Effects of PD-0332991 on gene expression of human pancreatic ductal adenocarcinoma (PDAC) cell lines
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Liu F
PROVIDER: S-ECPF-GEOD-39646 | biostudies-other | 2012 Oct
REPOSITORIES: biostudies-other
Similar Datasets
Project description:PD-0332991 is a small molecule inhibitor for Cdk4 and Cdk6. It exerted growth inhibitory effects on PDAC cell lines (AsPC-1 and COLO-357). Microarray analysis was used to characterize the changes in gene expression profiles of AsPC-1 and COLO-357 upon PD-0332991 incubation AsPC-1 and COLO-357 cells were treated in the absence or presence of 5 µM PD-0332991 for 24 h and 72 h. Each expreimental condition had biological triplicates. Twenty-four samples were analyzed in total.
2012-10-10 | E-GEOD-39646 | biostudies-arrayexpress
Project description:PD-0332991 is a small molecule inhibitor for Cdk4 and Cdk6. It exerted growth inhibitory effects on PDAC cell lines (AsPC-1 and COLO-357). Microarray analysis was used to characterize the changes in gene expression profiles of AsPC-1 and COLO-357 upon PD-0332991 incubation
2012-10-10 | GSE39646 | GEO
Project description:Pancreatic ductal adenocarcinoma (PDAC) has one of the worst survival rates of all cancers. ANO1 (TMEM16A) is a recently identified Ca(2+)-activated Cl(-) channel (CaCC) that is upregulated in several tumors. Although ANO1 was subject to extensive studies in the recent years, its pathophysiological function has only been poorly understood. The aim of the present study is to establish the significance of ANO1 in PDAC behavior and demarcate its roles in PDAC from those of the volume-regulated anion channel (VRAC). We performed qPCR and Western blot measurements on different PDAC cell lines (Panc-1, Mia PaCa 2, Capan-1, AsPC-1, BxPC-3) and compared the results to those obtained in a human pancreatic ductal epithelium (HPDE) cell line. All cancer cell lines showed an upregulation of ANO1 on mRNA and protein levels. Whole-cell patch-clamp recordings identified large Ca(2+) and voltage-dependent Cl(-) currents in PDAC cells. Using siRNA knockdown of ANO1 and three ANO1 inhibitors (T16Ainh-A01, CaCCinh-A01, and NS3728), we found that ANO1 is the main constituent of CaCC current in PDAC cells. We further characterized these three inhibitors and found that they had unspecific effects on the free intracellular calcium concentration. Functional studies on PDAC behavior showed that surprisingly inhibition of ANO1 did not influence cellular proliferation. On the other hand, we found ANO1 channel to be pivotal in PDAC cell migration as assessed in wound healing experiments.
| S-EPMC4464647 | biostudies-literature
Project description:BACKGROUND:Although the pancreatic ductal adenocarcinoma (PDAC) presents high mortality and metastatic potential, there is a lack of effective therapies and a low survival rate for this disease. This PDAC scenario urges new strategies for diagnosis, drug targets, and treatment. METHODS:We performed a gene expression microarray meta-analysis of the tumor against normal tissues in order to identify differentially expressed genes (DEG) shared among all datasets, named core-genes (CG). We confirmed the CG protein expression in pancreatic tissue through The Human Protein Atlas. It was selected five genes with the highest area under the curve (AUC) among these proteins with expression confirmed in the tumor group to train an artificial neural network (ANN) to classify samples. RESULTS:This microarray included 461 tumor and 187 normal samples. We identified a CG composed of 40 genes, 39 upregulated, and one downregulated. The upregulated CG included proteins and extracellular matrix receptors linked to actin cytoskeleton reorganization. With the Human Protein Atlas, we verified that fourteen genes of the CG are translated, with high or medium expression in most of the pancreatic tumor samples. To train our ANN, we selected the best genes (AHNAK2, KRT19, LAMB3, LAMC2, and S100P) to classify the samples based on AUC using mRNA expression. The network classified tumor samples with an f1-score of 0.83 for the normal samples and 0.88 for the PDAC samples, with an average of 0.86. The PDAC-ANN could classify the test samples with a sensitivity of 87.6 and specificity of 83.1. CONCLUSION:The gene expression meta-analysis and confirmation of the protein expression allow us to select five genes highly expressed PDAC samples. We could build a python script to classify the samples based on RNA expression. This software can be useful in the PDAC diagnosis.
