Abstract 4818: The predictive value of a 5-gene signature as a patient pre-selection tool in medulloblastoma for Hedgehog pathway inhibitor therapy
Authors: Amakye Dereck , Robinson Douglas , Rose Kristine , Cho Jae , Ligon Keith L. , Sharp Thad , Haider Asifa , Bandaru Raj , Ando Yuichi , Geoerger Birgit , Doz Francois , Ashley David , Hargrave Darren , Casanova Michela , Rodon Jordi , Thomas Anne , Mita Alain , MacDonald Tobey , Kieran Mark W. 
Published: August 2012

Abstract
Medulloblastoma (MB), an invasive primitive neuroectodermal tumor of the posterior fossa, is the most common brain tumor in children, comprising ∼20% of childhood and &lt;2% of adult brain tumors. Current standard of care treatment, surgery followed by craniospinal radiation and chemotherapy, can lead to significant long term toxicities, especially in very young patients. At the time of relapse, no standard salvage therapy exists. Therefore, targeted therapies are needed. Several studies have used gene expression profiling to identify distinct molecular subgroups of MB, including one characterized by activated Hedgehog (Hh) signaling. Using available gene expression data, a 5-gene Hh signature that can be assayed in formalin-fixed paraffin-embedded (FFPE) samples by standard RT-PCR was identified. Two sets of matched fresh frozen and FFPE MB specimens were used; one for development of the 5-gene signature and one for its independent validation. Hh activation status was determined in fresh frozen samples by gene expression profiling using the GeneChip human genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA) and in FFPE samples by RT-PCR analysis. The 5-gene Hh signature was selected from a larger panel of 73 genes that were associated with the Hh subgroup classification, as determined by standard Affymetrix gene expression profiling. Eighteen of these genes shown to be differentially expressed in FFPE were chosen for the RT-PCR gene card that formed the basis of the Elastic Net model building exercise. Based on the expression levels of the 5-gene signature, a predictive model was used to compute a propensity score (0-100%) representative of the Hh activation status of each tumor sample. The median propensity scores for the 17 non-Hh-activated tumors was 0.7% (range: 0.1-3.0%) compared to 87.9% (range: 69.1-97.6%) in the eight Hh-activated tumors. Hh activation status of 25 independent MB samples defined by the 5-gene signature and assayed by RT-PCR were in 100% agreement with the Hh activation status determined by gene expression profiling. In order to determine the predictive value of this assay as a tool to identify patients who might benefit from treatment with a Hh pathway inhibitor, MB samples from patients (n=13) enrolled in recent phase I trials of the Smoothened inhibitor LDE225 were analyzed and correlated with the respective tumor responses. Using the 5-gene signature, all patients (n=4) who responded to LDE225 treatment (PR or CR) were found to have Hh-pathway activated tumors, whereas all patients who did not respond (n=9) were found to have Hh non-activated tumors. These results suggest an association between Hh activation status determined by the 5-gene Hh signature and tumor response to LDE225 treatment. Data from an ongoing phase I/II trial in pediatric patients will enable determination of the predictive value of this patient pre-selection assay.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4818. doi:1538-7445.AM2012-4818