Human inositol polyphosphate multikinase regulates transcript-selective nuclear mRNA export to preserve genome integrity
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Vihandha Wickramasinghe
PROVIDER: E-GEOD-49658 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Background: The incidence of human papillomavirus (HPV) associated oropharyngeal carcinomas has increased rapidly over the last thirty years. These tumours behave as a distinct biological entity when compared to classical smoking- and alcohol-related disease. To gain more information regarding the pathway through pre-malignancy in HPV positive/HPV negative oropharyngeal carcinoma (OSCC), we investigated genomewide expression profiles in histopathologically confirmed tumour samples with site-matched normal epithelial controls. Methods: Twenty-four patients with primary oropharyngeal squamous cell carcinoma (4 with stage III and 20 with stage IV disease) were included in this prospective clinical trial (UKCRN11945). The tumour tissues were each assessed by a histopathologist with HPV status and typing by p16INK4A, consensus PGMY PCR, type-specific HPV16 DNA & RNA PCR and DNA sequencing. Fresh tissue samples were subjected to whole transcriptome analysis using the Illumina Bead Array (~47,000 transcripts) and the results validated with quantitative Real Time-PCR (qRT-PCR). In a separate cohort of twelve OSCC patients, laser capture micro-dissection of formalin fixed paraffin embedded (FFPE) tissue allowed RNA extraction from regions of in situ malignant change (with matched normal and invasive SCC samples). Results: The majority of OSCC patients (28/36) displayed evidence of high risk HPV positivity. Predictable fold changes of RNA expression in HPV-associated disease included multiple transcripts within the p53 oncogenic pathway (e.g. CDKN2A/CCND1). Other candidate transcripts found to have altered levels of expression in this study have not previously been established in HPV16 associated oropharyngeal cancer. These were involved in cell differentiation, proliferation and invasion and demonstrated considerable overlap with expression analysis data in other oncogenic pathways (SFRP1/CRCT1/DLG2/SYCP2/CRNN). SYCP2 showed the highest consistent fold change from baseline in both fresh frozen and FFPE tissue (qRT-PCR fresh frozen tissue [P<0.04]; FFPE tissue pre-invasive [P<0.01]; FFPE tissue invasive [P<0.01]), and aberrant expression of this meiosis-specific protein may contribute to genetic instability during HPV-associated cancer development. Conclusion: Investigation of differentially expressed genes in HPV-positive tumours may reveal unique pathways that can explain their different natural history and biological properties. The data from this study reveal SYCP2 (amongst others) as a potential biomarker in HPV positive oropharyngeal carcinoma, and if corroborated on a larger scale, may facilitate the development of a non-invasive screening tool. Twenty four samples (12 matched invasive oropharyngeal carcinoma and normal epithelial controls).
2015-11-01 | E-GEOD-56142 | biostudies-arrayexpress
Project description:Analysis of factors upregulated in highly aggressive 410.4 and 4T1 tumour cells compared to the less aggressive 4T07 tumour cells at gene expression level. The question addressed in the present study was which secreted factors are differentially expressed by these cells and therefore could account for the observed difference in fibroblast activation in these tumours. Results provide important characterisation of the ex vivo expression profiles of highly aggressive vs. non-aggressive tumour cells. 4T07, 410.4 or 4T1 cells were inoculated into the mammary fat pad of Ub-GFP mice and total RNA from FACSorted GFP-negative; CD45-negative tumour cells was isolated.
