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_:b418679830 , _:b418679831 ; ns1:pmcid "PMC0" ; bibo:doi "10.1371%2Fjournal.pone.0007752" . @prefix ns4: . ns4:contains _:b6404448 , _:b6404450 , _:b6404443 , _:b6404433 , _:b6404415 . _:b6404415 rdf:type ns4:Section . @prefix dc: . _:b6404415 dc:title "introduction" ; ns4:contains _:b6404432 , _:b6404424 , _:b6404425 , _:b6404426 , _:b6404427 , _:b6404428 , _:b6404429 , _:b6404430 , _:b6404431 , _:b6404416 , _:b6404417 , _:b6404418 , _:b6404419 , _:b6404420 , _:b6404421 , _:b6404422 , _:b6404423 . _:b6404416 rdf:type ns1:Context ; rdf:value "Glioblastoma (GBM) is the most common malignant brain tumor and is characterized by intratumoral heterogeneity, invasive growth pattern and poor response to treatment.[>>1<<]\u2013[4] While GBM comprises approximately 25% of all brain tumors in adults, in absolute numbers it is still an uncommon cancer." ; ns1:mentions . _:b6404417 rdf:type ns1:Context ; rdf:value "Glioblastoma (GBM) is the most common malignant brain tumor and is characterized by intratumoral heterogeneity, invasive growth pattern and poor response to treatment.[1]\u2013[>>4<<] While GBM comprises approximately 25% of all brain tumors in adults, in absolute numbers it is still an uncommon cancer." ; ns1:mentions . _:b6404418 rdf:type ns1:Context ; rdf:value "treatment approach contrasts with the wealth of molecular data on mutations, genomic aberrations and transcriptomal features in GBM which indicate potential therapeutic targets and resolve apparently distinct subclasses of these tumors.[>>3<<] We designed this investigation of signal transduction pathway activation in GBM with the expectation that tumor subclasses based on differential activation of glioma-relevant pathways would be of paramount utility for interpreting" ; ns1:mentions . _:b6404419 rdf:type ns1:Context ; rdf:value "two subtypes of GBM were distinguished based on histologic grade at clinical presentation. Primary GBMs present initially as grade 4 tumors while secondary GBMs present as lower grade gliomas and progress to GBMs over time.[>>5<<] Although primary and secondary GBM differ in the frequency of molecular abnormalities seen, they draw largely from a common palette of events:" ; ns1:mentions . _:b6404420 rdf:type ns1:Context ; rdf:value "a common palette of events: amplification and activating mutations in EGFR, over-expression of PDGF and its receptors and loss of the tumor suppressors INK4a/ARF, p53 and PTEN are well-documented, recurrent mutations in these tumors.[>>1<<] Recent large-scale efforts to characterize the glioblastoma genome have identified additional recurrent alterations in genes not previously implicated in glioma, such as ERBB2 and IDH1 mutation in primary and secondary GBM respectively," ; ns1:mentions . _:b6404421 rdf:type ns1:Context ; rdf:value "have identified additional recurrent alterations in genes not previously implicated in glioma, such as ERBB2 and IDH1 mutation in primary and secondary GBM respectively, and a significant incidence of mutation and genomic loss of NF1.[>>6<<]\u2013[8] While there is hope that further sequencing will yield new therapeutic targets, it should be noted that single-agent therapy trials of inhibitors directed to the two most commonly altered receptors have not been successful in" ; ns1:mentions . _:b6404422 rdf:type ns1:Context ; rdf:value "identified additional recurrent alterations in genes not previously implicated in glioma, such as ERBB2 and IDH1 mutation in primary and secondary GBM respectively, and a significant incidence of mutation and genomic loss of NF1.