| S-EPMC6995241 | biostudies-literature
Project description:BackgroundOne of the deadliest and most prevalent cancer is pancreatic ductal adenocarcinoma (PDAC). Microarray has become an important tool in the research of PDAC genes and target therapeutic drugs.ObjectivesThis study intends to clarify the promising prognostic and biomarker targets in PDAC using GSE78229 and GSE62452 datasets, publicly accessible at the Gene Expression Omnibus database.Materials and methodsUtilizing GEOquery, Bio base, gplots, and ggplot2 packages in the R program, this study detects 428 differentially expressed genes that are further applied to build a co-expression network by the weighted correlation network analysis (WGCNA). The turquoise module presented a higher correlation with PDAC progression. 79 candidate genes were selected based on the co-expression and protein-protein interaction (PPI) networks. In addition, the functional enrichment analysis was studied.ResultsFive significant KEGG pathways linked to PDAC were detected, in which the endoplasmic reticulum protein processing pathway was remarked to be vital. The resulting 19 hub genes as HSPA4, PABPC1, HSP90B1, PPP1CC, USP9X, EIF2S3, MSN, RAB10, BMPR2, P4HB, UBC, B2M, SLC25A5, MMP7, SPTBN1, RALB, DNAJB1, CENPE, and PDIA6 were identified by the Network Analyst web tool founded on PPI network by the STRING. These were identified as the most connected hub proteins. The quantification of the expression of levels and survival probabilities were analyzed overall survival (OS) of the real hub genes and were investigated by Kaplan-Meier (KM) plotter through The Cancer Genome Atlas Program (TCGA) database.ConclusionsThe protein-protein interactions and KEGG pathway enrichment by DAVID indicated that some pathways were involved in PDAC, such as "pathways in cancer (hsa05200)", "protein processing in the endoplasmic reticulum (hsa04141)", "antigen processing and presentation (hsa04612)", "dopaminergic synapse (hsa04728)", and "measles (hsa05162)"; in which these pathways, the "protein processing in endoplasmic reticulum (hsa04141)", was further studied because of its closely relationship with PDAC. The rest of the hub genes reviewed throughout the study might be promising targets for diagnosing and treating PDAC and relevant diseases.
| S-EPMC9284245 | biostudies-literature
Project description:Introduction: PDAC is a lethal malignancy with a clear unmet need; almost all patients fail 1st, 2nd, and 3rd line multi-agent cytotoxic chemotherapy. The mammalian target of rapamycin (mTOR) has been identified as a key signaling node enhancing tumor survival and drug resistance in PDAC; hence, it is considered a promising therapeutic target. Areas covered: We comprehensively reviewed the evidence from preclinical and phase I and II clinical trials, based on the authors'clinical experience and a PubMed, Cochrane library, Embase, and Google Scholar search everolimus + pancreatic cancer. Expert opinion: Everolimus has not demonstrated efficacy in PDAC; however, an mTOR inhibitor in combination with stroma-targeted therapies may be a promising area to explore in clinical trials.
