Down-regulation of the IKKb expression in glioma-infiltrating microglia/macrophages may results in defective inflammatory/immune gene responses in glioblastomas
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ABSTRACT: Samples of resected tumor from patients with low- and high-grade gliomas
Project description:Paired samples of resected tumor from glioblastoma patients: Pre and post Avastin-treatment samples for each patient in the cohort.
Project description:Glioblastoma (GBM) is the most frequent and most aggressive form of diffuse glioma. The prognosis is very poor, with a median overall survival of 15 months after maximum safe resection and radiochemotherapy.GBM is one of the most genetically unstable cancers. It is characterized by numerous chromosome (chr) copy number alterations (CNA), such as chr 7 gain, chr 9p loss, and chr 10 loss, along with CDKN2A homozygous deletion (chr 9p21) and EGFR amplification (chr 7p11).Chromosome instability (CIN) may be the cause or the consequence of GBM development. In high-grade diffuse gliomas (HGG), CIN may initiate tumorigenesis. To identify recurrent genomic abnormalities in IDH WT glioblastomas, SNP arrays (Illumina 850K CytoSNP) were analyzed for 123 IDH WT GBM cases.
Project description:Large lymphocytic leukemia (LGL) is a chronic clonal lymphoproliferative disorder, characterized by expansion of cytotoxic CD8+ T-cells or NK-cells. We compared gene expression of 3 LGL leukemia patients with STAT3 mutation (Patients 1, 2, and 3), 3 LGL leukemia patients with STAT5b mutation (Patients 4, 5, and 6), and 2 LGL leukemia patients without STAT3/STAT5b mutation (Patients 7 and 8) with CD8 and NK-cell samples from healthy controls to assess different gene expression patterns between samples.
Project description:LGL leukemia is chronic clonal lymphoproliferative disorder, characterized by expansion of cytotoxic CD8+ T-cells or NK-cells. We compared gene expression of 2 LGL leukemia patients with STAT3 mutation (Patients 11 and 12) and 2 LGL leukemia patients without STAT3/STAT5b mutation (Patients 9 and 10) with CD8 and CD4 samples from healthy controls to assess different gene expression patterns between samples.
Project description:Glioblastoma (GBM) is an aggressive malignancy associated with profound host immunosuppression. Microglia and macrophages infiltrating GBM acquire the pro-tumorigenic, M2 phenotype and support tumor invasion, proliferation, survival, angiogenesis and block immune responses both locally and systematically. Mechanisms responsible for immunological deficits in GBM patients are poorly understood. We analyzed immune/inflammatory gene expression in five datasets of low and high grade gliomas, and performed Gene Ontology and signaling pathway analyses to identify defective transcriptional responses. The expression of many immune/inflammatory response and TLR signaling pathway genes was reduced in high grade gliomas compared to low grade gliomas. In particular, we found the reduced expression of the IKBKB, a gene coding for IKKβ, which phosphorylates IκB proteins and represents a convergence point for most signal transduction pathways leading to NFκB activation. The reduced IKBKB expression and IKKβ levels in GBM tissues were demonstrated by qPCR, Western blotting and immunohistochemistry. The IKKβ expression was down-regulated in microglia/macrophages infiltrating glioblastoma. NFκB activation, prominent in microglia/macrophages infiltrating low grade gliomas, was reduced in microglia/macrophages in glioblastoma tissues. Down-regulation of IKBKB expression and NFκB signaling in microglia/macrophages infiltrating glioblastoma correlates with defective expression of immune/inflammatory genes and M2 polarization that may result in the global impairment of anti-tumor immune responses in glioblastoma.