[6]\u2013[>>8<<] While there is hope that further sequencing will yield new therapeutic targets, it should be noted that single-agent therapy trials of inhibitors directed to the two most commonly altered receptors have not been successful in unselected" ; ns1:mentions . _:b6404423 rdf:type ns1:Context ; rdf:value "hope that further sequencing will yield new therapeutic targets, it should be noted that single-agent therapy trials of inhibitors directed to the two most commonly altered receptors have not been successful in unselected populations.[>>9<<], [10] At least in some cases this may be due to failure of RTK inhibition to impact downstream or parallel signal transduction pathway activation." ; ns1:mentions . _:b6404424 rdf:type ns1:Context ; rdf:value "[9], [10] At least in some cases this may be due to failure of RTK inhibition to impact downstream or parallel signal transduction pathway activation.[>>11<<]" ; ns1:mentions . _:b6404425 rdf:type ns1:Context ; rdf:value "The importance of signal transduction activity downstream of tyrosine kinase receptors in glioma biology is emphasized by the fact that these pathways are abnormally active in these tumors and causal in their formation in mice.[>>12<<], [13] Therefore, there is significant interest in whether molecular subclasses of GBM might be identified based on distinct signaling characteristics, and whether such subclasses could be used to refine patient stratification in clinical" ; ns1:mentions . _:b6404426 rdf:type ns1:Context ; rdf:value "The importance of signal transduction activity downstream of tyrosine kinase receptors in glioma biology is emphasized by the fact that these pathways are abnormally active in these tumors and causal in their formation in mice.[12], [>>13<<] Therefore, there is significant interest in whether molecular subclasses of GBM might be identified based on distinct signaling characteristics, and whether such subclasses could be used to refine patient stratification in clinical trials" ; ns1:mentions . _:b6404427 rdf:type ns1:Context ; rdf:value "whether such subclasses could be used to refine patient stratification in clinical trials or help interpret treatment responses. Several studies have subdivided GBMs by expression array analysis measuring total cellular mRNA levels.[>>14<<]\u2013[19] However, because of differential translational efficiencies, total mRNA levels do not always correlate with protein levels." ; ns1:mentions . _:b6404428 rdf:type ns1:Context ; rdf:value "such subclasses could be used to refine patient stratification in clinical trials or help interpret treatment responses. Several studies have subdivided GBMs by expression array analysis measuring total cellular mRNA levels.[14]\u2013[>>19<<] However, because of differential translational efficiencies, total mRNA levels do not always correlate with protein levels." ; ns1:mentions . _:b6404429 rdf:type ns1:Context ; rdf:value "of proteins such as beta catenin. To further complicate matters, signal transduction activity may affect, through feedback mechanisms, the translational efficiencies of mRNAs encoding proteins with effects on the oncogenic phenotype.[>>20<<], [21] Therefore, direct measurements of active signaling components at the protein level are critical to fully characterize the signal transduction state of the cell." ; ns1:mentions . _:b6404430 rdf:type ns1:Context ; rdf:value "such as beta catenin. To further complicate matters, signal transduction activity may affect, through feedback mechanisms, the translational efficiencies of mRNAs encoding proteins with effects on the oncogenic phenotype.[20], [>>21<<] Therefore, direct measurements of active signaling components at the protein level are critical to fully characterize the signal transduction state of the cell." ; ns1:mentions . _:b6404431 rdf:type ns1:Context ; rdf:value "Such measurements have been made on glioma samples and have shown correlation between the levels of active pathway components.[>>20<<], [22]" ; ns1:mentions . _:b6404432 rdf:type ns1:Context ; rdf:value "Such measurements have been made on glioma samples and have shown correlation between the levels of active pathway components.