Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression data from postnatal day 7 subventricular zone (SVZ), IV ventricle and cerebellar white matter-derived neural stem cells (NSCs) and of cancer stem cells (CSCs) from Ptch het p53 wt and Ptch het p53 het mouse medulloblastomas

ABSTRACT: We exploited microarrays to detail the global program of gene expression underlying normal stem cells and cancer stem cells in the cerebellum and in medulloblastomas (MBs). To identify novel molecular mediators involved in medulloblastomagenesis, we compared the distinct postnatal hindbrain-derived NSC populations, which are potentially tumor-initiating, with murine single Ptch and compound Ptch/p53-mutant MB cancer stem cells (CSCs), the latter faithfully phenocopying the different variants of human MB in vivo. Transcriptome analysis of both hindbrain NSCs and MB CSCs resulted in the generation of well-defined gene signatures, each reminiscent of a specific human MB molecular subclass.

ORGANISM(S): Mus musculus

SUBMITTER: Rossella Galli

PROVIDER: E-GEOD-37316 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Putative N-glycoprotein markers of MCF-7/ADR cancer stem cells from N-glycoproteomics characterization of the whole cell lysate

Project description:Being the most malignant disease among females, breast cancer has morbidity and mortality in the first and second positions among various cancers [1]. Up to now, chemotherapy has been the most common therapy [2]; however, multidrug resistance (MDR) often occurs to give low overall survival rate. Thus, it is urgent to figure out the mechanism of chemotherapy resistance. The first step of drugs to attack tumor cells is to interact with the plasma membrane, and solute carrier (SLC) family proteins are uptake transporters [3]. On the other side, the efflux transporters (such as ATP-binding cassette, ABC) pump drug out of cancer cells [4]. The main mechanism of MDR is the upregulation of ATP-binding cassette (ABC) transporters [5]. Breast cancer resistance protein (ABCG2), multidrug resistance protein (ABCC1) and P-glycoprotein (P-gp) have been extensively studied [6,7]. Formation of CSCs [8], DNA damage [9] and cell apoptosis [10] and epithelial mesenchymal transition (EMT) are other mechanisms of MDR. To zoom in on the correlation between altered glycosylation and drug resistance and to find out the putative biomarkers, MS-based glycoprotomics is a method of choice. Here, we report our N-glycoproteomics study of differential N-glycosylation from the whole cell lysate of MCF-7/ADR CSCs (adriamycin-resistant MCF-7 CSCs) relative to MCF-7 CSCs. Intact N-glycopeptides from both cells were enriched with ZIC-HILIC, isotopically diethylated, mixed with 1:1 ratio, and the mixture was analyzed by C18-RPLC-ESI-MS/MS (HCD with stepped NCE). Differentially expressed N-glycopeptides (DEGPs) were identified and quantified with database search using GPSeeker.

2023-07-04 | PXD036095 | Pride

Cancer stem cells from lobular infiltrating breast tumor metastasize to bone and acquire a gene signature associated to bone tropism

Project description:We investigated the role of breast cancer stem-like cells (CSCs-like), isolated from primary tumor, in promoting bone metastases in a human-in-mice model. Luciferase-transduced CD44+CD24- breast CSCs-like were injected through subcutaneous (SC) and intracardiac (IC) route in nonobese/severe combined immunodeficient (NOD/SCID) mice carrying subcutaneous human bone implants. The implanted bone was viable, active and human neo-vascularization was present. By in vivo luciferase imaging, we monitored tumor growth and detected bone-localized breast CSCs-like, both after SC and IC injection. Bone metastatic lesions were histologically evident, and tumor cells expressed epithelial markers and vimentin. Bone metastatic cells isolated from bone implants showed a CD44-CD24+ phenotype and re-created tumors and bone metastases after injection in secondary mice. A “bone tropism” expression signature was found to distinguish bone-colonizing cells from parental CSCs-like and to persist at subsequent passages also in the absence of surrounding bone tissue. The bone tropism signature displayed significant enrichment in genes discriminating bone metastases of breast cancer from metastases at other organs. Our results demonstrate the ability of breast CSCs-like to promote bone metastasis and provide a CSCs-like bone tropism signature, with potential prognostic value. C10 breast cancer stem-like cells (CSCs-like) were derived as mammospheres from a lobular-infiltrating breast carcinoma (ER+, HER2-). Samples are organized in the following groups: (i) Breast CSCs-like (C10, duplicate); (ii) Luciferase-transduced CSCs-like (C10L, simplicate); (iii) Bone-isolated C10L metastatic cells (C10-bone, duplicate) and subsequently (iv) grown in vitro as spheroids (C10-CSC, simplicate) or (v) re-grown in subcutaneous implants (C10-SC, duplicate).