Project description:Tumorigenesis is characterised by changes in transcriptional regulation and the androgen receptor (AR) has been identified as a key driver in prostate cancer. In this study, we show that the hexosamine biosynthetic pathway (HBP) genes are overexpressed in clinical prostate cancer and androgen-regulated in cell-lines. HBP senses metabolic status of the cell and produces an essential substrate for O-GlcNAc transferase (OGT), which regulates target proteins via glycosylation. Using immunohistochemistry, we found that OGT is up-regulated in the protein level in prostate cancer (n=1987) and its expression correlates with high Gleason Score, pT and pN stages and biochemical recurrence (for all, p<0.0001). Both a small molecule inhibitor and siRNAs targeting OGT decreased prostate cancer cell growth. Microarray profiling revealed that the principal effects of the OGT inhibitor in prostate cancer cells are on cell cycle progression and DNA replication. We identified MYC as a candidate upstream regulator of these genes and found that OGT inhibitor caused a dose-dependent loss of c-MYC protein but not mRNA in cell lines. Finally, we observed a statistically significant co-expression between c-MYC and OGT in human prostate cancer samples (n=1306, p=0.0012). Total RNA was extracted and experiment has three biological replicates for each condition, conditions are: 12 hours ST045849, 24 hours ST045849, 12 hours vehicle, 24 hours vehicle, 12 hours siOGT, 24 hours siOGT, 12 hours scrambled, 24 hours scrambled
Project description:A hESC MESP1-MCHERRY reporter line was used to isolate and study the molecular character of MESP1 expressing pre-cardiac progenitors, derived from hESC. MESP1 is a key-transcription factor for pre-cardiac mesoderm and is marking the progenitor for almost all cells of the heart. This reporter line was used to study cardiac differentiation and the derivation of early cardiac progenitors in vitro. hESCs were differentiated towards the cardiac lineage, expressing MESP1-mCherry at day 3 of differentiation. Total RNA obtained from isolated MESP1-mCherry expressing progenitors was compared to that of non-MESP1-expressing progenitors and undifferentiated hESCs in order to characterize MESP1-specific transcription factors and proteins.
Project description:Prostate cancer is the commonest male cancer in Europe and the USA. The androgen receptor is a key transcription factor contributing to the development of all stages of the disease. In addition, other transcription factors have been associated with poor prognosis in prostate cancer, amongst which c-Myc is a well-established oncogene in many other cancers. We have previously reported that a role for the androgen receptor in prostate cancer is to promote glycolysis and anabolic metabolism. Many of these metabolic pathways are also c-Myc-regulated in other cancers. In this study we report that de novo purine biosynthesis is a c-Myc-dependent pathway in prostate cancer cells as determined by commensurate changes in the levels of enzymes in the pathway in response to siRNA knockdown of c-Myc and inducible overexpression of c-Myc. In addition c-Myc is recruited to the promoters of genes in the pathway as determined by chromatin immunoprecipitation. Using immunohistochemistry and real-time transcript detection we show that two enzymes (PAICS and IMPDH2) within the pathway are overexpressed in prostate cancers. An inhibitor of IMPDH2 reduces cell proliferation and significantly reduces the levels of guanosine triphosphate within treated cells. This imposes nucleolar stress on cells as determined by significant reductions in the levels of guanine nucleotide binding protein-like 3 (GNL3). In addition the levels of c-Myc, p53 and the androgen receptor are affected and the expression of tumour suppressive microRNA-34b is increased. Combining the IMPDH2 inhibitor with anti-androgens results in a combinatorial inhibition of cell proliferation. In conclusion we propose using enzymes within the de novo purine biosynthesis as cancer biomarkers and applying drugs to alter the flux through this pathway may represent an effective means of stratifying patients for therapy and sensitising some to AR-targeted therapies. Total RNA of three biological replicates for each condition was extracted using the RNeasy kit (Qiagen), conditions are: 5 h vehicle, 5 h Doxycycline, 12 h vehicle, 12 h Doxycyline
Project description:Microglia isolated from glioma patients gain anti-tumor activities upon poly (I:C) stimulation. Expression profiles of human tumor-infiltrating microglia/macrophages before (untreated) and after treatment with poly (I:C) for 48h (induced). Tumor-infiltrating microglia/macrophages were isolated from freshly excised brain tumors
Project description:The purpose of our study was to characterize methylomic status by comparing the zone of fetal membranes (site of rupture (ZAM) and away from the site (ZIM)) and the tissue layer (amnion and choriodecidua). Nine fetal membranes were collected by cesarean section at term before labor. . After classifying genes in specific biological processes, we highlight particular patterns like inflammation.