EXPRESSION OF VAV1 IN GLIOBLASTOMA MULTIFORME
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE24072 | GEO | 2010/09/30
SECONDARY ACCESSION(S): PRJNA130241
REPOSITORIES: GEO
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Project description:Background: Even though much progress has been made in the understanding of the molecular nature of glioma, the survival rates of patients affected of this tumour have not changed significantly during these years. Thus, a deeper understanding of this malignancy is still needed in order to predict its outcome and improve patient treatment. Here, we report that VAV1, a GDP/GTP exchange factor for Rho/Rac proteins with oncogenic potential that is involved in the regulation of cytoskeletal dynamics and cell migration. Methodology/Principal Findings: VAV1 is overexpressed in 32 patients diagnosed with high-grade glioma. Such overexpression is linked to the parallel upregulation of a number of genes coding for proteins also involved in cell invasion- and migration-related processes. Unexpectedly, immunohistochemical experiments revealed that VAV1 is not expressed in glioma cells. Instead, VAV1 is found in non-tumoral astrocyte-like cells that are located either peritumoraly or perivascularly, suggesting that its expression is linked to synergistic signalling cross-talk between cancer and infiltrating cells. Conclusions/Significance: Interestingly, we show that the pattern of expression of VAV1 is a good prognostic factor to unveil populations of high-grade glioma patients with different survival and progression free survival rates. 1. Oligonucleotide microarray analyses Total RNAs were extracted using the Triazol reagent (Life Technologies, Gaithersburg, MD, USA) and purified with the RNeasy Mini kit (Qiagen, Valencia, CA, USA). The integrity of RNA samples obtained was assessed using the 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA). Double-stranded cDNAs and biotinylated cRNAs were synthesized using a T7-polyT primer and the BioArray RNA labelling Kit (Enzo Farningdale, NY, USA), respectively. Labelled RNAs were then fragmented and hybridised to HU-133A oligonucleotide arrays (Affymetrix, Santa Clara, CA, USA) according to standard Affymetrix protocols. After hybridization and washes, arrays were scanned using the Gene Array Scanner (Affymetrix), and the expression value for each probe set calculated using the MAS 5.0 software (Affymetrix). All examples had a scaling factor lower than threefold and 3’/5’ of GAPDH probe set <2.5. Gene levels were transformed to base two logarithms. A median normalization approach was applied. Only genes with al least three “present” calls across all samples were selected. All these steps were done at the Genomics and Proteomics Unit of the “Centro de Investigación del Cáncer, Salamanca”. 2. Microarray data analyses To visualize clusters of genes with similar expression patterns, we used a hierarchical clustering method (Cluster and TreeView software) based on the average-linkage method with the centred correlation metric [26]. A multidimensional scaling method (BRB Arrays Tools version 3.0) was also utilized by using Euclidean distance criteria [27]. Supervised learning was used to identify genes with statistically significant changes in expression among different classes by using the Significant Analysis of Microarrays (SAM) algorithm [28]. All data were permuted over 100 cycles by using the two-class (unpaired) and multi-class response format. Significant genes were selected based on the lowest false discovery ratio (between 0.6 and 0.9). In addition, nonparametric tests such as Wilcoxon rank sum test and Kruskal-Wallis test to compare more than two unpaired group were also used (SPSS 18, SPSS Inc). 3. Functional annotation of microarray data Probe sets showing significant expression change were functionally annotated and grouped according to biological function criteria using GeneOntology biological process descriptions. The functional analysis to identify the most relevant biological mechanism, pathways and functional categories in gene dada sets was generated using the Ingenuity Pathway software (Ingenuity Systems, Mountain View, CA, USA) available in the web (www.ingenuity.com) [29]. A functional network was considered significant when it fulfilled the following criteria: i) to have a minimal score of 15; ii) to have a minimum of 20 direct functional interactions among the network members. 4. Quantitative reverse transcription-PCR Total RNA was quantified in a RNA 6000 Nano Chip (Agilent Technologies) and quantitative PCR performed using the QuantiTect SYBR Green RT–PCR kit (Qiagen). To quantify VAV1 mRNA levels, we used two different sets of probes: PAIR A (5’-AAC AAC GGG AGG TTC ACC CT-3’ and 5’-GGT CCC TCA TGG CAT CCA-3’) and PAIR B (5’-AGC CAT TGG ACC CTT TCT ACG-3’ and 5’-GCC ATG GAC ATA GGG CTT CA-3’). Amplifications were performed using the iCycler apparatus (Bio-Rad Laboratories, California, USA). Analyses of data were done using the iCycler iQ Optical System Software, version 3.0a (Bio-Rad Laboratories). Primers to GAPDH were used as intersample normalizing controls. Variations in expression of VAV1 mRNA were represented as the mean value of the fold change respect the VAV1 expression levels detected in sample #19209 with both pairs of oligonucleotide primers. 