Ethanol inhibits the proliferation of neural stem cells in the fetal, adolescent, and adult brain. The consequences are cognitive deficits associated with fetal alcohol spectrum disorder and alcohol use disorder. We tested the hypothesis that ethanol affects progression through cell cycle checkpoints by differentially modifying transcriptional processes. Monolayer cultures of NS-5 neural stem cells were treated for 48 hr with the mitogenic agent FGF2 or the anti-mitogenic TGF1 in the absence or presence of ethanol. Cell cycle elongation was induced by a global down-regulation of genes involved in cell cycle progression, including the cyclin E system. Checkpoint regulation occurred downstream of p21 and Jun-oncogene signaling cascades. Thus, ethanol can affect cell cycle progression by altering transcript expression of strategic genes downstream of the G1/S checkpoint.
Ethanol-induced methylation of cell cycle genes in neural stem cells.
Specimen part, TreatmentView Samples
The synthetic cost of cycling genes is higher than other genes, and the cyclic expression pattern of these genes is a strategy for reducing the overall energy usage of cells Overall design: Samples for both conditions were taken over two metabolic cycles. For the fast cycling condition one sample was taken every 13 minutes for ~4.25 hours. For the slow cycling condition, samples were taken every 36 minutes for ~14.5 hours. Cycling genes were identified using JTK_Cycle (Hughes et al. (2010) Journal of Biological Rhythms).
Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale.
Cell line, SubjectView Samples
Genome-wide association studies have identified a locus within the second intron of the FGFR2 gene that is consistently the most strongly associated with estrogen receptor-poisive breast cancer risk. However, we know little about the mechanisms by which the FGFR2 locus mediates risk or the pathways in which multiple risk loci may combine to cause disease. Previously, a systems biology approach was adopted to elucidate the regulatory networks operating in MCF-7 breast cancer cells in order to examine the role of FGFR2 in mediating risk. Here, the same approach has been employed using a number of different estrogen receptor-positive breast cancer cell lines in order to see if the previous findings are reproducible and consistent in estrogen receptor-positive disease.
Regulators of genetic risk of breast cancer identified by integrative network analysis.
Specimen part, Cell line, TreatmentView Samples
HCT116 cells were transfected with two different siRNA's targeting either DDX5, an siRNA targeting EBNA1, or no siRNA (mock). The siRNA targeting EBNA1 is used as a negative control since HCT116 cells do not have the EBNA1 gene. RNA was obtained from cultures at 24hrs post-siRNA transfection using the Qiagen RNeasy Minikit (cat. # 74104) with on-column DNase digestion performed as per the manufacturer's protocol. The RNA samples were isolated at 24hrs post-siRNA transfection since this timepoint precedes an impaired G1-to-S phase cell cycle progression phenotype that is evident at 48hrs post-siRNA transfection and so may reveal gene expression changes occuring before this effect on cell cycle. RNA samples were submitted to the Cold Spring Harbor Laboratory Microarray Faciity where cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip Human Gene 1.0 ST microarrays. Data from the arrays were processed using the RMA method with an up-to-data probe set definition (Biostatistics 4:249-264 and Nucleic Acids Research 33(20):e175. Gene set analysis was performed using generally applicable gene set enrichment (BMC Bioinformatics 10:161). The most differentially regulated gene ontology groups were selected with FDR q-value < 0.1.
DDX5 regulates DNA replication and is required for cell proliferation in a subset of breast cancer cells.
Cell lineView Samples
Non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide. The oxygen-sensitive Hypoxia Inducible Factor (HIF) transcriptional regulators HIF-1 and HIF-2 are overexpressed in many human NSCLCs, and constitutive HIF-2 activity can promote murine lung tumor progression, suggesting that HIF proteins may be effective NSCLC therapeutic targets. To investigate the consequences of inhibiting HIF activity in lung cancers, we deleted Hif-1 or Hif-2 in an established KrasG12D-driven murine NSCLC model. Deletion of Hif-1 had no obvious effect on tumor growth, whereas Hif-2 deletion resulted in an unexpected increase in tumor burden that correlated with reduced expression of the candidate tumor suppressor gene Scgb3a1 (HIN-1).