2013-11-30 | E-GEOD-36102 | biostudies-arrayexpress

mTORC1 promotes malignant large cell/anaplastic histology and is a therapeutically targetable vulnerability in SHH-TP53 mutant medulloblastoma

Project description:Distinct molecular subgroups and subtypes have been identified for medulloblastoma (MB), one of the most malignant brain tumors of childhood, with the sonic hedgehog (SHH)-activated subgroup of patients with mutations in p53 having a very severe outcome, associated with unfavorable histological large cell/anaplastic (LC/A) features. Aim of this study was to determine whether hyperactivation of mechanistic Target Of Rapamycin Complex 1 (mTORC1) pathway, whose role in molecular subtypes of MB is currently undefined, underlies the acquisition of LC/A histology in this subtype. MBs developing in p53-deficient Ptch+/- SHH mice show LC/A features that correlate with mTORC1 hyperactivation, which, mechanistically, is mediated by a decrease in the p53-dependent expression of the negative mTORC1 regulator Tsc2. Ectopic mTORC1 activation in mouse MB cancer stem cells (CSCs) promotes the acquisition of the LC/A phenotype. Furthermore, mTORC1 inhibition in both autochthonous p53-mutant SHH MBs and CSC-derived LC/A MBs results in reduced tumor burden and enhanced survival. Most remarkably, mTORC1 hyperactivation in tumor cells is detected only in human p53-mutant SHH MB samples and treatment with rapamycin of a human preclinical model phenocopying this subgroup decreases tumor growth and malignancy. As such, mTORC1 may act as a new and specific druggable target for this subset of SHH MB, thus resulting in the implementation of a more stringent MB risk stratification and in the potentially rapid translation of this precision medicine approach into the clinical setting.

2021-10-21 | GSE183901 | GEO

Altered expression of microRNAs in PC-3 sphere cells of prostate cancer compared with PC-3 adherent cells

Project description:Metastatic prostate cancer is a leading cause of cancer-related death in men. Cancer stem cells (CSCs) are involved in tumor progression and metastasis, including in prostate cancer. There is an obvious and urgent need for effective cancer stem cells specific therapies in metastatic prostate cancer. MicroRNAs (miRNAs) are an important class of pervasive genes that are involved in a variety of biological functions, especially in cancer. The goal of this study was to identify miRNAs involved in prostate cancer metastasis and cancer stem cells. Several published reports have demonstrated that non-adherent spheres culture is increasingly used as an effective method to enrich and identify stem cells or putative CSCs.In our previous study, we enriched prostate cancer stem cells from PC-3 sphere cells in serum-free suspension culture and characterized their CSCs properties.Thus, we used spheres as a prostate cancer stem cells model to elucidate its metastatic mechanisms. We examined the miRNA expression profiles of PC-3 sphere cells of prostate cancer compared with PC-3 adherent cells by miRNA microarray.

2013-04-01 | E-GEOD-44069 | biostudies-arrayexpress

human liver CSCs LC-MSMS in sgTRMT6/61A and control

Project description:To identify proteins regulated by TRMT6/TRMT61A complex, we depleted TRMT6/TRMT61A in human liver CSCs, and compared the differential proteins with control CSCs by LC-MS/MS.

2021-09-15 | PXD019576 | Pride

Gene expression data from postnatal day 7 subventricular zone (SVZ), IV ventricle and cerebellar white matter-derived neural stem cells (NSCs) and of cancer stem cells (CSCs) from Ptch het p53 wt and Ptch het p53 het mouse medulloblastomas

Project description:We exploited microarrays to detail the global program of gene expression underlying normal stem cells and cancer stem cells in the cerebellum and in medulloblastomas (MBs).