5. Immunohistochemical analyses The VAV1 antibody was generated in rabbits using a synthetic peptide and purified by affinity chromatography in Bustelo’s laboratory. This antibody recognizes VAV1 proteins from humans and mice but it does not recognize other VAV family members (unpublished data). For immunostaining, tissue sections were washed thrice with Xylene and once with 100% ethanol, rehydrated by sequential changes in 80%, 70%, and 50% ethanol and a final incubation in phosphate-buffered saline (PBS). Each rehydrating step involved 3 min incubations with the indicated solutions. Endogenous peroxidases were quenched by the addition of a 3% H2O2 solution in methanol for 30 min at room temperature (RT). Tissue sections were subsequently washed twice with PBS. Antigen retrieval was performed by incubation in 1 mM EDTA for 30 min at 37°C. The slides were washed twice in PBS and blocked in blocking buffer (Zymed, CA, USA) for 30 min at RT. Specimens were then incubated with the primary antibody (1:250 dilution) in blocking buffer. After an 1 hr incubation at 37°C, slides were washed three times in PBS, incubated with a biotinylated secondary antibody for 30 min at 37°C, washed thrice in PBS, incubated with horseradish peroxidase-streptavidin for 30 min at 37°C, washed three times in PBS, and developed using the AEC substrate (Zymed). Slides were then washed twice in water, counterstained with hematoxilin (Zymed), washed again in water, and mounted with GVA (Zymed). Samples were analyzed by light microscopy and images acquired suing an Axiophot imaging system (Zeiss, Munich, Germany). 6. Fluorescence in situ hybridization analyses FISH experiments were carried out in 40 cases of glioblastoma multiforme (grade IV) positive for VAV1 expression. For this purpose, we performed dual-colour FISH analyses with locus-specific probes for centromere 7 (Abbott Molecualr, Des Plaines) exactly as previously described.[30] Polysomies were defined when more than 10% of the nuclei surveyed contained three or more CEP signals (chromosome-specific FISH probes that hybridize to highly repetitive human satellite DNA sequences, usually located near centromeres). 7. Immunohistochemistry and fluorescence in situ hybridization (FISH) in paraffin-embedded tumours Four um sections were cut from routinely processed paraffin blocks and mounted onto glass slides with a charged coating. Sections were dewaxed in Xylene and then rehydrated using increasing concentrations of alcohol before being rinsed briefly in water. Slides were heated 2 min in 1 mM EDTA (pH 9.0) in a microwavable pressure cooker. After antigen retrieval, slides were incubated 1 h at RT in a moist chamber with a primary antibody diluted in PBS supplemented with 10% foetal calf serum. Slides were incubated for 1 h with fluorochrome-conjugated antibodies to the appropriate IgG isotypes in a moist chamber in the dark. Finally, slides were washed thrice in PBS containing 0.5% Tween 20 three before FISH analysis. 8. Degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) analyses After the staining of tissue sections with VAV1 antibodies (see above), the regions of the tumour were identified, microdissected, and collected using the PALM® microscope system (P.A.L.M. Microlaser Technologies, Munich, Germany). The genomic DNA was extracted as indicated by Isola et al [31] with modifications to small DNA amounts. Those included the resuspension of the microdissected sections in extraction buffer followed by a digestion with proteinase K (0.6 mg/ml). All samples were resuspended in 10 ul of 10 mM Tris-HCl (pH 7.4) and 0.1 mM EDTA. DOP-PCR amplification was performed in two steps. For the first, low-stringency step, 1 ul of sample was added to 4 ul of buffer A (2.5 ul of 600 uM dNTPs (Roche, Pleasanton, CA), 0.5 ul of 10 uM DOP primer 5’-CCGACTCGAGNNNNNNNATGTGG-3’, where N= A, C, G, or T) [32] and 1 ul of 5x Sequenase Reaction Buffer (Amersham, Cleveland, OH). Reactions were performed using 5 cycles of 30ºC for 5 min, 37ºC for 2 min, and 96ºC for 2 min, adding 0.65 units of Sequenase in each 30ºC step. The first phase product was then subjected to the second step usin
2010-09-30 | E-GEOD-24072 | biostudies-arrayexpress
Project description:Analysis of differential gene expression profiles in VAV1-/- versus VAV+/+ BM-macrophages , respectively. A distinct expression profile in VAV1-/- versus VAV1+/+ (wild-type) BM-macrophages allows to resolve molecular mechanisms. Total RNA was obtained froms BM-macrophages of VAV1+/+ and VAV1-/- mice
2013-03-08 | E-GEOD-36123 | biostudies-arrayexpress
Project description:Analysis of differential gene expression profiles in VAV1-/- versus VAV+/+ BM-macrophages , respectively. A distinct expression profile in VAV1-/- versus VAV1+/+ (wild-type) BM-macrophages allows to resolve molecular mechanisms.