2016-01-18 | E-GEOD-50471 | biostudies-arrayexpress
Project description:Comparison of gene expression in labouring and non-labouring myometrium. In this work, gene expression in 48 (22 labouring, 26 non-labouring) myometrial samples was measured using Illumina HT-12 v4.0 BeadChips. Biopsy samples of full thickness lower segment specimens of human myometrium were selected from the Edinburgh Reproductive Tissue Biobank (ERTBB, http://www.crh.ed.ac.uk/biobank/). All tissue samples were collected during Caesarean section from participant tissue donors with informed and written consent, according to the ethical approval and governance granted to the Edinburgh Reproductive Tissues BioBank by the West of Scotland Research Ethics Committee 4 (09/S0704/3). In order to maximise biological replicates on the array, all 22 labouring samples that fulfilled our inclusion criteria and that were stored in the ERTBB as of August 2012 were selected. In order to minimise inter-group variation in baseline characteristics, a second group of non-labouring samples (n=26) were selected by matching to labouring samples on maternal BMI, gestational age, parity and maternal age. We did not exclude smokers or women who had received medication to induce labour. We restricted the number of non-labouring samples to 26 so that all samples (n=48) could fit on three array chips. Forty-five of the samples had been transferred into RNAlater® (Life Technologies, Invitrogen, Carlsbad, CA, USA) immediately after collection and then stored at -80°C. Three labouring samples had not been transferred to RNAlater® before freezing but were also included in the array analysis in order to maximise the number of labouring samples. Total RNA was isolated using TRI Reagent® and the Qiagen RNeasy Lipid Tissue kit protocol (Qiagen, Valencia, CA, USA). The quantity and quality of RNA was assessed using a NanoDrop 1000 (Thermo Scientific, Wilmington, DE, USA). RNA quality was further assessed in the biotin-labelled samples by the Wellcome Trust Clinical Research Facility, Edinburgh using a Bioanalyzer 2100 (Agilent Technologies, Wilmington, DE, USA). To prepare samples for the microarray experiment, 450ng total RNA was amplified and biotin-labelled using the Illumina® TotalPrepTM RNA Amplification Kit (Ambion, Austin, TX, USA). Samples were split randomly over four Illumina HT-12 v4.0 BeadChips to minimise any effect of inter-chip variability. One sample was used per well. The chips were imaged using a BeadArray Reader and raw data was obtained with Illumina BeadStudio software. Raw data were preprocessed using the Lumi package in R version 2.14.1. The data was subjected to Robust Multichip Average (RMA) background correction before quantile normalisation to remove non-biological systematic variation.
2015-01-01 | E-MTAB-3136 | biostudies-arrayexpress
Project description:STAC3 was identified as a nutritionally regulated gene from an Atlantic salmon subtractive hybridization library with highest expression in skeletal muscle. Salmon STAC3 mRNA was highly correlated with myogenin and myoD1a expression during differentiation of a salmon primary myogenic culture and was regulated by amino acid availability. In zebrafish embryos, STAC3 was initially expressed in myotomal adaxial cells and in fast muscle fibres post-segmentation. Morpholino knockdown resulted in defects in myofibrillar protein assembly, particularly in slow muscle fibres, and decreased levels of the hedgehog receptor patched. The function of STAC3 was further characterized in vitro using the mammalian C2C12 myogenic cell line. STAC3 mRNA expression increased during the differentiation of the C2C12 myogenic cell line. Knockdown of STAC3 by RNAi inhibited myotube formation, and microarray analysis revealed that transcripts involved in cell cycle, focal adhesion, cytoskeleton and the pro-myogenic factors IGFBP-5 and IGF2 were down regulated. RNAi-treated cells had suppressed AKT signalling and exogenous IGF2 was unable to rescue the phenotype, however, IGF/AKT signalling was not blocked. Overexpression of STAC3, which results in increased levels of IGFBP-5 mRNA, did not lead to increased differentiation. In synchronized cells, STAC3 mRNA was most abundant during the G1 phase of the cell cycle. RNAi-treated cells were smaller, had higher proliferation rates and decreased proportion of cells in G1 phase when compared to controls, suggesting a role in the G1 phase checkpoint. These results identify STAC3 as a new gene required for myogenic differentiation and myofibrillar protein assembly in vertebrates. We identified STAC3 as being essential for myogenic differentiation. The goal of the microarray analysis was to identify genes that were up- or down-regulated in C2C12 cells when STAC3 expression was inhibited by interfering RNA (RNAi). The microarray compares the C2C12 mouse myogenic cell line between control samples to samples treated with an interfering RNA directed at STAC3. The mouse C2C12 cell line was used at two time points: day 0, which was 24 hours after adding the RNAi, with cells growing in growth media (non-differentiating), and day 1, which was 48 hours after the interfering RNAi was added, and 24 hours after switching to differentiation media. RNAi-treated cells were transfected with an RNAi directed against STAC3, and control cells were transfected with a high-GC content control RNAi. Total RNA was extracted from control and RNAi-treated samples at two time points, at day 0 (24 h after treating with RNAi, while samples were still in growth media), and at day 1 (cells grown in differentiation media for 24h, 48 h after RNAi treatment). At each time point, STAC3 RNAi-treated cells were compared to controls. For the array comparison, at day 0, triplicate biological samples + one technical replicate were used for the controls, and four biological samples were used for the RNAi-treated cells. At day 1, four biological samples and one technical replicate were used for controls and RNAi-treated cells. Technical replicate identifiers are appended by _r.
