Gastrointestinal (GI) stromal tumors, albeit historically subjected to numerous classification schemes, are no exception to this new molecular-profiling trend. It now appears that molecular characteristics may critically impact the ultimate biologic behavior of the tumor(s) and these molecular endpoints may serve to add precision to an otherwise imprecise classification system. Until recently, outside of the pathology literature, GIST remained a relatively obscure clinical entity. Progress in molecular medicine with the development and clinical implementation of targeted molecular therapies provided the impetus for renewed attention to this otherwise, rare, soft tissue tumor. The overwhelming success of the tyrosine kinase inhibitor imatinib mesylate (Gleevec; Novartis) in patients with CML parallels initial clinical trial successes in patients with metastatic GISTs.

Initially, GIST emerged as a prototypical solid tumor model destined for this new genre of molecular medicine. Histopathologic definition of these tumors was unreliable based on conventional techniques. Clinically, surgery was the only option for resectable tumors and even these patients did poorly. Conventional adjuvant therapies were unsuccessful. GISTs represent an incurable malignancy for patients with metastatic or unresectable disease. Histologic, molecular genetic, and immunohistochemistry advances heralded a new era for GISTs and GIST patients. The common denominator in most GISTs is the KIT protein. KIT, a type III tyrosine kinase growth factor receptor, has similarities to receptors of macrophage colony stimulating factor and platelet derived growth factor. CD117, the epitope for KIT, was introduced as a new, reliable phenotypic marker useful for distinguishing between GISTs versus non-GIST spindle cell tumors of the gastrointestinal tract. CD117, the protein product of the proto-oncogene c-kit, represents upregulated tyrosine kinase activity, a central pathogenetic event in most GISTs. The pharmaceutical development and therapeutic implications of protein tyrosine kinase inhibitors has refocused our attentions on GIST, a disease where uncontrolled and constitutive activation of KIT signaling leads to uncontrolled cell proliferation and resistance to apoptosis.

It is now known that most overexpression of KIT/CD117 is in direct response to mutations in the c-kit gene, mapped to chromosomal region 4q11-21. Most GISTs, both benign and malignant, carry mutations in c-kit. Supplemental information has shown that these mutations vary among these tumors and no definitive genotype/phenotype correlations have been established. The molecular story of GISTs is complex, however, and the spectrum of mutations and their functional consequences are yet to be refined. Furthermore, KIT activation is still thought to occur regardless of the presence of a kit mutation. Activating or gain-of-function mutations in the juxtamembrane domain (exon 11) of the c-kit gene appear to cause GIST, as compared with mutations in the tyrosine kinase domain (exon 17) that are more often associated with aggressive mastocytosis. The c-kit exon 11 mutations occur in 21 to 57% of GIST and portend a more aggressive tumor behavior. The fact that GIST with c-kit mutations have a higher mitotic count and more frequently have necrosis and/or hemorrhage supports the correlation of c-kit mutations with a poorer clinical outcome. C-kit mutations in exon 11, 9 and 13 were recently associated exclusively with the spindle cell phenotype. Mutations in exon 9 may also define tumors by site in addition to prognosis. These mutational hotspots, including exon 11 and to a lesser degree exons 9 and 13, create unique subsets of GISTs that 1) delineate malignant forms from benign, 2) may not necessarily show a correlation with CD117 expression, and 3) segregate poor prognoses patient subsets.

Other pathways cannot be excluded when molecularly characterizing GISTs. Mutations in kit enable the receptor to phosphorylate various substrate proteins, resulting in activation of a signal transduction cascade, which regulates cell proliferation, apoptosis, chemotaxis and adhesion. Aberrations of these processes may be manifested via other mechanisms, aside from classical mutations and/or protein expression. Conventional cytogenetic analysis has revealed that GISTs demonstrate karyotypes far less complex than those in other spindle cell tumors of comparable histologic grade. Other mechanisms of investigating genetic changes in GISTs have focused on genomic profiling by comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH) studies. GISTS have been shown to have relatively noncomplex cytogenetic profiles that show del(14q) and 22q as common mechanisms of cytogenetic aberration. CGH showed that DNA sequence copy number changes are more prominent in metastatic disease > malignant >benign tumors (El_Rifai, 2000). FISH and CGH have been used to correlate loss of 14q and 22q in tumors with c-kit mutations. A cytogenetic continuum has been suggested (Heinrich 2002) whereby benign GISTs more frequently show a normal karyotype with occasional partial loss of chromosome 14 (14q32). Intermediate or borderline malignant lesions have a consistent loss of chromosome 14, but show additional acquired abnormalities such as loss of 1p, 9p, 11 p, or 22q. High grade (malignant) GISTs predictably have 3 or more of the previously mentioned aberrations. Additionally, other abnormalities, 8q or 17q gains are shown to be associated almost exclusively with the malignant GISTs. Thus, while there is overlap in chromosomal/mutational changes, there appears to be a spectrum of genetic events with a fairly defined repertoire of accumulated genetic changes and tumor progression.

Will molecular profiling segregate GISTs into groups and identify which are most likely to respond to molecular targeting? Should we be routinely testing clinically for mutations in c-kit exons that herald a poor prognosis in these patients? Laboratory verification of mutations in c-kit may be clinically useful as an adjunct in confirming and stratifying patients with GISTs (versus GANTs and other benign or malignant neoplasms). The mutation, particularly the in-frame deletion in exon 11, is unique to GISTS, both in somatic tumor cells and in leukocytes of patients with a family history of GISTs. Monitoring c-kit mutations may be helpful in assessing residual tumor burden and monitoring patients for recurrent disease. Should we be investigating cytogenetic abnormalities in these patients? Likely so, but clinical outcome and other answers are only yet beginning to unravel. Inconsistencies in diagnosis, treatment, treatment response, mutational status, chromosomal aberrations, and mutations in genes yet undefined all contribute to our tenuous grasp on the role of molecular genetics as a predictor of biologic behavior in GISTs.

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