A Five-Gene Hedgehog Signature Developed as a Patient Preselection Tool for Hedgehog Inhibitor Therapy in Medulloblastoma

Abstract

Purpose: Distinct molecular subgroups of medulloblastoma, including hedgehog (Hh) pathway–activated disease, have been reported. We identified and clinically validated a five-gene Hh signature assay that can be used to preselect patients with Hh pathway–activated medulloblastoma. Experimental Design: Gene characteristics of the Hh medulloblastoma subgroup were identified through published bioinformatic analyses. Thirty-two genes shown to be differentially expressed in fresh-frozen and formalin-fixed paraffin-embedded tumor samples and reproducibly analyzed by RT-PCR were measured in matched samples. These data formed the basis for building a multi-gene logistic regression model derived through elastic net methods from which the five-gene Hh signature emerged after multiple iterations. On the basis of signature gene expression levels, the model computed a propensity score to determine Hh activation using a threshold set a priori. The association between Hh activation status and tumor response to the Hh pathway inhibitor sonidegib (LDE225) was analyzed. Results: Five differentially expressed genes in medulloblastoma (GLI1, SPHK1, SHROOM2, PDLIM3, and OTX2) were found to associate with Hh pathway activation status. In an independent validation study, Hh activation status of 25 medulloblastoma samples showed 100% concordance between the five-gene signature and Affymetrix profiling. Further, in medulloblastoma samples from 50 patients treated with sonidegib, all 6 patients who responded were found to have Hh-activated tumors. Three patients with Hh-activated tumors had stable or progressive disease. No patients with Hh-nonactivated tumors responded. Conclusions: This five-gene Hh signature can robustly identify Hh-activated medulloblastoma and may be used to preselect patients who might benefit from sonidegib treatment. Clin Cancer Res; 21(3); 585–93. ©2014 AACR.

A Phase I, Multicenter, Open-Label, First-in-Human, Dose-Escalation Study of the Oral Smoothened Inhibitor Sonidegib (LDE225) in Patients with Advanced Solid Tumors

“…Importantly, all responses occurred in patients with hedgehog-activated medulloblastoma (18,(26)(27)(28)(29). Complete and partial responses have been observed in patients with medulloblastoma in our study and in a phase I/II study of sonidegib in children with tumors thought to be dependent on hedgehog signaling (phase I) and children and adults with hedgehog-activated medulloblastoma (18).…”

“…Taken together, these data suggest that GLI1 is an ideal marker for SMO inhibitor therapy, but not a marker for tumor response. Molecular alterations in other hedgehog pathway components in the patients who responded are unknown as mutational analyses were not conducted in this study; however, hedgehog pathway activity was assessed using the 5-gene hedgehog signature assay, an RT-PCR-based assay, in fresh-frozen paraffin-embedded tumor samples-a strong association between tumor response and activated hedgehog pathway was observed in patients with BCC and medulloblastoma (18,19).…”

“…To date, responses in medulloblastoma have been reported only for sonidegib and vismodegib (3,18,(26)(27)(28)(29). Importantly, all responses occurred in patients with hedgehog-activated medulloblastoma (18,(26)(27)(28)(29).…”

“…In patients with BCC and medulloblastoma, there was a strong association between tumor response and hedgehog pathway activation, as determined by a 5-gene hedgehog signature RT-PCR assay (Supplementary Table S2; ref. 18). Best overall response of stable disease was observed in 24 patients (23%), with duration of stable disease > 6 months in 3 patients with lung adenocarcinoma, spindle cell sarcoma, and BCC.…”

“…RNA was extracted from tissue samples and analyzed by reverse transcriptase-PCR (RT-PCR) to measure GLI1 expression and hedgehog pathway activation status, based on the 5-gene hedgehog signature assay (18,19).…”