HIF-2alpha deletion promotes Kras-driven lung tumor development.
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Tissue samples were collected from patients diagnosed with HNSCC (oropharynx, hypopharynx, larynx). Samples were taken from the tumor site (tumor samples) and from a site distant to the tumor (normal samples) prior to therapy.
Prognostic biomarkers for HNSCC using quantitative real-time PCR and microarray analysis: β-tubulin isotypes and the p53 interactome.
Age, Specimen part, SubjectView Samples
We identified 4,356 genes with expression differences associated with a high-fat diet, with 184 genes exhibiting a sex-by-diet interaction. Dietary fat dysregulated several pathways, such as cytokine-cytokine receptor interaction, chemokine signaling, and oxidative phosphorylation. Grant: Funding source: American Heart Association Grant number: 16PRE26420105 Title: The effect of maternal over-nutrition on obesity, epigenetics, and gene expression Awarded to Madeline Keleher Overall design: We performed RNA-seq in 21 total libraries, each with two mice of the same sex and diet pooled together (There were 6 low-fat-fed female libraries, 5 libraries of high-fat-fed females, 5 libraries of low-fat-fed males, and 5 libraries of high-fat-fed males). A 1x50 single read sequencing run was done on an Illumina HiSeq 2500 machine (Illumina Inc.)
A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice.
Sex, Specimen part, Cell line, SubjectView Samples
In the cancer stem cell model a cell hierarchy has been suggested as an explanation for intratumoral heterogeneity, and tumor formation is thought to be driven by this tumor cell subpopulation. The identification of cancer stem cells in osteosarcoma (OS) and the biological processes dysregulated in this cell subpopulation, also known as tumor-initiating cells (TICs), may provide new therapeutic targets. The goal of this study, therefore, was to identify and characterize the gene expression profiles of TICs isolated from human OS cell lines. We analyzed the self-renewal capacity of OS cell lines and primary OS tumors based upon their ability to form sphere-like structures (sarcospheres) under serum-starving conditions. TICs were identify from OS cell lines using the long-term label retention dye PKH26. OS TICs and the bulk of tumor cells were isolated and used to assess their ability to initiate tumor in NOD/SCID mice. Gene expression profiles of OS TICs were obtained from fresh orthotopic tumor samples. We observed that increased sarcosphere efficiency correlated with an enhanced tumorigenic potential in OS. PKH26High cells were shown to constitute OS TICs based upon their capacity to form more sarcospheres, as well as to generate both primary bone tumors and lung metastases efficiently in NOD/SCID mice. Genomic profiling of OS TICs revealed that both bone development and cell migration processes were dysregulated in this tumor cell subpopulation. PKH26 labeling represents a valuable tool to identify OS TICs and gene expression analysis of this tumor cell compartment evidences potential therapeutic targets.
Identification and gene expression profiling of tumor-initiating cells isolated from human osteosarcoma cell lines in an orthotopic mouse model.
Specimen partView Samples
Recent studies suggest that PDEF is required for secretory cell differentiation in several epithelial tissues. To investigate PDEF in the mammary gland, we examined the effect of this transcription factor on gene expression using microarray based profiling of MCF-10A cells. These cells are non-transformed mammary epithelial cells that express protein and gene expression programs of basal epithelial cells and undetectable levels of endogenous PDEF. Bioinformatics analysis of the genes induced or repressed by PDEF overexpression in MCF10A cells revealed a striking effect on expression of luminal and myoepithelial cell markers.
PDEF promotes luminal differentiation and acts as a survival factor for ER-positive breast cancer cells.
Cell line, TreatmentView Samples