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Development of gene signatures for doxorubicin resistance and cancer stem cell CD44+, CD24-/low ALD+ isolated from canine mammary adenocarcinoma cell line (microRNA)

ABSTRACT: CMT-Stylo is a canine mammary gland adenocarcinoma cell line. From this cell line, a doxorubicin resistant subline called CMT-Star was developed by culturing the cells in the presence of doxorubicin from low concentration to 100 nM doxorubicin (to induce drug resistance). The CMT-Stylo cells were maintained in Dulbecco’s modified eagles medium (DMEM) supplemented with 10% Foetal bovine serum (FBS) and 1% Penicillin-Streptomycin (ThermoFisher Scientific, USA) in 5% CO2 at 370C. The CMT-Star cell line was maintained in additional 5 nM doxorubicin to maintain its resistant phenotype.

ORGANISM(S): Canis lupus familiaris

PROVIDER: GSE114889 | GEO | 2020/12/31

REPOSITORIES: GEO

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Development of gene signatures for doxorubicin resistance and cancer stem cell CD44+, CD24-/low ALD+ isolated from canine mammary adenocarcinoma cell line (mRNA)

Project description:CMT-Stylo is a canine mammary gland adenocarcinoma cell line. From this cell line, a doxorubicin resistant subline called CMT-Star was developed by culturing the cells in the presence of doxorubicin from low concentration to 100 nM doxorubicin (to induce drug resistance). The CMT-Stylo cells were maintained in Dulbecco’s modified eagles medium (DMEM) supplemented with 10% Foetal bovine serum (FBS) and 1% Penicillin-Streptomycin (ThermoFisher Scientific, USA) in 5% CO2 at 370C. The CMT-Star cell line was maintained in additional 5 nM doxorubicin to maintain its resistant phenotype.

2020-12-31 | GSE114888 | GEO

Transcriptomic analysis of undifferentiated human embryonic stem cells (hESCs) and day-25 differentiated cortical neuronal progenitor cells from 5 isogenic hESC lines with low and high levels of alpha-synuclein expression

Project description:Purpose: To compare the cortical neuroonal differentiation capacity of clonal isogenic hESC lines with different levels of alpha-synuclein (aSyn) expression. Methods 1: Shef4 hESCs was used as a parental line to create an allelic series of clonal transgenic hESC lines expressing a human SNCA (encoding aSyn) contruct. Clonal transgenic lines with high (S8, S37) and low (S9, S34) aSyn expression were established and characterized. Methods 2: hESCs were cultured on Laminin-521 (BioLamina) in StemMACS iPS-Brew XF self-renewal media (Miltenyi) prior to lifting for isolation of total RNA. Methods 3: Cortical neuronal progenitor cells were differentiated from hESCs on Laminin-111 coated (Biolamina) 24-well plates at an initial plating density of 80,000 cells/cm2. Differentiation commenced in neural induction media (NIM) consisting of 50% DMEM/F12 (ThermoFisher Scientific), 50% Neurobasal Media (ThermoFisher Scientific), B27 supplement with Retinoic Acid (ThermoFisher Scientific), N2 supplement (ThermoFisher Scientific) and 2 mM L-Glutamine (ThermoFisher Scientific), 10μM SB431542 (Tocris) and 100 nM LDN-193189 (Miltenyl Biotec). From day 4 onwards, the base media was changed to 50% NIM, 25% DMEM/F12 and 25% Neurobasal Media. SB431542 (10 μM) and LDN-193189 (100 nM) were present for the first 12 days of differentiation. Cells were lifted and re-plated at day 12 and day 17 with Collagenase Type IV (Life Technologies). At day 25, differentiated cells were lifted for total RNA isolation.

2022-02-04 | GSE195877 | GEO

Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters

Project description:To investigate the function of the doxorubicin treatment in differentiation expression of human genes, we performed gene expression profiling analysis using data obtained from RNA-seq of three different conditions: control (DMSO-treatment) and doxorubicin treatment (200 nM and 340 nM).

2023-03-31 | GSE215321 | GEO

Gene expression profile in response to doxorubicin-rapamycin combined treatment of HER-2 overexpressing human mammary epithelial cell lines

Project description:HER-2 positive breast cancers frequently sustain elevated AKT/mammalian target rapamycin (mTOR) signaling which has been associated with resistance to doxorubicin treatment in the clinic. In our study we investigated if the mTOR inhibitor rapamycin increased the sensitivity to doxorubicin therapy in HB4a, a luminal normal mammary cell line; C5.2, a transformed cell derived from HB4a transfected with HER-2 and SKBR3 that exhibits HER-2 amplification. Flow cytometry analysis showed that the combination treatment for 24 hours with rapamycin 20nM and doxorubicin caused accumulation of HB4a and C5.2 cells in S-G2/M. Otherwise in SKBR3 cells, we observed a relative depletion of cells in S-G2/M and concomitant accumulation in G0/G1 of 10% of the cells. The analysis of IC50 of doxorubicin alone and in combination with rapamycin indicated that the sensitivity was increased 2.37 fold in HB4a, 2.46 in C5.2 and 1.87 in SKBR3, suggesting that rapamycin might have enhanced the effects of doxorubicin. Changes in gene expression resulting from co-treatment demonstrated that functional groups of genes with roles in cell cycle, proliferation, apoptosis regulation were represented in the 3 cells analysed. Other biological functions were exclusively associated with each cell suggesting that the inhibition of mTOR activation induced by HER-2 is complex and depends on the cellular context. Five independent experiments were performed for each treatment conditions: HB4a, C5.2 and SKBR3 cell lines were treated with vehicle (DRC), 20 nM of RAPAMYCIN alone (R) and 30 nM of DOXORUBICIN alone (D). The combined treatment consisted of 20 nM of RAPAMYCIN associated with 30 nM DOXORUBICIN of (DR). Total RNA extraction and hybridization on Affymetrix microarrays.

