Whole genome pooled shRNA screen to characterize Raptinal-induced apoptosis in the MIA PaCa-2 cell line
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE66423 | GEO | 2018/02/27
REPOSITORIES: GEO
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Project description:Pancreatic ductal adenocarcinoma, caused by activating mutation in K-Ras, is an aggressive malignancy due to its early invasion and matastasis. Ral GTPases, negatively regulated by RalGAP, are activated downstream of Ras and play a crucial role in development and progression of pancreatic ductal adenocarcinoma. However, the underlying mechanisms remain unclear. We used microarrays to detail the global programme of gene expression underlying the human pancreatic ductal adenocarcinoma cell line, MIA PaCa-2 with RalGAPβ deficiency or not, and identified distinct classes of Ral activation-related mRNA.
2023-04-24 | GSE223382 | GEO
Project description:Among solid tumors, pancreatic cancer (PC) remains a leading cause of death. In PC, the protein ANXA1 has been identified as an oncogenic factor acting in an autocrine/paracrine way, and also as a component of tumor-deriving extracellular vesicles. Here, we proposed the experimental protocol to obtain spheroids from the two cell lines, wild-type (WT) and Annexin A1 (ANXA1) knock-out (KO) MIA PaCa-2, this last previously obtained through CRISPR/Cas9 genome editing system. The use of three-dimensional (3D) models, like spheroids, can be useful to mimic tumor characteristics and for preclinical chemo-sensitivity studies. By using PC spheroids, we have assessed the activity of intracellular and extracellular ANXA1. Indeed, we have proved that the intracellular protein influences in vitro tumor development and growth by spheroids analysis, in addition to defining the modification about cell protein pattern in ANXA1 KO model compared to the WT one. Moreover, we have tested the response to FOLFIRINOX chemotherapy regimen whose cytostatic effect appeared notably increased in ANXA1 KO spheroids. Additionally, this study has highlighted that the extracellular ANXA1 action is strengthened through the EVs supporting spheroids growth and resistance to drug treatment, mainly affecting tumor progression. Thus, our data interestingly suggest the relevance of ANXA1 as a potential therapeutic PC marker.
| S-EPMC9563593 | biostudies-literature
Project description:A library of active genome regulatory elements (putative promoters and enhancers) from MIA PaCa-2 pancreatic adenocarcinoma cells was constructed using a specially designed lentiviral vector and a massive parallel reporter assay (ChIP-lentiMPRA). Chromatin immunoprecipitation of the cell genomic DNA by H3K27ac antibodies was used for primary enrichment of the library for regulatory elements. Totally, 11,264 unique genome regions, many of which are capable of enhancing the expression of the CopGFP reporter gene from the minimal CMV promoter, were identified. The regions tend to be located near promoters. Based on the proximity assay, we found an enrichment of highly expressed genes among those associated with three or more mapped distal regions (2 kb distant from the 5'-ends of genes). It was shown significant enrichment of genes related to carcinogenesis or Mia PaCa-2 cell identity genes in this group. In contrast, genes associated with 1-2 distal regions or only with proximal regions (within 2 kbp of the 5'-ends of genes) are more often related to housekeeping functions. Thus, ChIP-lentiMPRA is a useful strategy for creating libraries of regulatory elements for the study of tumor-specific gene transcription.