2012-12-01 | E-GEOD-34474 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-01-28 | E-GEOD-43626 | biostudies-arrayexpress
Project description:Identification of cell-type specific enhancers is important for understanding the regulation of programs controlling cellular development and differentiation. Enhancers are typically marked by the co-transcriptional activator protein p300 or by groups of cell-expressed transcription factors. We hypothesized that a unique set of enhancers regulates gene expression in human erythroid cells, a highly specialized cell type evolved to provide adequate amounts of oxygen throughout the body. Using chromatin immunoprecipitation followed by massively parallel sequencing, genome-wide maps of candidate enhancers were constructed for p300 and four transcription factors, GATA1, NF-E2, KLF1, and SCL, using primary human erythroid cells. These data were combined with gene expression analyses and candidate enhancers identified. Consistent with their predicted function as candidate enhancers, there was statistically significant enrichment of p300 and combinations of co-localizing erythroid transcription factors within 1-50 kb of the TSS of genes highly expressed in erythroid cells. Candidate enhancers were also enriched near genes with known erythroid cell function or erythroid cell phenotypes. Candidate enhancers exhibited only moderate conservation with mouse and minimal conservation with nonplacental vertebrates. Candidate enhancers were mapped to a data set of erythroid-associated, biologically relevant, SNPs from the GWAS catalog of the NHGRI. Fourteen candidate enhancers, representing 10 genetic loci, mapped to sites associated with biologically relevant erythroid traits. Fragments from these loci directed statistically significant expression in reporter gene assays. Identification of enhancers in human erythroid cells will allow a better understanding of erythroid cell development, differentiation, structure, and function, and provide insights into inherited and acquired hematologic disease. CD34+-selected stem and progenitor cells were expanded for three days in the absence of EPO, and total RNA was isolated from a portion of the cells. The cells were further cultured in the presence of EPO, and RNA was isolated after cells differentiated into R3/R4 nucleated erythroid cells. There were 3 replicates of CD34 cells and 9 replicates of R3/R4 erythroid cells.
2013-01-28 | E-GEOD-43624 | biostudies-arrayexpress
Project description:Our previous studies have revealed that treatment of pregnant rats with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, 1 M-NM-<g/kg) at gestational day (GD) 15 reduces the pituitary synthesis of luteinizing hormone (LH) during late fetal and early postnatal period, leading to imprinting of defects in sexual behaviors at adulthood. However, it remains obscure how the attenuation of pituitary LH links to sexual immaturity. To address this issue, we firstly performed a DNA microarray analysis to identify the gene(s) responsible for dioxin-induced sexual immaturity, using the pituitary and hypothalamus of male pups, at the age of postnatal day (PND)70, born from TCDD-treated dams. Among the reduced genes, we focused on gonadotropin-releasing hormone (GnRH) in the hypothalamus, because of its role in sexual behaviors suggested so far. The present study strongly suggests that maternal exposure to TCDD fixes the status of the lowered expression of GnRH in the offspring by reducing steroidogenesis at perinatal stage, and this is the mechanism for the imprinting of defects in sexual behaviors at adulthood. Total RNA was isolated from the pituitary and hypothalamus of PND70 male pups born from the dams treated with TCDD (1 M-NM-<g/kg) or vehicle at GD15, using an RNeasy Mini Kit (QIAGEN). To identify the gene(s) the altered expression of which is fixed and linked to defects in sexual behaviors, the profile of gene expression was analyzed using the Illumina RatRef-12 Expression BeadChip. This series includes two dataset; hypothalamic and pituitary samples (each case; N=3x2). The normalization applied each dataset.
