized. We used an integrative genomic and functional approach to identify amplified oncogenes on 5p and to evaluate the relevance of AMACR amplification at 5p13.3 and its overexpression in gastrointestinal stromal tumors. Thirty-seven tumor samples, imatinib-sensitive GIST882 cell line, and imatinib-resistant GIST48 cell line were analyzed for DNA imbalances using array-based genomic profiling. Forty-one fresh tumor samples of various risk categories were enriched for pure tumor cells by laser capture microdissection and quantified for AMACR mRNA expression. AMACR-specific fluorescence in situ hybridization and immunohistochemistry were both informative in tissue microarray sections of 350 independent primary gastrointestinal stromal tumors, including 213 cases with confirmed KIT /PDGFRA genotypes. To assess the oncogenic functions of AMACR, GIST882 and GIST48 cell lines were stably silenced against their endogenous AMACR expression. In 59% of cases featuring 5p gains, two major amplicons encompassed discontinuous chromosomal regions that were differentially overrepresented in high-risk cases, including the one harboring the mRNA-upregulated AMACR gene. Gene amplification was detected in 19.7% of cases (69/350) and strongly related to protein overexpression (p<0.001), although 52% of AMACR-overexpressing cases exhibited no amplification. Both gene amplification and protein overexpression were significantly associated with epithelioid histology, larger size, increased mitoses, higher risk levels, and unfavorable genotypes (all p≦0.03). They were also independently predictive of decreased disease-free survival (overexpression, p<0.001; amplification, p=0.020) in the multivariate analysis. Concomitant with downregulated cyclin D1, cyclin E, and CDK4, AMACR knockdown suppressed cell proliferation and induced G1-phase arrest, but did not affect apoptosis in both GIST882 and GIST48 cells. In conclusion, AMACR amplification is a mechanism driving increased mRNA and protein expression and conferring aggressiveness through heightened cell proliferation in gastrointestinal stromal tumors.
Highlights
As the most common mesenchymal tumors of the digestive tract, gastrointestinal stromal tumors (GISTs) are believed to derive from interstitial Cajal cells or their precursors [1, 2]
Based on the conventional comparative genomic hybridization studies, 5p gain represents non-random chromosomal alterations in GISTs that preferentially occur in the later stages of tumor evolution and have variable prognostic impacts [12, 13]
In our oligonucleotide-based array-based comparative genomic hybridization (aCGH) profiling, the ultra-high resolution and sufficient sample number enabled refined mapping of genomewide copy number alterations (CNAs) that were differentially involved in highrisk samples
Summary
As the most common mesenchymal tumors of the digestive tract, gastrointestinal stromal tumors (GISTs) are believed to derive from interstitial Cajal cells or their precursors [1, 2]. The losses of other chromosomal regions or arms, such as -1p, -9p, and -9q, preferentially occur in aggressive GISTs with or without concomitant chromosomal gains, +5p, +5q, and +8q [12,13,14]. Of these chromosomal aberrations occurring at later stages, we previously profiled the DNA copy number alterations on chromosome 9 and characterized the clinical relevance of homozygous MATP gene deletion at 9p21.3 in GISTs [22]. To search for candidate oncogenes relevant to tumor progression, we performed global genomic profiling analysis of two cell lines and 37
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
