Gene Expression and Histone Modification Profiles in GBM Tumors

The primary goal of this study was to collect and analyze genomic data from primary glioblastoma multiforme tumors. Our collaborators at St David's Medical Center (SDMC) obtained informed consent from patients undergoing surgery to remove a tumor in the brain. After consent was obtained, specimens were removed from the operating suite and flash frozen in liquid nitrogen. Tumors were analyzed if they were a grade III (anaplastic astrocytoma) or grade IV glioma (glioblastoma multiforme). Tumors were transported from SDMC to UT Austin, then weighed and homogenized. Chromatin immunoprecipitation was performed for 7 proteins in each tumor (histone modifications H3K4me3, H3K4me1, H3K9ac, H3K9me3, H3K27ac, H3K27me3, and the multifunctional insulator binding protein CTCF) and no-antibody input was also sequenced. An aliquot of tumor material was set aside for isolation of total RNA.]]>
Tumors were analyzed if they were a grade III (anaplastic astrocytoma) or grade IV glioma (glioblastoma multiforme) lesion. Patients were included in this study if they consented to tissue donation during surgery to remove a brain tumor. Study participants ranged in age from 28 to 70. Six participants were male and seven were female. No minors were included in this study.]]>
The 13 samples comprising the tumor samples in this study were collected, then homogenized. The homogenized tissue was subjected to chromatin immunoprecipitation for 7 proteins in each tumor (histone modifications H3K4me3, H3K4me1, H3K9ac, H3K9me3, H3K27ac, H3K27me3, and the multifunctional insulator binding protein CTCF), and RNA isolation. Libraries for sequencing were made from the resulting DNA (and cDNA in the case of isolated RNA) and were sequenced at M.D. Anderson Cancer Center at Science Park (Smithville, Texas) using an Illumina HiSeq 2500. Several samples were sequenced at the Genome Sequencing and Analysis Facility (GSAF) at the University of Texas at Austin, also using an Illumina HiSeq 2500.]]>