Project description:Most B cell lymphomas arise in the germinal center (GC), where humoral immune responses evolve from potentially oncogenic cycles of mutation, proliferation, and clonal selection. Although lymphoma gene expression diverges significantly from GC-B cells, underlying mechanisms that alter the activities of corresponding regulatory elements (REs) remain elusive. Here we define the complete pathogenic circuitry of human follicular lymphoma (FL), which activates or decommissions transcriptional circuits from normal GC-B cells and commandeers enhancers from other lineages. Moreover, independent sets of transcription factors, whose expression is deregulated in FL, target commandeered versus decommissioned REs. Our approach reveals two distinct subtypes of low-grade FL, whose pathogenic circuitries resemble GC-B or activated B cells. Remarkably, FL-altered enhancers also are enriched for sequence variants, including somatic mutations, which disrupt transcription factor binding and expression of circuit-linked genes. Thus, the pathogenic regulatory circuitry of FL reveals distinct genetic and epigenetic etiologies for GC-B transformation. Molecular profiling of follicular lymphoma, resting peripheral blood and tonsillar B cells using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) and chromatin immunoprecipitation (H3ac and H3K27ac).
Project description:Mice with (i) PR-Cre; (ii) PR-Cre, Fbxw7 R482Q/+; (iii) PR-Cre, Pten fl/fl; (iv) PR-Cre, Pten fl/fl, Fbxw7 R482Q/+ Uterine RNA was harvested at 8 weeks age and expression profiling done by Affymetrix Clariom S Mouse HT array
Project description:Caco-2 cells (a human gastrointestinal epithelial cell line) grown to form confluent cell layers on permeable membrane supports were treated with variously (A) iron depleted medium, (B) iron depleted medium with 10 uM ferric nitrilotiracetate added to the apical medium or (C) iron depleted medium with 30 uM human holo-transferrin added to the basolateral medium for 7 days (days 14-21 after cell seeding). RNA was extract from the cells on day 21 for transcription profiling by array.
Project description:MiRNAs differentially expressed in normal pancreatic cell line (Human Pancreatic Ductal Epithelial cell line) vs MIA PaCa-2 (Pancreatic cancer cell line) were first identified by profiling >1900 miRNAs using an array approach. Subsequently, miRNAs differentially expressed in DZNep treated cells (as compared to untreated) were also identified. We also checked for miRNA changes with gemcitabine treatment as well as combination treatment.
Project description:Fibroblasts can be directly reprogrammed to induced renal tubular epithelial cells (iRECs) using four transcription factors. These engineered cells may be used for disease modeling, cell replacement therapy or drug and toxicity testing. Direct reprogramming induces drastic changes in the transcriptional landscape, protein expression, morphological and functional properties of cells. However, how the metabolome is changed by reprogramming and to what degree it resembles the target cell type remains unknown. Using untargeted gas chromatography-mass spectrometry (GC-MS) and targeted liquid chromatography-MS, we characterized the metabolome of mouse embryonic fibroblasts (MEFs), iRECs, mIMCD-3 cells, and whole kidneys. Metabolic fingerprinting can distinguish each cell type reliably, revealing iRECs are most similar to mIMCD-3 cells and clearly separate from MEFs used for reprogramming. Treatment with the cytotoxic drug cisplatin induced typical changes in the metabolic profile of iRECs commonly occurring in acute renal injury. Interestingly, metabolites in the medium of iRECs, but not of mIMCD-3 cells or fibroblast could distinguish treated and non-treated cells by cluster analysis. In conclusion, direct reprogramming of fibroblasts into renal tubular epithelial cells strongly influences the metabolome of engineered cells, suggesting that metabolic profiling may aid in establishing iRECs as in vitro models for nephrotoxicity testing in the future.
Project description:Here we describe the generation and application of a gene expression signature for the Rheb pathway. Affymetrix array data obtained from human mammary epithelial cells over expressing Rheb or GFP were used to generate a Rheb/mTOR activation signature. To test the capacity of the signature to predict patient response to everolimus we treated patient-derived colorectal cancer explants (PDCCEs) predicted to have high and low Rheb pathway activity withthe mTOR inhibitor everolimus.
Project description:To investigate the effects of a late deletion of Gata3 on CD4 T cell gene expression profiles in experimental autoimmune encephalomyelitis, we performed a RNA-Seq analysis of Gata3-sufficient (i.e., Cd45.1/Cd45.2 or vehicle treated Cd45.2/Cd45.2 Cre-ERT2 Gata3 fl/fl) and Gata3-deficient (i.e., tamoxifen-treated Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl) CNS-infiltrating CD4+ effector T cells from mixed congenic co-transfer recipient mice. We performed a gene expression profiling analysis using data obtained from RNA-seq from 2 mixed congenic adoptive transfer receipient vehicle-treated mice and 2 mixed congenic adoptive transfer receipient tamoxifen-treated mice for a total of 8 biological samples.
Project description:PP2A regulates inflammatory cytokine/chemokine gene expression by dephosphorylating protein kinases at multiple signaling pathways from stimulated cells. In this dataset, Affymetrix mouse Gene ST 2.1 Array was used to assay total RNA extracted from LPS-treated PP2ACα knockout BMDM (PP2ACαfl/fl;lyM-Cre) and the control BMDM (PP2ACαfl/fl) In this dataset, we include the expression data obtained from LPS-stimulated PP2ACα conditional knockout BMDM (PP2ACαfl/fl;lyM-Cre) and control BMDM (PP2ACαfl/fl). The data are used to obtain 1080 genes that are differentially expressed in response to LPS stimulation