Additional file 1: of Serum long noncoding RNA HOTAIR as a novel diagnostic and prognostic biomarker in glioblastoma multiforme

Supplementary materials and methods. (DOCX 109 kb

Additional file 2: of Serum long noncoding RNA HOTAIR as a novel diagnostic and prognostic biomarker in glioblastoma multiforme

Figure S1. HOTAIR expression detected in our biomarker assay is derived mostly from circulating RNA, not DNA. 3 GBM serum samples were selected at random and the relative HOTAIR expression in GBM serum with and without reverse transcription (RT)-PCR was determined. The HOTAIR RNA was reverse-transcribed into HOTAIR cDNA and qPCR was performed. The circulating HOTAIR DNA in the serum was detected by qPCR without RT. The considerable difference between HOTAIR expression with and without RT demonstrates that the HOTAIR we are detecting in our qRT-PCR reactions is derived from RNA and not DNA. (PDF 1003 kb

Additional file 3: of Serum long noncoding RNA HOTAIR as a novel diagnostic and prognostic biomarker in glioblastoma multiforme

Figure S2. A longitudinal study on a single GBM patient was carried out in order to monitor the changes in serum HOTAIR expression over time. 3 different time points were included in this study: pre-op (the blood was drawn right before the surgery started), post-op (at least 24 h after surgery) and during the 2 week follow-up (F/U) with the neurosurgeon. We show that the level of HOTAIR decreases after surgery and at the follow-up visit. (PDF 430 kb

Correlation networks identified that intersect epigenetic pathways/signaling pathways with patient specific DE genes.

<p>Connections were calculated for gene-gene pairs emanating from epigenetic pathways or genes in the Notch, SHH, or WNT pathways and genes that were Differentially Expressed in each patient.</p

Correlation networks created by using the top gene pairs for each patient.

<p>The number of connections we identified were compared to those previously described in the literature (red). Yellow indicates connections, which were identified in protein-protein interaction databases.</p

Gene Networks created by Pairs with high PCC (greater than 0.7) and high hypergeometric p-value yield less experimentally verified interactions.

<p>The number of connections identified was calculated for gene pairs with high PCC and high hypergeometric p-values. These connections were then compared to those identified in the literature. Note that few connections were found to be experimentally validated.</p

Additional file 3: of Curcumin decreases malignant characteristics of glioblastoma stem cells via induction of reactive oxygen species

Figure S3. N-acetylcysteine (NAC) rescues curcumin-induced p-STAT3 (Tyr705) activation in additional GBM stem cell lines. Expression of p-STAT3 (Tyr705) and STAT3 was assessed in non-treated (NT), 5 mM NAC treated, 25 μM curcumin treated, and pretreated 5 mM NAC followed by 25 μM curcumin treated GSCs after 8 h. Alpha-tubulin was used as a loading control. (TIFF 345 kb

Additional file 2: of Curcumin decreases malignant characteristics of glioblastoma stem cells via induction of reactive oxygen species

Figure S2. The effects of curcumin on MAPKs in additional GBM stem cell lines. Expression of p-jun, jun, p-p38, p38, p-ERK and ERK were assessed by western blot analysis in non-treated (NT) GSCs and 8 h after 25 μM of curcumin. Alpha-tubulin was used as a loading control for all experiments. (TIFF 562 kb

Pipeline for identifying patient-specific gene association in GBM.

<p>Our first step in our pipeline is to identify Differentially Expressed (DE) genes that are represented in 3 out of 4 algorithms. Next, we filter this DE gene list for those genes that overlapped with DE genes in the TCGA GBM Database. We then calculate the Correlation Coefficient and a hypergeometric p-value for every gene pair. Finally, by selecting the gene pairs with the highest correlation values we create a patient specific gene correlation network, which can be experimentally verified. As a starting point for our experiments, we can use the sub-networks in which, already verified connections exist in the literature.</p

Additional file 1: of Curcumin decreases malignant characteristics of glioblastoma stem cells via induction of reactive oxygen species

Figure S1. No primary controls for stem cell immunofluorescence shown in Fig. 1a. For control staining, antibody diluent without primary antibody was used, followed by the secondary antibody. Cells were counterstained with DAPI to identify nucleus. No stem cell marker fluorescence was observed in control cells. Scale bar: 100 μm. (TIFF 1896 kb