[20], [>>22<<]" ; ns1:mentions . _:b6404433 rdf:type ns4:Section ; dc:title "results" ; ns4:contains _:b6404434 , _:b6404435 , _:b6404436 , _:b6404437 , _:b6404438 , _:b6404439 , _:b6404440 , _:b6404441 , _:b6404442 . _:b6404434 rdf:type ns1:Context ; rdf:value "1 and 2 and downstream Notch target HES1. The Wnt pathway was assessed by beta catenin levels and the SHH pathway by SHH levels. NF1 was assayed in preserved lysates at a later date, after mutations were reported for this gene in GBM.[>>7<<], [8] Quantified bands for 55 antibodies were normalized against actin or tubulin." ; ns1:mentions . _:b6404435 rdf:type ns1:Context ; rdf:value "2 and downstream Notch target HES1. The Wnt pathway was assessed by beta catenin levels and the SHH pathway by SHH levels. NF1 was assayed in preserved lysates at a later date, after mutations were reported for this gene in GBM.[7], [>>8<<] Quantified bands for 55 antibodies were normalized against actin or tubulin." ; ns1:mentions . _:b6404436 rdf:type ns1:Context ; rdf:value "aberrations commonly described in GBM: focal amplification of EGFR, MET and PDGFRA; gain of chr7 without focal amplification; loss of chr10 or 10q23 region spanning PTEN; loss and/or homozygous deletion of 9p21 including Ink4a/ARF.[>>1<<], [23], [24] Figure 2 summarizes the finding of focal amplification of MET and EGFR, gain of chromosome 7, homozygous deletion spanning the Ink4a/ARF locus, and loss at PTEN locus." ; ns1:mentions . _:b6404437 rdf:type ns1:Context ; rdf:value "commonly described in GBM: focal amplification of EGFR, MET and PDGFRA; gain of chr7 without focal amplification; loss of chr10 or 10q23 region spanning PTEN; loss and/or homozygous deletion of 9p21 including Ink4a/ARF.[1], [>>23<<], [24] Figure 2 summarizes the finding of focal amplification of MET and EGFR, gain of chromosome 7, homozygous deletion spanning the Ink4a/ARF locus, and loss at PTEN locus." ; ns1:mentions . _:b6404438 rdf:type ns1:Context ; rdf:value "[1], [23], [>>24<<] Figure 2 summarizes the finding of focal amplification of MET and EGFR, gain of chromosome 7, homozygous deletion spanning the Ink4a/ARF locus, and loss at PTEN locus." ; ns1:mentions . _:b6404439 rdf:type ns1:Context ; rdf:value "class showed EGFR-region amplification and four showed point mutations in the extracellular domain (ECD) previously described in GBM as activating mutations: A289V (GBM.10 and GBM.6), T263P (GBM.8), G598V (GBM.1) and R108K (GBM.6).[>>25<<] The only tumor in the EGFR signaling cluster that did not show focal EGFR amplification was found to harbor amplification of a narrow region including MET." ; ns1:mentions . _:b6404440 rdf:type ns1:Context ; rdf:value "subset of tumors with EGFR or Met amplifications. The PDGFRA-cocluster showed high expression of GRIA2, OLIG2, and NCAM1/2 as well as other genes which are signatures of the \u201CProneural\u201D transcriptomal class of GBM previously described.[>>19<<] Conversely, signature genes of the \u201CMesenchymal\u201D GBM class such as YKL40/CHI3L1, IGFBP2 and VEGFA were most highly expressed in the NF1-cocluster transcriptomal group (Figure S5)." ; ns1:mentions . _:b6404441 rdf:type ns1:Context ; rdf:value "gliomas and found no correlation between mRNA expression and levels of protein even though the latter were highly variable (Figure S7). This reflects the strong regulation of PDGF at the level of translation rather than transcription.[>>27<<], [28] It is likely that some signaling proteins in our study are closely coupled to mRNA levels while many others are regulated independently (or in negative feedback) with corresponding mRNA." ; ns1:mentions . _:b6404442 rdf:type ns1:Context ; rdf:value "and found no correlation between mRNA expression and levels of protein even though the latter were highly variable (Figure S7). This reflects the strong regulation of PDGF at the level of translation rather than transcription.