Project description:To investigate differential gene expression, we analyzed the entire transcriptomes of tumor and matched normal brain tissues obtained from a patient who had glioblastoma multiforme. We extracted and sequenced the mRNA using Illumina GA2 platform. The raw data was analyzed using our recently developed program called RNASEQR, as well as ERANGE, MapSplice, SpliceMap, and TopHat. Tumor and matched control brain tissues were obtained from a Han-Chinese patient.
Project description:To investigate differential gene expression, we analyzed the entire transcriptomes of tumor and matched normal brain tissues obtained from a patient who had glioblastoma multiforme. We extracted and sequenced the mRNA using Illumina GA2 platform. The raw data was analyzed using our recently developed program called RNASEQR, as well as ERANGE, MapSplice, SpliceMap, and TopHat.
Project description:glioblastoma multiforme genomic profiling by single nucleotide polymorphism microarray<br><br>Human GBM (glioblastoma multiforme)cell lines (U87, U118, U138, U343, U373, T98G) were maintained in Dulbecco's modified Eagle's medium with 10 % fetal calf serum, 10 U/ml penicillin-G, and 10 mg/ml streptomycin. All cells were incubated at 37 oC in 5% CO2.<br><br>Four primary GBM explants were established from patients with glioblastoma multiforme undergoing surgery as following described: Tumor specimens were immediately transported to the laboratory, finely minced to single cell suspension and cultured in complete medium [Ham's F-12/DME High Glucose medium containing 10% fetal calf serum, 10 U/ml penicillin-G, and 10 mg/ml streptomycin and 2 mM glutamax-1 into 100 cm2 tissue culture plastic dishes the second passage. All cells were incubated at 37 oC in 5% CO2.<br><br>GBM (glioblastoma multiforme) tissue samples were quick frozen. <br><br>Standard proteinase K-phenol-chloroform extraction method was used to extract DNA from GBM samples, cell lines and explants.<br><br>The matched peripheral blood data can be used as normalized data for their matched tumor tissue data. <br><br>The cell lines samples and two explants without normalized data, but they can be normalized by one of the peripheral blood DNA data.
Project description:This model is based on paper:
Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy
Abstract:
Glioblastoma multiforme is one of the most invasive type of glial tumors, which rapidly grows and commonly spreads into nearby brain tissue. It is a devastating brain cancer that often results in death within approximately 12 to 15 months after diagnosis. In this work, optimal control theory was applied to regulate intracellular signaling pathways of miR-451–AMPK–mTOR–cell cycle dynamics via glucose and drug intravenous administration infusions. Glucose level is controlled to activate miR-451 in the up-stream pathway of the model. A potential drug blocking the inhibitory pathway of mTOR by AMPK complex is incorporated to explore regulation of the down-stream pathway to the cell cycle. Both miR-451 and mTOR levels are up-regulated inducing cell proliferation and reducing invasion in the neighboring tissues. Concomitant and alternating glucose and drug infusions are explored under various circumstances to predict best clinical outcomes with least administration costs.
Project description:This model is based on paper, based on its cell cycle dynamics model:
Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy
Abstract:
Glioblastoma multiforme is one of the most invasive type of glial tumors, which rapidly grows and commonly spreads into nearby brain tissue. It is a devastating brain cancer that often results in death within approximately 12 to 15 months after diagnosis. In this work, optimal control theory was applied to regulate intracellular signaling pathways of miR-451–AMPK–mTOR–cell cycle dynamics via glucose and drug intravenous administration infusions. Glucose level is controlled to activate miR-451 in the up-stream pathway of the model. A potential drug blocking the inhibitory pathway of mTOR by AMPK complex is incorporated to explore regulation of the down-stream pathway to the cell cycle. Both miR-451 and mTOR levels are up-regulated inducing cell proliferation and reducing invasion in the neighboring tissues. Concomitant and alternating glucose and drug infusions are explored under various circumstances to predict best clinical outcomes with least administration costs.
Project description:Glioblastoma multiforme is the most common and aggressive type of brain cancer. Little is known about the complex relationship between genomic and epigenomic as tumour progresses. We present the following base resolution whole genome maps of matched tumour/margin and blood samples from a glioblastoma multiforme patient:<br>* Single nucleotide variations (SNVs), copy number variations (CNVs) and structural variations (SVs) as revealed by DNA sequencing. </br> <br>* 5-methylcytosine and 5-hydroxymethylcytosine levels obtained using (oxidative)bisulfite sequencing. </br> <br>* Transcript levels produced using RNA sequencing.</br> <br>For the three samples with very large bam raw data files ('Blood DNA-seq', 'Margin DNA-seq' and 'Tumour DNA-seq'), bai index files are available from https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5171/E-MTAB-5171.additional.1.zip
Project description:RNA-seq profiling of murine hGFAPCreXrcc4f/fp53f/f malignant gliomas with characteristic features of human glioblastoma multiforme (GBMs). Comparison to control neurospheres generated from the hGFAPCreXrcc4f/fp53f/f postnatal day 1-3 brain.
Project description:Extensive infiltration of the surrounding healthy brain tissue is a critical feature in glioblastoma. Several miRNAs have been related to gliomagenesis, some of them related with the EGFR pathway. We have evaluated whole-genome miRNA expression profiling associated with different EGFR amplification patterns, studied by fluorescence in situ hybridization in tissue microarrays, of 30 cases of primary glioblastoma multiforme, whose clinicopathological and immunohistochemical features have also been analyzed.