2013-03-08 | GSE36123 | GEO
Project description:Mutations in VAV1, a multifunctional signaling protein essential for T lymphocytes, have been recently found in peripheral T cell lymphoma (PTCL) and other tumors. However, their pathobiological significance remains unsettled. Here, we show that these mutations belong to several subclasses according to the spectra of VAV1 signaling branches deregulated by them. These mutations target both known and new regulatory hotspots as well as transitional activation states of the protein. The most frequent VAV1 mutant subclass drives PTCL formation in mice by exacerbating normal VAV1- dependent signaling responses in follicular helper T cells.
2021-09-01 | GSE165006 | GEO
Project description:Glioblastoma multiforme (GBM) is the most common form of malignant glioma and is characterized by marked genetic instability, extensive intra-tumoral histopathological variability, and unpredictable variation in its clinical behavior. We investigated global gene expression in surgical samples of primary brain tumors. Gene expression profiling revealed large differences between normal brain samples and tumor tissues and between GBMs and lower grade oligodendroglial tumors. Extensive differences in gene expression were found among GBMs, particularly in genes involved in angiogenesis, immune cell infiltration, and extracellular matrix re-modeling. Significantly, we found that the global gene expression patterns in paired specimens from the same GBM invariably were more closely related to each other than to any other tumor, even when the paired specimens had strikingly divergent histologies. Survival analyses revealed a set of approximately 70 genes that were more highly expressed in rapidly progressing tumors and which stratified GBMs into two groups that differed by more than four-fold in median duration of survival. We further investigated one gene from the group, FABP7, and confirmed its association with survival in two unrelated cohorts totaling 105 patients. Expression of FABP7 enhanced the motility of glioma-derived cells in vitro. Our analyses thus provide a series of prognostic markers and suggest that their expression may enhance the invasive potential of tumor cells. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Using regression correlation
2006-01-18 | E-GEOD-4058 | biostudies-arrayexpress
Project description:VAV1 mutations have been recently found in peripheral T cell lymphoma and non-small cell lung cancer. To understand their pathogenic potential, we generated a gene-edited mouse model that expresses a Vav1 mutant protein that recapitulates the signaling alterations present the VAV1 mutant subclass most frequently found in tumors. We could not detect any overt tumorigenic process in those mice. However, the concurrent elimination of the Trp53 tumor suppressor gene in them drives T cell lymphomagenesis. This process represents an exacerbation of the normal functions that wild-type Vav1 plays in follicular helper T cells. We also found that, in combination with an oncogenic Kras mutation, the Vav1 mutant version favors progression of non-small cell lung cancer. These data indicate that VAV1 mutations play critical, although highly cell typespecific roles in tumorigenesis. They also indicate that such functions are contingent on the mutational landscape of the tumors involved.
