Gene-Pair Test Distinguishes GIST From Leiomyosarcoma

HOUSTON—Researchers have developed a two-gene test that can accurately distinguish between two common forms of gastrointestinal cancers. The two cancers, gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS), are almost phenotypically identical but respond quite differently to chemotherapy. The new test holds promise for improving the outcomes of patients with the two types of tumors, and as a prototype for tests aimed at more individualized diagnoses and determining how other cancers may respond to treatment.

"This simple and accurate test has the potential to be relatively quickly implemented in the clinic to benefit patients by guiding appropriate treatment," said senior author Wei Zhang, PhD, professor of pathology at M.D. Anderson Cancer Center.

For years, GIST was considered a subtype of LMS because both tumors develop in the smooth muscle cells of the GI tract; thus, differentiating between them was not regarded as clinically relevant. In recent years, however, it has become obvious that GIST responds far better to the molecularly targeted drug imatinib (Gleevec) than to traditional chemotherapy, and that LMS responds to chemotherapy but not imatinib.

"Thus, there is a clear clinical importance in distinguishing between these two entities to guide the most effective therapy," wrote first author Nathan D. Price, PhD, a research scientist at the Institute for Systems Biology (ISB) in Seattle, and colleagues from ISB and M.D. Anderson. They reported their work in the February 27 issue of the Proceedings of the National Academy of Sciences (104:3414-3419, 2007).

Currently, the most accurate test to differentiate GIST from LMS is Kit immunostaining, which is subjective and variable due to cellular heterogeneity that may result in false-negative diagnoses. Kit staining has a reported accuracy of 87%, considerably less than that obtained with the new test.

The team first measured gene expression in 68 well-characterized GIST or LMS tumor samples using whole genome microarrays. Then, instead of trying to identify multiple genes whose expression distinguished the two GI tumors from one another, the researchers analyzed the expressions of all possible gene pairs.

This technique, called Top Score Pairing analysis, pinpointed two genes—OBSCN and C9orf65—whose expression ratio best distinguished the two cancers from each other. When the OBSCN gene expressed more RNA than the C9orf65 gene, that difference identified the cancer as GIST. If the C9orf65 gene produced the greater amount of RNA, this ratio pinpointed the tumor as LMS.

Of the 68 microarrayed tumors, the test accurately identified 67. The one exception proved to be a tumor in which the two genes had an expression ratio of almost 1:1. Further testing, including an additional 19 tumor samples not included in the original 68 samples, yielded an accuracy of 99.3% on the microarray samples and an estimated accuracy of 97.8% on future cases.

Top Score Pairing analysis appears highly accurate for two reasons, the authors said. Its simplicity reduces the problem of overfitting data, and the use of gene pairs eliminates normalization issues. "It is possible that, in the future, this approach may be used not only to differentiate ambiguous histologies and to assess prognosis but also to determine who will benefit from chemotherapy, which type of chemotherapy to use, and which patients are at risk for local or distant relapse," the researchers said.