The Neuro-Oncology Branch Laboratory of translational science is divided into three major areas:Project 1: The molecular and genetic characterization of human gliomas for the purpose of redefining a glioma taxonomy and for the identification and ultimate validation of new molecular targets and patient specific subgroups for therapeutic drug discovery.The creation of a national, multi-institutional effort to prospectively molecularly characterize over 1000 gliomas: The Glioma Molecular Diagnostic Initiative (GMDI): We have constructed a national, publicly funded effort that we call the GMDI, which coupled with its bioinformatics counterpart (REMBRANDT), is designed to breach the gap between biological and corresponding clinical data related to primary brain tumors in order to better understand the molecular pathogenesis of gliomas and ultimately help patients receive more rationally tailored treatment specific to their tumor's biology. Through our national protocol, patient accrual to the GMDI began approximately 30 months ago. All tissue collected is sent to our laboratory for processing. Clinical data on the patients is collected prospectively until the patient's death, through the NCI-sponsored brain tumor clinical trials consortia. DNA, RNA and proteins are assayed using different genomic-scale technologies to determine levels of expression, mutations and chromosomal abnormalities. Beyond the generation of the molecular data and the data population of REMBRANDT, we are also analyzing the data in order to identify new targets for therapy thereby furthering the mission of the NOB. As a first step in this data mining process, we have analyzed the results from the genomic survey in our retrospective sample of 180 gliomas.. We have used the data obtained from the SNP array in two different but complementary ways: a) Analysis of Copy Number Alterations (CNA); and b) Loss of heterozygosity (LOH). CNA analysis of these tumors yielded a large number of areas with deletions and amplifications, some of which had been previously reported, as in the case of CDKN2B and EGFR whereas many never previously described areas were detected. We have been able to identify novel regions of LOH while confirming known ones (PTEN on Chr 10, 1p/19q, etc) The high correlation between the results of the LOH and CNA analyses allows us to confirm the regions of loss. An example of how data generated from GMDI may lead to promising new molecular targets is demonstrated by our analyses of chemotherapy sensitive oligodendrogliomas with 1p/19q chromosomal deletions compared to chemotherapy resistant oligodendrogliomas with maintenance at that locus. CGH and SNP analysis allowed us to separate a cohort of 10 oligodendrogliomas with LOH and 24 without. Gene expression profiles between the two groups of tumors revealed 97 genes differentially expressed. One of the most significantly differentially expressed genes was histone deacytelase I (HDAC-1)74, with HDAC1 levels significantly lower in gliomas with 1p/19q LOH compared to those with maintenance of the locus. HDAC1 levels were much lower in chemotherapy sensitive oligodendrogliomas and much higher in other chemotherapy resistant gliomas of all types such as GBMs. This led to a series of in vitro experiments using HDAC1 siRNA and HDAC inhibitors (i.e. valproic acid) demonstrating that down-regulation of HDAC-1 is not only intrinsically toxic to glioma cell lines that normally express high levels of HDAC1, but also sensitize glioma cells to both radiation and a broad array of alkylating agents. We have used these data to convince investigators at CTEP to allow us to conduct a NABTC-sponsored, multi-institutional phase I/II trial of the HDAC inhibitor, Depsipeptide75, in patients with recurrent high-grade gliomas.. A variety of future research paths are opening due to the wealth of molecular data generated through the GMDI effort.
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