| S-EPMC9740945 | biostudies-literature
Project description:Studies using cell lines should always characterize these cells to ensure that the results are not distorted by unexpected morphological or genetic changes possibly due to culture time or passage number. Thus, the aim of this study was to describe those MIA PaCa-2 and PANC-1 cell line phenotype and genotype characteristics that may play a crucial role in pancreatic cancer therapeutic assays, namely neuroendocrine chemotherapy and peptide receptor radionuclide therapy. Epithelial, mesenchymal, endocrine and stem cell marker characterization was performed by immunohistochemistry and flow cytometry, and genotyping by PCR, gene sequencing and capillary electrophoresis. MIA PaCa-2 (polymorphism) expresses CK5.6, AE1/AE3, E-cadherin, vimentin, chromogranin A, synaptophysin, SSTR2 and NTR1 but not CD56. PANC-1 (pleomorphism) expresses CK5.6, MNF-116, vimentin, chromogranin A, CD56 and SSTR2 but not E-cadherin, synaptophysin or NTR1. MIA PaCA-1 is CD24(-), CD44(+/++), CD326(-/+) and CD133/1(-), while PANC-1 is CD24(-/+), CD44(+), CD326(-/+) and CD133/1(-). Both cell lines have KRAS and TP53 mutations and homozygous deletions including the first 3 exons of CDKN2A/p16(INK4A), but no SMAD4/DPC4 mutations or microsatellite instability. Both have neuroendocrine differentiation and SSTR2 receptors, precisely the features making them suitable for the therapies we propose to assay in future studies.
| S-EPMC4756684 | biostudies-literature
Project description:This a model from the article:
Computational insights on the competing effects of nitric oxide in regulating
apoptosis.
Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. PLoS One
2008 May 28;3(5):e2249 18509469
,
Abstract:
Despite the establishment of the important role of nitric oxide (NO) on
apoptosis, a molecular-level understanding of the origin of its dichotomous pro-
and anti-apoptotic effects has been elusive. We propose a new mathematical model
for simulating the effects of nitric oxide (NO) on apoptosis. The new model
integrates mitochondria-dependent apoptotic pathways with NO-related reactions,
to gain insights into the regulatory effect of the reactive NO species N(2)O(3),
non-heme iron nitrosyl species (FeL(n)NO), and peroxynitrite (ONOO(-)). The
biochemical pathways of apoptosis coupled with NO-related reactions are
described by ordinary differential equations using mass-action kinetics. In the
absence of NO, the model predicts either cell survival or apoptosis (a bistable
behavior) with shifts in the onset time of apoptotic response depending on the
strength of extracellular stimuli. Computations demonstrate that the relative
concentrations of anti- and pro-apoptotic reactive NO species, and their
interplay with glutathione, determine the net anti- or pro-apoptotic effects at
long time points. Interestingly, transient effects on apoptosis are also
observed in these simulations, the duration of which may reach up to hours,
despite the eventual convergence to an anti-apoptotic state. Our computations
point to the importance of precise timing of NO production and external
stimulation in determining the eventual pro- or anti-apoptotic role of NO.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. (2008) - version=1.0
The original CellML model was created by:
Wendy Kang
wkan014@aucklanduni.ac.nz
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1006230026 | BioModels
Project description:This a model from the article:
Computational insights on the competing effects of nitric oxide in regulating
apoptosis.
Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. PLoS One
2008 May 28;3(5):e2249 18509469
,
Abstract:
Despite the establishment of the important role of nitric oxide (NO) on
apoptosis, a molecular-level understanding of the origin of its dichotomous pro-
and anti-apoptotic effects has been elusive. We propose a new mathematical model
for simulating the effects of nitric oxide (NO) on apoptosis. The new model
integrates mitochondria-dependent apoptotic pathways with NO-related reactions,
to gain insights into the regulatory effect of the reactive NO species N(2)O(3),
non-heme iron nitrosyl species (FeL(n)NO), and peroxynitrite (ONOO(-)). The
biochemical pathways of apoptosis coupled with NO-related reactions are
described by ordinary differential equations using mass-action kinetics. In the
absence of NO, the model predicts either cell survival or apoptosis (a bistable
behavior) with shifts in the onset time of apoptotic response depending on the