2022-10-12 | GSE189221 | GEO
Project description:Glioblastoma multiforme (GBM) is a grade IV human glioma and is the most malignant primary central nervous system tumor in adults, accounting for around 15% of intracranial neoplasms and 40–50% of all primary malignant brain tumors. However, the median survival time of GBM patients is still less than 15 months, even after treatment with surgical resection, concurrent chemoradiotherapy, and adjuvant chemotherapy with temozolomide (TMZ). Telomere mainte-nance 2 (TELO2) mRNA is highly expressed in high-grade glioma patients, and its expression correlates with shorter survival outcomes. Hence, it is urgent to address the functional role of TELO2 in the tumorigenesis and TMZ treatment of GBM. In this study, we knocked down TELO2 mRNA in GBM8401 cells, a grade IV GBM, compared with TELO2 mRNA overexpression in hu-man embryonic glial SVG p12 cells and normal human astrocyte (NHA) cells. We first analyzed the effect of TELO2 on the Elsevier pathway and Hallmark gene sets in GBM8401, SVG p12, and NHA via an mRNA array analysis. Later, we further examined and analyzed the relationship between TELO2 with fibroblast growth factor receptor 3, cell cycle progression, epithelial–mesenchymal transient (EMT), reactive oxygen species (ROS), apoptosis, and telomerase activity. Our data showed that TELO2 is involved in several functions of GBM cells, including cell cycle progression, EMT, ROS, and apoptosis, telomerase activity. Finally, we examined the crosstalk between TELO2 and the responsiveness of TMZ or curcumin mediated through the TE-LO2-TTI1-TTI2 complex, the p53-dependent complex, the mitochondrial-related complex, and signaling pathways in GBM8401 cells. In summary, our work provides a new insight that TELO2 might modulate target proteins mediated through the complex of phosphatidylinositol 3‑kinase‑related kinases in its involvement in cell cycle progression, EMT, and drug response in GBM patients.
2023-06-14 | GSE231503 | GEO
Project description: Not available
| S-ECPF-GEOD-24072 | biostudies-other
Project description:In this study, we combined mouse genetics and quantitative proteomics to characterize in a comprehensive manner the VAV1 interactome. A line of knock-in mouse expressing endogenous VAV1 molecules with a genetic tag permitting affinity purification was generated and combined with affinity purification and mass spectrometry (AP-MS) to analyze the VAV1 signaling complex that assembles in primary CD4+ T cells over 300 s of activation. This allowed us to describe in a time-resolved manner the interactome of VAV1 in primary CD4+ T cells and to identify 44 previously unknown bindings partners of VAV1. The dataset contains mass spectrometry results from the analysis of AP-MS purifications (based on affinity purification on Streptactin beads of One-Strep-tagged proteins) starting from CD4+ T cells which were either non stimulated or stimulated with pervanadate for different time lengths. Control samples for each time point were prepared from wild-type mice. 8 different conditions were thus analyzed: - VAV1-OST transgenic mice, CD4+ T cells non stimulated (noted Vav_0) - VAV1-OST transgenic mice, CD4+ T cells stimulated 30s (noted Vav_30) - VAV1-OST transgenic mice, CD4+ T cells stimulated 120s (noted Vav_120) - VAV1-OST transgenic mice, CD4+ T cells stimulated 300s (noted Vav_300) - WT mice, CD4+ T cells non stimulated (noted WT_0) - WT mice, CD4+ T cells stimulated 30s (noted WT_30) - WT mice, CD4+ T cells stimulated 120s (noted WT_120) - WT mice, CD4+ T cells stimulated 300s (noted WT_300) Four biological replicates were prepared for these 8 different conditions (noted S1, S2, S3, S4), yielding 32 analyzed samples. Three technical nanoLC-MS runs were acquired for each sample (noted R1, R2, R3), except for some samples of the biological series S4 for which 2 technical nanoLC-MS runs were performed. This led to 91 nanoLC-MS raw files composing the dataset.
2018-06-26 | PXD004217 | Pride
Project description:Glioma represents a serious health burden in terms of morbidity and mortality. The prognostic significance of the lymphoid and myeloid infiltrates in glioma is not clearly determined. Moreover, the characterization of different leukocyte subsets in the tumor microenvironment relies mainly on immunohistochemistry observations, and data about their association with prognosis are contradictory. Here, we performed acomprehensive study of both the tumor-infiltrating and circulating immune compartments of patients with high-grade glioma. We identified prognostic tumor and peripheral immune signatures, which associate increased inflammation, immune infiltration and activation with shorter overall survival in high-grade glioma patients. Importantly, we confirmed our observations by flow cytometry analysis and validated the tumor-signature using the TCGA dataset. In addition, both tumor genotype and grade associated with the degree of glioma immune infiltration. Unlike in the majority of cancers, lymphocyte infiltration at the tumor site is anegative prognostic factor in glioma, suggesting the ambivalent pro-tumorigenic role of immune responses in glioma.
2021-11-16 | GSE188812 | GEO