Pancreatic cancer stem-like cells display aggressive behavior mediated via activation of FoxQ1
Ontology highlight
ABSTRACT: A microarray approach was used to measure and compare whole genome expression in non-sorted cell population and in subsets of cultured cells, including stem-like cancer cell and non-stem like cancer cell populations, MiaPaCa-2 pancreatic cancer cells from culture were sorted by Fluorescence Activated Cell Sorting (FACS) using 3 markers: CD44, CD133 and EpCAM. Three resulting populations, i.e., not sorted, sorted triple positive and sorted triple negative, were analyzed. 4 cultures were sorted independently to arrive at 4 biological replicates.
Project description:The aim of our study was to assess the impact of simvastatin on the amount of cytosolic lipid droplets (LDs), which are implicated in many biological processes including proliferation, inflammation, carcinogenesis, apoptosis, necrosis or growth arrest. Human pancreatic cancer cells MiaPaCa-2 were treated with simvastatin (6 and 12 _M) for 24 hours. Changes in expression of genes related to lipid metabolism in the simvastatin-treated cells were examined by DNA microarray analysis. The treatment of the cells with simvastatin increased their intracellular content of LDs, partially due to the uptake of cholesterol and triacylglycerides from medium; but in particular, due to enhanced synthesis of triacylglycerides as proved by detection of significant overexpression of genes related to de novo synthesis of triacylglycerides and phospholipids. Further, simvastatin markedly influenced expression of genes directly affecting cell proliferation and signaling.
Project description:Nuclear Protein 1 (NUPR1) is a nuclear intrinsically disordered protein of 82 amino acids that plays an important role in stress response and in cancer development. The project was aimed at identifying binding partners of NUPR1 in MiaPaCa-2 cells, in control and after stress condition: glucose starvation during 24h. Lysates from MiaPaCa-2 cells (transfected with NUPR1-Flag or NUPR1-GFP) were used for immunoprecipitation, performed with agarose beads coated with anti-Flag or anti-GFP antibodies. After immunoprecipitation, the eluted proteins were analyzed by LC-MS/MS.
Project description:This is data for the evaluation of a new way of counting sgRNAs in CRISPR screens using padlock probes and UMIs. It is compared to the typical PCR-based approach. In particular, a dropout screen was performed in MiaPaCa-2 cells using the Human Kinome CRISPR pooled library (Addgene #75314)
Project description:Metastatic lesions are typically not found until patients self-report symptoms or they become radiologically evident. We have developed an engineered metastatic niche (scaffold) that recruits aggressive tumor cells prior to their colonization in other organs. The engineered niche can be monitored for dynamic gene expression, and changes at this site are analogous to those in a native metastatic site (lung) for triple negative breast cancer (4T1 cells). We were able to develop a 10-gene signature from the scaffold that accurately monitors disease progression and recurrence or resistance to resection therapy. This data set acts to dissect the heterogeneity of the cell populations in the engineered and native metastatic niche and identify the cell types that contribute to the success of the signature.
Project description:Triple-negative breast cancer represents approximately 15–20% of all reported breast cancer cases, and is characterized by a shorter survival time and higher mortality rates compared to other breast cancer sub-types. Tumor microenvironment (TME) refers to the internal and external environment of tumor tissue. Increasing evidence indicates that a tumor’s microenvironment is tightly associated with the immunological surveillance and defense during the development of breast cancer. Although oncology studies employing digital dissection methodologies have provided some insight on the biological features of TME, the development of methods to investigate the cellular composition of the tumor microenvironment remain an important research priority. In this study, we extracted whole transcriptome from 30 Triple-negative breast cancer (TNBC) patients and then used bioinformatics approaches to characterize cell type content in tumor tissue compared with para-cancerous tissue. We identified 4 types of enriched immune cells and 6 types of downregulated immune cells in the tumor tissue samples. After comprehensive bioinformatics analyses, we developed an ‘immune infiltration score’ (IIS) to quantitatively model immune cell infiltration in TNBC. To demonstrate the utility of the IIS, we used 2 independent datasets for validation. We found that patients with a higher IIS showing a longer progression-free survival time and significantly better prognosis than those with a lower IIS value. In sum, we explored the immune infiltration landscape in 30 TNBC patients and provided a novel and reliable biomarker IIS to evaluate the progression-free survival and prognosis in the TNBC patients.
Project description:This experiment is performed to reveal the novel binding sites of Snai1 transcription factor globally in triple negative breast cancer cell line Hs578T. We also reveal the effect of TGF cytokine on the binding sites of Snai1.
Project description:This experiment is performed to reveal the novel binding sites of ZEB1 transcription factor globally in triple negative breast cancer cell line Hs578T. We also reveal the effect of TGF cytokine on the binding sites of ZEB1.
Project description:Human mesenchymal stem cells (hMSCs) were transduced using lentivirus containing the the triple fusion reporter gene fluc-mrfp-ttk. Microarray studies of hMSCs after transduction with the triple reporter genes using lentivirus were performed to study the effects of transduction on stem cell properties using an oligonucleotide human microarray. Transduced cells were sorted by FACS. Cells with high and low signals were ftacrtionated, and gene expression profiles were determined. Experiment Overall Design: In this study, 8 samples were experimentally evaluated. 2 samples were used as the control without undergoing any transduction. 2 samples were transduced with the virus containing only the backbone. 2 samples were transduced with the lentivirus containing the triple reporter and has high MGFP (>10^3), while 2 samples <10^3.
Project description:Breast cancers enriched for the triple negative breast cancer phenotype with extensive clinico-pathological features were profiled to establish their comprehensive transcriptional profiles
Project description:The goal of the experiment was to demonstrate if the overexpression of human-Prune-1 in Triple Negative breast cancer cells induces M2-polarization of macrophages in vitro. For this purpose, murine primary cells from breast tumor developed by Genetically Engineered Mouse Models (GEMMs) of TNBC (i.e., MMTV-Wnt1) and metastatic TNBC overexpressing both human Prune-1 and Wnt1 in mammary gland (i.e., MMTV-Prune-1/Wnt1) were obtained. Conditioned media were collected from these primary cells (1x106 cells) after 24 hours. Murine macrophages (J774A.1 and Raw264.7; 1x106) were starved for six hours and then grown for 48 hours in those conditioned media collected from MMTV-Wnt1 and MMTV-Prune-1/Wnt1 cells. Untreated macrophages were used as negative control for the experiment.