Gastrointestinal stromal tumor (GIST) has emerged as a clinically distinct type of sarcoma with frequent overexpression and mutation of the c-Kit oncogene and a favorable response to imatinib mesylate [also known as STI571 (Gleevec)] therapy. However, a significant diagnostic challenge remains in the differentiation of GIST from leiomyosarcomas (LMSs). To improve on the diagnostic evaluation and to complement the immunohistochemical evaluation of these tumors, we performed a whole-genome gene expression study on 68 well characterized tumor samples. Using bioinformatic approaches, we devised a two-gene relative expression classifier that distinguishes between GIST and LMS with an accuracy of 99.3% on the microarray samples and an estimated accuracy of 97.8% on future cases. We validated this classifier by using RT-PCR on 20 samples in the microarray study and on an additional 19 independent samples, with 100% accuracy. Thus, our two-gene relative expression classifier is a highly accurate diagnostic method to distinguish between GIST and LMS and has the potential to be rapidly implemented in a clinical setting. The success of this classifier is likely due to two general traits, namely that the classifier is independent of data normalization and that it uses as simple an approach as possible to achieve this independence to avoid overfitting. We expect that the use of simple marker pairs that exhibit these traits will be of significant clinical use in a variety of contexts.cancer ͉ classification ͉ diagnostic ͉ machine learning ͉ molecular signature G astrointestinal stromal tumors (GISTs) and leiomyosarcomas (LMSs) are common mesenchymal tumors with remarkably similar phenotypic features (1, 2). Until recently, the differentiation between these two entities had not been thought to be clinically relevant. Chemotherapeutic agents, such as doxorubicin and ifosfamide used in the treatment of soft-tissue sarcomas have resulted in response rates of 0-10% in patients with advanced GIST (3-5). However, the use of the selective tyrosine kinase inhibitor imatinib mesylate [also known as STI571 (Gleevec; Novartis Pharmaceuticals Corp., East Hanover, NJ)] has resulted in response rates of Ͼ50% for patients with GIST (6, 7, **). Conversely, patients with advanced LMS expect response rates of 27-53% when treated with doxorubicin or newer regimens combining gemcitabine with docetaxel (8, 9) but do not benefit from imatinib therapy (10, 11, † †). Thus, there is clear clinical importance in distinguishing between these two entities to guide the most effective therapy. Currently, the best marker to differentiate GIST from LMS is Kit immunostaining, which is subjective and variable due to cellular heterogeneity that may result in false-negative diagnoses. Kitnegative GISTs and Kit-expressing LMS have been reported on the basis of tumor cell morphology and other markers such as CD34, desmin, and smooth muscle actin ( ‡ ‡). The occurrence of Kit-negative GIST in the literature is Ϸ4-10% (2, 12). We used whole human genome microarray d...

Our previous studies have shown that insulin-like growth factor binding protein 2 (IGFBP-2) is frequently overexpressed in the highly invasive glioblastoma multiforme (GBM). By using a yeast two-hybrid system, we identified a gene, invasion inhibitory protein 45 (IIp45), whose protein product bound to IGFBP-2 through the thyroglobulin-RGD region of the C terminus of IGFBP-2. The IIp45 gene is located on chromosome 1p36 and has nine exons. The IIp45 protein has three SEG (segment of low compositional complexity) domains and an integrin-binding RGD motif. The IIp45 protein was not expressed in some GBMs. Functional studies showed that IIp45 inhibited GBM cell invasion both in vitro and in xenograft model. Gene expression profiling studies showed that IIp45 consistently inhibited the expression of cell invasion-associated genes, such as the transcriptional NFB, and its downstream target gene, intercellular adhesion molecule 1. Thus, we report here the isolation and characterization of a gene, IIp45, whose protein product binds to IGFBP-2 and inhibits glioma cell invasion.

The vast majority of Friedreich ataxia patients are homozygous for large GAA triplet repeat expansions in intron 1 of the X25 gene. Instability of the expanded GAA repeat was examined in 23 chromosomes bearing 97-1250 triplets in lymphoblastoid cell lines passaged 20-39 times. Southern analyses revealed 18 events of significant changes in length ranging from 69 to 633 triplets, wherein the de novo allele gradually replaced the original over 1-6 passages. Contractions and expansions occurred with equal frequency and magnitude. This behavior is unique in comparison with other large, non-coding triplet repeat expansions [(CGG)(n)and (CTG)(n)] which remain relatively stable under similar conditions. We also report a rare patient who, having inherited two expanded alleles, showed evidence of contracted GAA repeats ranging from nine to 29 triplets in DNA from two independent peripheral blood samples. The GAA triplet repeat is known to adopt a triplex structure, and triplexes in transcribed templates cause enhanced mutagenesis. The poly(A) tract and a 135 bp sequence, both situated immediately upstream of the GAA triplet repeat, were therefore examined for somatic mutations. The poly(A) tract showed enhanced instability when in cis with the GAA expansion. The 135 bp upstream sequence was found to harbor a 3-fold excess of point mutations in DNA derived from individuals homozygous for the GAA triplet repeat expansion compared with normal controls. These data are likely to have important mechanistic and clinical implications.

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BACKGROUND.Imatinib has demonstrated marked clinical efficacy against gastrointestinal stromal tumor (GIST). Microarray technology, real‐time polymerase chain reaction (PCR) validation, and fluorodeoxyglucose‐positron emission tomography (FDG‐PET) imaging were used to study the early molecular effects of imatinib antitumor activity in GIST.METHODS.After exposure of sensitive and resistant sarcoma cell lines to imatinib for 24 to 48 hours, the changes in gene expression were evaluated using a 1146 unique pathway array with Western blot validation. Real‐time PCR was used to confirm changes in gene expression in human GIST samples (preimatinib biopsy and postimatinib surgical specimen after 3–7 days of therapy). FDG‐PET was performed to correlate radiographic findings with the effects of imatinib on gene expression in GIST.RESULTS.In all, 55 genes demonstrated a ≥ 2‐fold change after imatinib treatment of the GIST882 cells. Among these genes there was up‐regulation of insulin‐like growth factor binding protein‐3 (IGFBP‐3), a protein that modulates proliferation and apoptosis. Western blot analysis confirmed the increase of IGFBP‐3 only in imatinib‐sensitive GIST882 cells. Up to a 7‐fold induction (49% mean increase; P = .08) of IGFBP‐3 mRNA was found in tumor samples from patients with low residual FDG uptake, whereas there was an up to 12‐fold reduction (−102% mean decrease; P = .03) in IGFBP‐3 in those patients with high residual FDG uptake after imatinib therapy.CONCLUSIONS.In the current study, imatinib appears to regulate numerous genes and specifically induces IGFBP‐3 in GIST cells and tumor samples. IGFBP‐3 levels also were found to be inversely correlated with residual FDG uptake in GIST patients early in imatinib therapy. These initial observations suggest that IGFBP‐3 is an important early marker of antitumor activity of imatinib in GIST. Cancer 2006. © 2006 American Cancer Society.