2013-08-21 | E-GEOD-48100 | biostudies-arrayexpress
Project description:ERYTHROID CELL-TYPE SPECIFIC GENE EXPRESSION Post-translational histone modifications, acting alone or in a context-dependent manner, influence numerous cellular processes via their regulation of gene expression. Monomethylation of histone H3 lysine 27 (K27me1) is a poorly understood histone modification. Some reports describe depletion of K27Me1 at promoters and transcription start sites (TSS), implying its depletion at TSS is necessary for active transcription, while others have associated enrichment of H3K27me1 at TSS with increased levels of mRNA expression. Tissue- and gene-specific patterns of H3K27me1 enrichment and their correlation with gene expression were determined via chromatin immunoprecipitation on chip microarray (ChIP-chip) and human mRNA expression array analyses. Results from erythroid cells were compared to those in neural and muscle cells. H3K27me1 enrichment varied depending on levels of cell-type specific gene expression, with highest enrichment over transcriptionally active genes. Over individual genes, the highest levels of H3K27me1 enrichment were found over the gene bodies of highly expressed genes. In contrast to H3K4me3, which was highly enriched at the TSS of actively transcribing genes, H3K27me1 was selectively depleted at the TSS of actively transcribed genes. There was markedly decreased to no H3K27me1 enrichment in genes with low expression. At some locations, H3K27 monomethylation was also found to be associated with chromatin signatures of gene enhancers. The gene expression profiles of three replicates of 4 human cell lines were obtained using Illumina microarrays.
2011-12-06 | E-GEOD-32135 | biostudies-arrayexpress
Project description:TMEM88 is indispensable for heart development and acts in the pre-cardiac mesoderm to specify lineage commitment of the cardiovascular progenitor cell through inhibition of Wnt signaling. 2 different lentiviruses expression shRNA targeting different domains of the TMEM88 locus were transduced into undifferentiated hES cells. Cells were puromycin selected then differentiated along the cardiac lineage. Total RNA was taken at day 5 of differentiation when the cardiovascular progenitor cell arises. 1 sample for each shRNA and 2 samples for control shRNA were analyzed by array
2013-10-21 | E-GEOD-43805 | biostudies-arrayexpress
Project description:The DALIA-1 trial was designed to evaluate the safety and immunogenicity of a DC-based vaccine generated by culturing blood monocytes with GM-CSF and IFN-a. DCs were pulsed for 24 hrs with the ANRS LIPO5 peptide pool and activated for the last 6 hrs with LPS. In total, 19 asymptomatic HAART-treated patients were included in the study. Microarray samples were collected in both the treatment phase and follow-up phase of the study. Whole blood RNA samples were collected at two time points prior to the first vaccination (Weeks -8 and -4) and served as a pre-vaccination baseline. Additional whole blood RNA samples were collected at the time of vaccination (Weeks 0, 4, 8, 12) and post-vaccination at weeks 16, 22, and 24. At week 24, an analytical treatment interruption (ATI) was initiated during which HAART was suspended. During this post-ATI follow-up phase, whole blood RNA samples were collected at weeks 25, 26, 27, 28, 32, 36, 40, , 44, and 48). Additionally, at weeks -4, 16, and 48 patients were apheresed. 18 samples are constituents of both the pre-ATI and post-ATI datasets, which were normalized separately. The normalised data underwent the following preprocessing: First a normal-exponential convolution model was applied (Xie et al, Bioinformatics, 2009; Shi et al, Nucleid Acids Research, 2010) to correct for the background noise. An offset of 16 (default value) was then added to the data (to improve precision and avoid a compression of the fold changes) before a quantile-quantile normalization was performed. Finally, data were log2 transformed. Only probes whose pval-detection (provided by Illumina Genome-Studio software) was below 0.01 in at least one sample were kept further on. At last, the ComBat method (Johnson et al, Biostatistics, 2007) was applied to those data in order to correct for batch effects (namely a small hybridization chamber effect, that was identified through Principal Variance Component Analysis - Li et al, chap. 12, Batch Effects and Noise in Microarray Experiments: Sources and Solutions, Wiley, 2009).
2015-05-22 | E-GEOD-46734 | biostudies-arrayexpress