Project description:Taking the advantage that B16F10 cells retain the wild-type p53, we introduced the p53 partner into these cells, the p19Arf. Also, in order to induce a immune stimulation in experiments *in vivo*, we introduced the interferon-beta cDNA. This combination induced several benefits when compared to the use of these factors alone, as seen by propidium iodide staining, tunel staining, several gene expression analysis, tumor growth, mice survival, among others. Because of this, we had the interest to study the effects of the combination of p19Arf plus interferon-beta upon gene regulation of B16F10 cells, compared to the effects of these transgenes alone. Previous works from our group that show several benefits of p19Arf plus interferon-beta combination upon B16F10 cells are described in Merkel et al (2010) doi: 10.1186/1471-2407-10-316, Merkel et al (2013) doi:10.1038/cgt.2013.23 and Medrano et al (2016) doi: 10.1007/s00262-016-1807-8 .
Project description:Fungal effectors play important roles in inciting disease development on host plants. We identified an effector (Secreted in Xylem4, SIX4) in an Arabidopsis infecting isolate (Fo5176) of the root-infecting fungal pathogen Fusarium oxysporum and demonstrated this effector is required for full virulence. To explore the role of Fo5176_SIX4 we use whole transcriptome profiling of root tissues from plants overexpressing this effector (35sSIX4) versus wild-type (Col-0) plants after F. oxysporum infection. Published in DOI:10.1007/978-3-319-42319-7_4. Belowground Defence Strategies in Plants.
Project description:Breast cancer risk is influenced by parity in an age-dependant manner, however human tissue remodelling induced by pregnancy and lactation is not well understood. In most cases, it is difficult to acquire human breast tissue during these key stages of development. Here, we present an approach to overcome this using single-cell RNA sequencing to examine viable primary mammary epithelial cells isolated from human milk (n=1, LMC) compared to resting, non-lactating human breast tissue (n=1, NMC, ran over 3 lanes of a 10x Genomics chip). We identified all documented mammary subpopulations within our breast tissue samples and found that milk contains distinct secretory luminal cells together with myeloid and lymphocytic hematopoietic lineage cells. Comparing the luminal transcriptional profiles of cells isolated from the resting and lactating state identified differences in mammary cell function and metabolism between these maturation states. This data may be used to provide an insight into how parity influences human luminal cell metabolism and breast cancer risk.
Project description:We investigated whether mouse serum autoantibody binding patterns on random-sequence peptide microarrays (immunosignaturing) can be used for diagnosing and predicting the onset of lupus and its central nervous system (CNS) manifestations. Submitter states "We have no processed data to submit. We have no gpr files to submit." To identify possible predictive and diagnostic peptides of lupus and CNS-lupus, we carried out two studies and selected peptides in common across both studies. In the first study we tested 3-6 MRL/lpr, MRL/mp and C3H/HeJ mice at four months of age. For study two we tested 9-10 MRL/lpr and MRL/mp at 1.5 and 4 months of age. In both studies the mice sera were diluted 1/500 and analyzed using microarray peptides from platform GPL14921. We ran each sample in triplicate. The MRL/lpr and MRL/mp are the autoimmune strains and the C3H/HeJ is the control strain.
Project description:Ex vivo colorectal adenocarcinoma samples were analysed by desorption electrospray ionisation using an Orbitrap mass spectrometer. The samples were analysed in negative mode over the m/z range 600-1000. Some of the samples presented in this dataset were analysed as part of [1]. The study makes available imzML files of profile and centroid mode data, as well as low- and high- resolution optical image files of H&E-stained sections. These files can be found in the zip file named after each tissue section. </p> Ref:</br> [1] Gerbig S, Golf O, Balog J, Denes J, Baranyai Z, Zarand A, Raso E, Timar J, Takats Z. Analysis of colorectal adenocarcinoma tissue by desorption electrospray ionization mass spectrometric imaging. Anal Bioanal Chem. 2012 Jun;403(8):2315-25. doi:10.1007/s00216-012-5841-x. PMID:22447214</br>
Project description:A functional genetic screen to identify genes causing tamoxifen resistance in an estrogen-dependent human breast cancer cell model was performed. By insertion of defective retrovirus into the genome, individual genetic changes were introduced at random in ZR-75-1 cells. Subsequently, infected cells were selected for their ability to proliferate while being exposed to tamoxifen, and from these cultures stable cell lines were established. The retrovirus insertion sites were mapped enabling the identification of several candidate breast cancer anti-estrogen resistance (BCAR) genes. By cDNA transfection of estrogen-dependent cells resulting in their transformation into a tamoxifen-resistant phenotype, proof was provided for the causative role of BCAR genes.A functional genetic screen to identify genes causing tamoxifen resistance in an estrogen-dependent human breast cancer cell model was performed. By insertion of defective retrovirus into the genome, individual genetic changes were introduced at random in ZR-75-1 cells. Subsequently, infected cells were selected for their ability to proliferate while being exposed to tamoxifen, and from these cultures stable cell lines were established. The retrovirus insertion sites were mapped enabling the identification of several candidate breast cancer anti-estrogen resistance (BCAR) genes identified. By cDNA transfection of estrogen-dependent cells resulting in their transformation into a tamoxifen-resistant phenotype, proof was provided for the causative role of BCAR genes (Van Agthoven et al, Breast Cancer Res Treat DOI:10.1007/s10549-008-9969-5, 2008). To elucidate the mechanisms how these individual BCAR genes induce cell proliferation in growth-arrested ZR-75-1 cells, we assessed the gene expression patterns between the different groups of cell lines. Keywords: Expression profiling, reference design RNA was isolated from two independent cultures of 69 tamoxifen-resistant cell lines. Detailed information regarding these cell lines with respect to the viral integration sites, was described previously (Van Agthoven et al, Breast Cancer Res Treat DOI:10.1007/s10549-008-9969-5, 2008). Each sample was hybridized in duplicate/triplicate and once in a dye-swap. The mixture of cell lines used as a reference was detailed previously (Jansen et al, J Clin Oncol 23, 732, 2005).
Project description:This experiment aimed to measure gene expression in glucose-responsive beta-cells. RNA was extracted using RNeasy Mini kit. Quantity and quality of extracted RNA were assessed by the NanoDrop spectrophotometer ND-1000 and Experion RNA StdSens Analysis Kit, respectively. Background correction, normalization, and probe summarization were performed by the Robust Multichip Average method. More details can be found in J Biol Chem (doi: 10.1074/jbc.M112.422527).