2011-01-13 | E-GEOD-26599 | biostudies-arrayexpress

Malignant canine mammary epithelial cells shed exosomes containing differentially expressed microRNA that regulate oncogenic networks

Project description:Breast (mammary) cancers in human (BC) and canine (CMT) patients share clinical, pathological, and molecular similarities that suggest dogs may be a useful translational model. Many cancers, including BC, shed exosomes that contain microRNAs (miRs) into the microenvironment and circulation, and these may represent biomarkers of metastasis and tumor phenotype. Three normal canine mammary epithelial cell (CMEC) cultures and 5 CMT cell lines were grown in serum-free media. Exosomes were isolated from culture media by ultracentrifugation then profiled qualitatively. CMEC and CMT cell lines shed round, “cup-shaped” exosomes approximately 150-200 nm by dynamic light scattering (DLS) and immunopositive for exosomal marker CD9 using Western blot. Exosomal small RNA was deep-sequenced on an Illumina HiSeq2500 sequencer and validated by qRT-PCR. Deep-sequencing averaged ~15 million reads/sample. 338 unique miRs were detected, with 145 having > ±1.5-fold difference between one or more CMT and CMEC samples. Gene ontology analysis revealed that the upregulated miRs in this exosomal population regulate a number of relevant oncogenic networks. Several miRNAs including miR-18a, miR-19a and miR-181a were predicted in silico to target the canine estrogen receptor (ESR1α). CMEC and CMT cells shed exosomes in vitro that contain differentially expressed miRs. CMT exosomal RNA expresses a limited number of miRs that are up-regulated relative to CMEC, and these are predicted to target biologically relevant hormone receptors and oncogenic pathways. These results may inform future studies of circulating exosomes and the utility of miRs as biomarkers of breast cancer in women and dogs.

2018-08-13 | GSE116881 | GEO

Transcription profiling of mouse embyonic fibroblasts from wild type and Elavl1knock-out embryos

Project description:Mouse embryonic fibroblasts (MEF) were isolated via enzymatic dissociation of 3 E14.5 embrya bearing epiblast specific inactivation of the murine Elavl1 locus as 3 littermate controls. Individual Fibroblast cultures were maintained in complete DMEM medium containing 10%FBS at 370C with 5%CO2. Cultures were passaged for 3 times and harvested for RNA isolation when they reached 60-70% conflunecy.

2009-03-15 | E-MEXP-1785 | biostudies-arrayexpress

REVERSIR platform for the tailored control of GalNAc-siRNA conjugate pharmacology

Project description:Primary mouse hepatocytes were treated with 1 nM TTR-siRNA and 10 nM scrambled or TTR-REVERSIR by in vitro free uptake for 24 h. RNA extracted with the Purelink RNA kit (ThermoFisher) was used for cDNA library preparation with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on the NextSeq500 desktop sequencer (Illumina), all according to manufacturers’ instructions. Raw RNA-seq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using fastq-mcf. Filtered reads were aligned to the Mus musculus genome (NCBIM37) using STAR with default parameters. Uniquely aligned reads were counted by featureCounts. Differential gene expression (DEG) analysis was performed by the R package DESeq2. Here, we report the rapid and potent reversal of GalNAc-siRNA-mediated RNAi activity in vivo with REVERSIR technology, which is based on short, synthetic high-affinity oligonucleotide complementary to the siRNA guide strand. The modular, sequence-specific nature of the REVERSIR platform has the potential to enhance the therapeutic profile of any long-acting GalNAc-siRNA conjugate to enable fine-tuned control of RNAi pharmacology

2018-05-02 | GSE110620 | GEO

Resveratrol-Induced Gene Expression Profiles in Human Prostate Cancer Cells

Project description:Cell Culture and Treatments The LNCaP cell line was obtained from American Type Culture Collection (Manassas, VA) and maintained in RPMI medium with 10% fetal bovine serum (CDT; Hyclone Laboratories, Logan, UT) and penicillin/streptomycin (Mediatech, Herndon, VA) in an environment of 95% air and 5% CO2 at 370C. Upon reaching 75% confluence, cells were treated with either DMSO control or purified resveratrol at several concentrations (LKT Laboratories, St. Paul, MN), dissolved in DMSO, and incubated for varying lengths of time. Final concentration of DMSO in media was 0.01%. Total RNA was prepared from cells using TRIzol (Invitrogen Life Technologies, Carlsbad, CA). An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs

2006-02-25 | GSE4299 | GEO

Resveratrol-Induced Gene Expression Profiles in Human Prostate Cancer Cells

2006-02-24 | E-GEOD-4299 | biostudies-arrayexpress

Sustained Activation of Non-canonical NF-kB Signalling Drives Glycolytic Reprogramming in Doxorubicin-resistant DLBCL

Project description:The transcriptomic profiles of two resistant (HT and OCI-LY3) and two sensitive (SUDHL5 and OCI-LY19) DLBCL cell lines before and after doxorubicin treatment were analysed by RNA-seq. To further investigate the molecular basis underlying the development of doxorubicin resistance, acquired doxorubicin-resistant cells (OCI-LY19R) were generated by periodically treating the parental doxorubicin-sensitive OCI-LY19 cells (OCI-LY19S) with increasing doses of doxorubicin over a prolonged period till its IC50 exceeded 200 nM. RNA-seq analysis was then performed using OCI-LY19R and OCI-LY19S cell lines to examine the transcriptomic changes following acquisition of doxorubicin resistance.

2022-12-01 | GSE215900 | GEO

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