strength of extracellular stimuli. Computations demonstrate that the relative
concentrations of anti- and pro-apoptotic reactive NO species, and their
interplay with glutathione, determine the net anti- or pro-apoptotic effects at
long time points. Interestingly, transient effects on apoptosis are also
observed in these simulations, the duration of which may reach up to hours,
despite the eventual convergence to an anti-apoptotic state. Our computations
point to the importance of precise timing of NO production and external
stimulation in determining the eventual pro- or anti-apoptotic role of NO.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. (2008) - version=1.0
The original CellML model was created by:
Wendy Kang
wkan014@aucklanduni.ac.nz
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1006230064 | BioModels
Project description:Mitochondria drive apoptosis by releasing pro-apoptotic proteins that promote caspase activation in the cytosol. The rhomboid-like protease PARL, an intramembrane cleaving peptidase in the inner membrane, regulates mitophagy and cell death pathways, but its role in apoptosis remained enigmatic. Here, we employed PARL-based proteomics to define its substrate spectrum. Our data identified the mitochondrial pro-apoptotic protein Smac/DIABLO as a PARL substrate. In apoptotic cells, Smac/DIABLO is released into the cytosol and promotes caspase activity by inhibiting IAPs. Intramembrane cleavage of Smac/DIABLO by PARL generates an amino terminal IAP-binding motif, which is required for its apoptotic activity. Loss of PARL impairs proteolytic maturation of Smac/DIABLO, which fails to bind XIAP. Smac/DIABLO peptidomimetics, downregulation of XIAP or cytosolic expression of cleaved Smac/DIABLO restores apoptosis in PARL-deficient cells. Our results discover a pro-apoptotic function of PARL and identify PARL-mediated Smac/DIABLO processing and cytochrome c release facilitated by OPA1 dependent cristae remodeling as two independent pro-apoptotic pathways in mitochondria. Please note that these data are overlapping with data uploaded under: PXD004914. Exclusively in this upload, you will find the S277A mutant immunoprecipitations.
2017-03-01 | PXD005712 | Pride
Project description:Small molecule inhibitors of key apoptosis regulators have been developed that bind to anti-apoptotic molecules like BCL-2, leading to release of pro-apoptotic proteins and cell death induction. This study shows that functional analysis of the interplay of apoptosis regulators in precursor B-ALL predicts preclinical in vivo activity of the BCL-2 inhibitor venetoclax and provides a robust assay for upfront identification of leukemias eligible for therapy.
2019-08-06 | GSE123883 | GEO
Project description:To determine the C1GALT1 regulated gene expression profile in MIA PaCa-2 cells.
2017-12-04 | GSE90668 | GEO
Project description:In colorectal cancer, p53 is commonly inactivated, associated with chemo-resistance, and marks the transition from non-invasive to invasive disease. Cancers, including colorectal cancer, are thought to be diseases of aberrant stem cell populations, as stem cells are able to self-renew, making them long-lived enough to acquire mutations necessary to manifest the disease. We have shown that extracts from sweet sorghum stalk components eliminate colon cancer stem cells (CCSC) in a partial p53-dependent fashion. However, the underlying mechanisms are unknown. In the present study, CCSC were transfected with short hairpin-RNA against p53 (CCSC p53 shRNA) and treated with sweet sorghum phenolics extracted from different plant components (dermal layer, leaf, seed head and whole plant). While all components demonstrated anti-proliferative and pro-apoptotic effects in CCSC, phenolics extracted from the dermal layer and seed head were more potent in eliminating CCSC by elevating caspases 3/7 activity, PARP cleavage, and DNA fragmentation in a p53-dependent and p53-independent fashion, respectively. Further investigations revealed that the anti-proliferative and pro-apoptotic effects were associated with decreases in beta-catenin protein levels, and beta-catenin targets cyclin D1, cMyc, and survivin. These results suggest that the anti-proliferative and pro-apoptotic effects of sweet sorghum extracts against human colon cancer stem cells are via suppression of Wnt/beta-catenin pro-survival signaling in a p53-dependent (dermal layer) and partial p53-independent (seed head) fashion. LCMS used to identify phenolic compounds associated with extract activity
2014-05-01 | MTBLS69 | MetaboLights