Genome-wide analysis of gene expression in mouse pancreas tumors [FAP and aSMA depletion]
ABSTRACT: Gene expression analysis of pancreatic tumors from genetically engineered mice (Pdx-Cre;LSL-KRASG12D;TGFBRIIf/f) with depletion of aSMA+ or FAP+ cells. The pancreas tumors were harvested and analysed for gene expression profiles comparisons. Overall design: Total RNA was isolated from the pancreas tumors of 3 PKT FAP control mice, 3 PKT FAP depleted mice, 3 PKT aSMA control mice, 3 PKT aSMA depleted mice
Project description:Genetically engineered mice developed spontaneous pancreas cancer (Pdx-Cre;LSL-KRASG12D;P53Mut). Mice were also engineered to develop similar spontaneous pancreas cancer without Twist or Snail (conditional gene knockout). The pancreas tumors were harvested and analysed for gene expression profiles comparisons. Total RNA was isolated from the pancreas tumors of 2 mice with wild-type Twist and Snail, from 2 mice without Twist expression in the pancreas, and from 2 mice without Snail expression in the pancreas.
Project description:Pooled KRC (LSL-KrasG12D; Rb1L/L; Pdx1-Cre: oncogenic Kras and deleted Rb1 in the pancreas) cells derived from 2 month old mice were compared to pooled KC (LSL-KrasG12D; Pdx1-Cre: oncogenic Kras in the pancreas) cells derived from 8 month old mice.
Project description:This study used Illumina RNA-sequencing to examine transcriptomic profile of mice with Klf5 knockout in context of oncogenic Kras expression. The study analyzed total RNA extracted from pancreas of mice 2 days after cerulein-induce pancreatitis. In addition, this study include 2 biological replicate of mice with each of the following genotypes: Ptf1aCreERTM, Ptf1aCreERTM;Klf5fl/fl, Ptf1aCerERTM;LSL-KrasG12D, and Ptf1aCreERTM;LSL-KrasG12D;Klf5fl/fl. Overall design: Transcriptomic profiling of pancreata from 2 Ptf1aCreERTM mice, 2 Ptf1aCreERTM;Klf5fl/fl mice, 2 Ptf1aCerERTM;LSL-KrasG12D mice, and 2 Ptf1aCreERTM;LSL-KrasG12D;Klf5fl/fl mice 2 days after cerulein-induced pancreatitis.
Project description:FAP+ cells had been reported to be present only in healing wounds and at sites of tissue remodelling. We have found FAP+ cells in many normal tissues and aimed to investigate whether these cells were related or whether FAP is upregulated in response to an external stimulus on a variety of cells. Furthermore we wanted to investigate whether FAP+ cells are simply fibroblasts and so compared their transcriptomic profiles to that of a typical fibroblastic population, the murine embryonic fibroblast. FAP+ cells were sorted from two mesenchymal tissues, visceral adipose and skeletal muscle, and from an epithelial organ, the pancreas. These were compared to MEFs. Cells were isolated in duplicate experiments and these were analysed separately. These were compared to previously published publically available CD4+ T-cell subset data.
Project description:Analysis of differentially expressed genes in CAF associated with PDAC vs NF. Genetically engineered mice with spontaneous pancreas cancer were generated. Their genotype is Ptfa-cre/+:LSL KrasG12D/+;Tgfrb2flox/flox. Cancer associated fibroblasts were expanded in vitro from the tumors of these mice (CAF). Normal fibroblasts (NF) were also expanded from normal pancreas of mice. The experiement consists in comparing the expression profile of CAF vs. NF. Expanded cultures of fibroblasts in vitro from pancreas tumor and normal pancreas tissue were lyzed in TRIzol and RNA extracted from them.
Project description:Purpose: determine RNA expression differences in an unbiased fashion between UPS tumors derived from LSL-KrasG12D;Trp53-/- (KP) mice, and UPS tumors derived from LSL-KrasG12D;Trp53-/-;Epas1-/- (KPH2) mice. Epas1 encodes HIF-2alpha protein. RNA-seq was performed on KP (n = 4) and KPH2 (n = 4) derived UPS tumors using Illumina HiSeq 2000.
Project description:Analysis of myofibroblast ablation at the gene expression level of PDAC tumors. Total RNA optained from pancreas of PDAC mice with and without aSMA myofibroblast ablated In addition, late stage aSMA ablated mice were treated with anti-CTLA4 treatment
Project description:A subset of human pancreatic ductal adenocarcinoma cells (PDACs) is characterized by high Fosl1 expression and Fosl1 is linked to the control of pro-inflammatory pathways and growth of PDAC cells. To mimick the human disease in mice (> 90% of PDAC patients harbour Kras mutations) the mutated LSL-KrasG12D allele was combined with the pancreas specific Cre recombinase Ptf1aCre (p48Cre). The two pancreatic cancer cell lines (Ptf1aCre, LSL-KrasG12D/+) were isolated from these mice and used for transcriptomics studies. The two different murine pancreatic cancer cell lines (Ptf1aCre, LSL-KrasG12D) were treated with two different Fosl1 siRNAs and one control siRNA, each. 72h after transfection a sufficient knockdown was tested by immunoblotting and qPCR. Total mRNA was isolated and checked for integrity. According to manufacture's recommendation the samples were subjected to microarray analysis using the Affymetrix Mouse Gene ST 1.0 array chip to discover differentially expressed genes.
Project description:These experiments aimed to determine the global gene expression patterns in p120WT, p120HET, and p120NULL cells in the context on oncogenic mutant KrasG12D Overall design: p120ctn was deleted using in vitro lentiviral Cre recombinase in pancreatic ductal cells isolated from LSL-KrasG12D;Ctnnd1wt/wt (KC-p120ctnWT), LSL-KrasG12D;Ctnnd1fl/wt (KC-p120ctnHET) , and LSL-KrasG12D;Ctnnd1fl/fl (KC-p120ctnNULL) mice.