[27], [>>28<<] It is likely that some signaling proteins in our study are closely coupled to mRNA levels while many others are regulated independently (or in negative feedback) with corresponding mRNA." ; ns1:mentions . _:b6404443 rdf:type ns4:Section ; dc:title "methods" ; ns4:contains _:b6404444 , _:b6404445 , _:b6404446 , _:b6404447 . _:b6404444 rdf:type ns1:Context ; rdf:value "6, 8, 10, or 12% SDS-PAGE gel, and transferred onto polyvinylidene difluoride membrane (Millipore). For qualitative comparison, analysis included normal brain cortex lysate as previously described (Analytical Biological Services Inc).[>>30<<] Membranes were blocked with 5% nonfat milk in PBS-0.1% Tween 20. Primary and secondary antibodies were diluted in the blocking solution." ; ns1:mentions . _:b6404445 rdf:type ns1:Context ; rdf:value "Activated K-ras (K-ras-GTP) was tested by using 500 \u00B5g samples for activated Ras pull-down with 10 \u00B5g of glutathione-conjugated Raf-1 GST-RBD beads (Upstate Biotechnology) as previously described.[>>31<<]" ; ns1:mentions . _:b6404446 rdf:type ns1:Context ; rdf:value "9.5.3.1 (Agilent). Fluorescence ratios of the scanned images were calculated and the raw aCGH profiles were processed to identify statistically significant transitions in copy number using the Circular Binary Segmentation algorithm.[>>32<<] Each profile was centered so that log2 ratio of zero is assigned to the predominant copy number, determined by the mode of the distribution of the mean log2 ratio for each segment, weighted by the number of probes per segment ." ; ns1:mentions . _:b6404447 rdf:type ns1:Context ; rdf:value "A description of TCGA data types, platforms and analyses are as previously described.[>>8<<] Processed genomic datasets were downloaded from The Cancer Genome Atlas public data portal (http:" ; ns1:mentions . _:b6404448 rdf:type ns4:Section ; dc:title "discussion" ; ns4:contains _:b6404449 . _:b6404449 rdf:type ns1:Context ; rdf:value "strong pS6 immunopositivity was localized in reactive astrocytes rather than tumor cells per se (data not shown), concordant with recent observations of mTOR activation in reactive astrocytes under experimental conditions of injury.[>>29<<] These cells were more common in PDGF-class tumors. We found a trend for treated tumors to be in the PDGF proteomic class and PDGFB levels were significantly higher in treated compared to untreated tumors." ; ns1:mentions . _:b6404450 rdf:type ns4:Section ; dc:title "supporting information" ; ns4:contains _:b6404451 . _:b6404451 rdf:type ns1:Context ; rdf:value "Tumor profiles in each subclass are assessed for enrichment of signature genes defining the Proneural and Mesenchymal transcriptomal classes of GBM previously described [>>19<<]. Box plots show the distribution of mean percentile rank for expression of Proneural and Mesenchymal signature gene sets courtesy of Kenneth Aldape, MD: Proneural\u200A=\u200A BMP2, GRIA2, OMG, NCAM1&2, OLIG2, BCAN, RTN1, SNAP91, GABBR1&2, and" ; ns1:mentions . _:b418678914 rdf:type ns1:RelevantBibliographicResource . @prefix xsd: . _:b418678914 ns1:RelevantScore "83"^^xsd:nonNegativeInteger ; ns1:hasRelevantPaperId . _:b418678915 rdf:type ns1:RelevantBibliographicResource ; ns1:RelevantScore "62"^^xsd:nonNegativeInteger ; ns1:hasRelevantPaperId . _:b418678916 rdf:type ns1:RelevantBibliographicResource ; ns1:RelevantScore "55"^^xsd:nonNegativeInteger ; ns1:hasRelevantPaperId . _:b418678917 rdf:type ns1:RelevantBibliographicResource ; ns1:RelevantScore "42"^^xsd:nonNegativeInteger ; ns1:hasRelevantPaperId . _:b418678918 rdf:type ns1:RelevantBibliographicResource ; ns1:RelevantScore "26"^^xsd:nonNegativeInteger ; ns1:hasRelevantPaperId . _:b418678919 rdf:type ns1:RelevantBibliographicResource ; 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