Gene Expression data from Pdx-1CreAPC+/LP53L/L pancreatic ductal adenocarcinoma (PDAC) cells versus Pdx-1CreP53L/L normal pancreatic ductal cells
ABSTRACT: Analysis of primary PDAC cells established from Pdx-1CreAPCL/+p53L/L and Pdx-1Crep53L/L mice. APC haploinsufficiency combined with P53 loss in the pancreas drives MCN progression in mice. Results provide insight into molecular mechanisms invloved in the MCN formation of Pdx-1Cre APCL/+P53L/L mice. Pdx-1CreAPC+/LP53L/L PDAC cell lines and 2 Pdx-1CreP53L/L ductal cell lines were analyzed.
Project description:Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis of all common cancers, but divergent outcomes are apparent between patients. To delineate the intertumor heterogeneity that contributes to this, we aimed to identify clinically distinct gene expression-based subgroups. From a cohort of 345 resected pancreatic cancer cases, 90 samples with confirmed diagnosis of PDAC and sufficient tumor content were available for gene expression analysis by RNA sequencing. Unsupervised classification was applied, and a classifier was constructed. Species-specific transcript analysis on matching patient-derived xenografts (PDX, N=14) allowed construction of tumor- and stroma-specific classifiers for use on PDX models and cell lines.
Project description:Mouse CD8+ T cells affected by ID3 (Inhibitor of DNA binding 3) display patterns of gene expression suggesting enhanced persistance and survival. In this study, we identified genes differentially expressed between ID32a transduced and mock transduced, and ID32a knockout and wild type mouse CD8+ T cells. Most prominent functions of differentially expressed genes include DNA replication-associated repair, maintenance of chromosome stability and mitotic cell divison machinery. Overall, these data suggest that ID3 acts in favor of maintained survival in CD8+ mouse T cells. Two independent microarray experiments were carried out using separate array batches, one comparing Id32aThy1.1 (ID32a transduced) with Thy1.1 pmel-1 (mock transduced) CD8+ T cells sorted 5 days after infection, and a second experiment comparing Id32a-/- (Id32a knockout)CD8+ T cells with Id32a+/+ (Id32a wild type) controls, both in an upaired design. Individual array samples were generated by pooling equal amounts of total RNA derived from purified T cells of four individual mice. Each experimental group consisted of four such microarrays (statistical group size n=4, pooled samples derived from 16 mice per assay group total).
Project description:miRNAs are known to be involved in PDAC tumorigenesis, but only a few biologically relevant gene targets have been identified. Here we show that three miRNAs (miR-21, miR-23a and miR-27a) act in concert for the cooperative suppression of several tumor suppressor genes of which we experimentally validated PDCD4, BTG2 and NEDD4L. The synergistic inhibition of this triple miRNA combination is capable of reducing PDAC growth in a mouse model greater than inhibition of oncomiR-21 alone. Patients samples of normal pancreas (n=6) or pancreatic ductal adenocarcinoma (PDAC; n=6) were retrieved during surgery and placed in RNA Later stabilization fluid and then kept at minus 80 until required.
Project description:Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease with limited effective treatment options. PDAC tumors frequently harbor the constitutively activated form of KRAS which drives proliferative signaling, but directly targeting KRAS has so far been unsuccessful. To overcome this limitation, combinatorial treatment strategies have been developed to inhibit upstream activators and downstream effectors of KRAS signaling. One such combination using trametinib, a MEK1/2 inhibitor, and lapatinib, an EGFR/HER2 inhibitor, substantially reduced tumor growth in a patient-derived xenograft (PDX) model of PDAC. Although trametinib and lapatinib are both known to inhibit the canonical MAPK signaling cascade, the effects of this combination on other important pathways in pancreatic cancer remains unclear. To investigate this, we analyze global gene expression profiles from PDX models of PDAC treated with trametinib, lapatinib, or their combination. Our results show that trametinib induces similar yet less significant expression changes compared to combination while lapatinib has little to no effect as a monotherapy in the acute treatment setting. In the chronic treatment setting, we show that tumors exposured to prolonged treatment with trametinib plus lapatinib eventually leads to adapative resistance. Expression analyses of resistant tumors revealed concominant gene expression changes in upstream receptor tyrosine kinases (RTKs). Overall design: Patient-derived xenografts (PDX) from patients with pancreatic adenocarcinoma (PDAC) were explanted onto the pancreata of nude mice to evaluate the effects of trametinib (a MEK inhibitor), lapatinib (an EGFR/HER2 inhibitor) after acute (24 hours) exposure and chronic (3 months) exposure. In a factorial design, tripliate samples were obtained from T366, T608, and T738 tumors treated acutely with trametinib (3 mg/kg) plus lapatinib (65 mg/kg), trametinib (3 mg/kg) alone, lapatinib (65 mg/kg) alone, or vehicle controls.