2012-04-17 | GSE37316 | GEO

CD109 expression regulates the phenotype of cancer stem-like cells or cancer-initiating cells in epithelioid sarcoma with possible impact on clinical prognosis

Project description:Several human cancers contain a small subpopulation of cells called cancer stem-like cells (CSCs)/cancer initiating cells (CICs), which are defined by the ability of self- renewal, multi-differentiation potential, and tumorigenesis. In current study, we focused on epithelioid sarcoma, which is very rare caner, and isolated CSCs/CICs from epitheloid sarcoma cell line ESX based on ALDH activity using ALDEFLUOR assay towards identification of a new CIC/CSC marker. We performed gene profiling between ALDHhigh and ALDH low cells using cDNA microarray for the identification of good markers of CSCs/CICs of epithelioid sarcoma.

2014-01-07 | E-MEXP-3826 | biostudies-arrayexpress

Transcription profiling of human primary bronchial/tracheal epithelial cells treated with 10 different sources of cigarette smoke condensates

Project description:Nine cigarette smoke condensates (CSCs) were produced under a standard ISO smoking machine regimen and one was produced by a more intense smoking machine regimen. These CSCs were used to treat primary normal human bronchial epithelial cells for 18 hours. Experiment Overall Design: Primary human bronchial/tracheal epithelial cells were grown in culture and treated with 10 different sources of cigarette smoke condensates.

2009-10-03 | E-GEOD-18235 | biostudies-arrayexpress

Comparing gene expression of human cardiac stem cells between automatic cell culture and manual handling culture

Project description:BACKGROUND: Cell-based regeneration therapies hold great promise and potential for new area in clinical medicine, although some obstacles still remain to be overcome for a wide range of clinical applications. One of the major impediments in this field is difficulties in large-scale production of cells of interest with reproducibility. Current protocol of cell therapy requires a long-time laborious manual process. To solve this problem, we focused on the robotics of automated and high throughput cell culture system. To date, an automated robotic cultivation of stem or progenitor cells in clinical trials has not been reported. METHODS: The system, AutoCultureÂ®, used in this study can automatically replace the medium, centrifuge cells, split the cells, and take a photograph for their morphology. We examined the feasibility to use it in the clinical field by comparing the growth rate and the characteristics of cardiac stem cells (CSCs) cultivated by AutoCulture and the manual handling culture, which protocol is the exact same as current performing clinical trial in our institute. RESULTS: We demonstrated similar characteristics in both culture methods, in terms of growth rates, gene expression profiles, cell surface profiles by FACS, carbon hydrate structures on the cell surface, and genomic DNA stability. IMPLICATIONS: The results of this study showed that AutoCulture is feasible to cultivate human cells for regenerative medicine. An automated cell-processing machine for cell therapy will play more important role, as it will be widespread from multi-center trials to off-the-shelf cell products. The cells were cultured by manual handling or by the automatic cell culture apparatus. Total RNA was extracted from these cells at day 7 by the RNeasy Plus Mini Kit (QIAGEN). Gene expression analysis was performed using the Agilent Whole Human Genome Microarray chips G4112F (Agilent). Raw data were normalized and analyzed by GeneSpring GX11 software.

2013-03-31 | E-GEOD-44032 | biostudies-arrayexpress

Human Breast LC-MSMS - Quantitative site- and structure-specific N-glycoproteomics characterization of differential N-glycosylation in MCF-7/ADR cancer stem cells

Project description:Cancer stem cells (CSCs) are reported to be responsible for tumor initiation, progression, metastasis, and therapy resistance where P-glycoprotein (P-gp) as well as other glycoproteins are involved. Identification of these glycoprotein markers is critical for understanding the resistance mechanism and developing therapeutics. Here we report our comparative N-glycoproteomics study of MCF‐7/ADR vs. MCF-7 cells. With zic-HILIC enrichment, isotopic diethyl labeling, RPLC-MS/MS (HCD) analysis and GPSeeker DB search, differentially expressed N-glycosylation was quantitatively characterized at the intact N-glycopeptides levels.

2020-02-21 | PXD013836 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data