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Project description:Deficient DNA mismatch repair status (dMMR)/high microsatellite instability have been shown to be predictive biomarkers for immune checkpoint inhibitor drugs which block the programmed death protein-1/programmed death ligand-1 (PD-1/PD-L1) interaction between tumor cells and activated T cells. The aim of this study was to determine the prevalence of MMR status and quantification of PD-L1 expression in pancreatic endoscopic ultrasound-guided fine-needle biopsy (EUS FNB) specimens. Immunochemistry (IHC) was performed on consecutive archived treatment-naïve formalin-fixed paraffin-embedded EUS-FNB samples. The specimens were considered to have PD-L1 expression if PD-L1 was expressed in ≥1% of tumor cells and a high level of expression if ≥50%. Tumors with absent nuclear staining of DNA mismatch repair proteins (MLH1, MSH2, MSH6, or PMS2) were classified as dMMR. A total of 28 treatment-naïve patients who underwent EUS-FNB and had a final diagnosis of pancreatic ductal adenocarcinoma (PDAC) were included in the study. All the EUS-FNB samples were adequate for the evaluation of MMR and PD-L1 expression. None of the patients with PDAC included in the study had a dMMR tumor. PD-L1 expression was identified in 39% of the cohort (n = 11). Expression thresholds of ≥1%, ≥10%, and ≥50% in tumor cells were identified in 11 (39%), 4 (14%), and 1 (4%) patients, respectively. The evaluation of MMR status and PD-L1 can be successfully performed on EUS-FNB pancreatic specimens. Furthermore, MMR expression failed to show utility in recognizing immunotherapy vulnerability in pancreatic cancer; the only recommendation for testing remains for patients with heritable cancers. Meanwhile high PD-L1 expression was correlated with poor prognosis. This association may identify a subgroup of patients where immune checkpoints inhibitors could provide therapeutic benefits, spotlighting the role of EUS-FNB in the field of immune-oncology.
| S-EPMC8871161 | biostudies-literature
Project description:Pancreatic cancer is one of the most fatal cancers and is associated with limited diagnostic and therapeutic modalities. Currently, gemcitabine is the only effective drug and represents the preferred first-line treatment for chemotherapy. However, a high level of intrinsic or acquired resistance of pancreatic cancer to gemcitabine can contribute to the failure of gemcitabine treatment. To investigate the underlying molecular mechanisms for gemcitabine resistance in pancreatic cancer, we performed label-free quantification of protein expression in intrinsic gemcitabine-resistant and - sensitive human pancreatic adenocarcinoma cell lines using our improved proteomic strategy, combined with filter-aided sample preparation, single-shot liquid chromatography-mass spectrometry, enhanced spectral counting, and a statistical method based on a power law global error model. We identified 1931 proteins and quantified 787 differentially expressed proteins in the BxPC3, PANC-1, and HPDE cell lines. Bioinformatics analysis identified 15 epithelial to mesenchymal transition (EMT) markers and 13 EMT-related proteins that were closely associated with drug resistance were differentially expressed. Interestingly, 8 of these proteins were involved in glutathione and cysteine/methionine metabolism. These results suggest that proteins related to the EMT and glutathione metabolism play important roles in the development of intrinsic gemcitabine resistance by pancreatic cancer cell lines.
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Project description:Lymph node (LN) metastasis occurs frequently in pancreatic ductal adenocarcinoma (PDAC), representing an advanced disease stage and independently predicting patient survival. Current nodal staging is inadequate preoperatively and even less so postoperatively, and molecular biomarkers are needed to improve prognostication and selection of therapy. Recent data have suggested important roles of miRNAs in PDAC tumorigenesis and progression. The aim of the present study was to identify miRNA expression signature for nodal spread in PDAC patients. Using PDAC human tissue specimens, we identified 39 miRNAs which were differently expressed in LN positive compared to LN negative PDAC samples. Of them, six miRNAs have been reported to play a role in cancer invasion and metastasis. A high versus low six- miRNA signature score was predictive of LN metastasis in the PDAC validation cohort. We demonstrated a similar expression pattern of four out of the six miRNAs in the plasma of PDAC patients. The results of our in-vitro studies revealed that miR-141 and miR-720 are involved in the process of epithelial to mesenchymal-transition in PDAC. These miRNAs significantly inhibited in vitro proliferation, migration and invasion of PDAC cells as evidence by gain- and loss- of function studies, specifically, via ZEB-1 and TWIST1 transcription factors, as well as through the activation of the MAP4K4/JNK signaling pathway.
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Project description:This SuperSeries is composed of the SubSeries listed below.
2014-11-10 | GSE63158 | GEO