Project description:Engraftment of primary pancreas ductal adenocarcinomas (PDAC) in mice to generate patient derived xenograft (PDX) models is a promising platform to for biological and therapeutic studies in this disease. However, these models are still incompletely characterized. Here, we measured the impact of the murine environment on the gene expression of the engrafted human tumoral cells. We have analyzed gene expression profiles from 35 new PDX models and compared them with previously published microarray data from PDAC and hepatocellular carcinoma (HCC). Our results showed that PDX models derived from PDAC, or HCC, were clearly different to the cell lines derived from the same cancer tissues. Indeed, PDAC- and HCC-derived cell lines are indistinguishable one from the other based in their gene expression profiles. In contrast, the transcriptomes of PDAC and HCC PDX models are clearly different and more similar to their original tumor than to PDX models from the other tumor type. Interestingly, the main differences between pancreatic PDX models and human PDAC is the expression of genes involved in pathways related with extracellular matrix interactions and cell cycle regulation likely reflecting the adaptations of the tumors to the new environment. Furthermore, most of these differences are detected in the first passages after the tumor engraftment, indicating early phases of the adaptation process. In conclusion, different from conventional cancer cell lines, PDX models of PDAC retain similar gene expression profiles of PDAC. Expression changes are mainly related to genes involved in stromal pathways likely reflecting the adaptation to new environments. We also provide evidence of the stability of gene expression patterns over subsequent passages. We have analyzed gene expression profiles from 35 new PDX models and compared them with previously published in GEO microarray data. We used PDX models, primary tumors and cell lines from PDAC and hepatocellular carcinoma. All these public data were re-process in order to compare with our 35 samples
Project description:We generated novel patient derived xenograft (PDX) and cell line -derived xenograft models for pancreatic ductal adenocarcinoma (PDAC) which reflect different molecular subtypes. Pancreatic ductal adenocarcinoma is currently the tumor with the fourth highest mortality rate. Recently, subtypes of PDAC have been reported by Collisson et al (Nat. Med. 17(4) 2011. DOI: 10.1038/nm.2344). However current fetal calf serum (FCS) cultured cell lines do not accurately model these subtypes. We thus generated novel serum-free cell lines derived from primary patient xenografts. We here analyse the gene-expression profiles of the xenografts and the derived cell lines. We show that indeed three different subtypes can be separated in our models based on gene-expression data. Further, we identify upregulation of a drug-detoxification pathway specifically in xenografts and cell lines of one of the subtypes. These models and data will help to better understand inter-patient heterogeneity in PDAC and identify novel drug targets and diagnostic markers.
Project description:Pancreatic adenocarcinoma (PDAC) is one of the most lethal human malignancies and a major health problem. Patient-derived xenografts (PDX) are appearing as a prime approach for preclinical studies despite being insufficiently characterized as a model of the human disease and its diversity. We generated subcutaneous PDX from PDAC samples obtained either surgically or using diagnostic biopsies (endoscopic ultrasound guided fine needle aspirate). The extensive multiomics characterization of the xenografts demonstrated that PDX is a suitable model for preclinical studies, representing the diversity of the primary cancers. We generated subcutaneous PDX from PDAC samples obtained either surgically or using diagnostic biopsies (endoscopic ultrasound guided fine needle aspirate). The variable 'MultiOmicsClassification' indicates the resulting sample's group. 'CIMPclass' is the CpG island methylator phenotype as estimated from the methylation arrays analysis. In this dataset, Illumina Infinium HumanCode-24 BeadChips SNP arrays were used to analyze the DNA xenografts samples from pancreatic ductal adenocarcinoma.
Project description:The mechanisms involved in promoting metastasis of pancreatic ductal adenocarcinoma have yet to be elucidated. Here, we show that AnnexinA2 regulates the secretion of Semaphorin3D from pancreatic tumor cells allowing it to bind to its receptor PlexinD1 on the surface of the tumor cell, which induces invasion and metastasis. Knockdown of AnnexinA2 or Semaphorin3D decreases the metastatic potential of pancreatic tumor cells, while over expression of AnnexinA2 or Semaphorin3D is sufficient to rescue the invasion capacity of these cells. Clinically, we found that Semaphorin3D expression correlates with poor survival and increased metastatic potential in human PDA patients. This study identified a novel axon guidance pathway downstream of AnnexinA2 that can be targeted in the treatment of metastatic pancreatic cancer. Two primary pancreatic tumor cell lines were analyzed. The first primary line was derived from a KrasG12D/p53172H/Pdx-1Cre mouse, which served as the reference sample. The second primary line was derived from a KrasG12D/p53R172H/Pdx-1Cre/AnxA2-/- mouse.
Project description:Pancreatic adenocarcinoma (PDAC) is one of the most lethal human malignancies and a major health problem. Patient-derived xenografts (PDX) are appearing as a prime approach for preclinical studies despite being insufficiently characterized as a model of the human disease and its diversity. We generated subcutaneous PDX from PDAC samples obtained either surgically or using diagnostic biopsies (endoscopic ultrasound guided fine needle aspirate). The extensive multiomics characterization of the xenografts demonstrated that PDX is a suitable model for preclinical studies, representing the diversity of the primary cancers. this dataset, describe the RNA sequencing data used in the multiomics study.
Project description:Endothelial cells from nine steady state tissues and two regenerating tissues (bone marrow and liver) were intravitally labeld, isolated via flow sorting, and immediately processed for RNA extraction. When of sufficient quality, the RNA was amplified and hybridized. For comparison, Human Emybryonic Stem Cell-derived Endothelial cells (hESC-ECs) were differentiated and isolated based on similarities to the adult mouse counterparts. Endothelial cells were labeled via intravitally labeling of the vascular bed 8 minutes prior to sacrifice with minimally three markers to identify endothelial cells followed by flow sorting.