Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bromodomain-containing protein BRPF1 as a therapeutic target for metastatic ovarian cancer

ABSTRACT: Total RNA was extracted using TRIzol from PEO4 and OVCAR-3 cells treated for 72 hours with 10uM GSK6853 or DMSO as a control. In case of BRPF1 silencing experiment, RNA extraction was performed from cells transfected with BRPF-targeting siRNA or nontarget (scramble) siRNA 96 hours post-transfection using TRIzol and Zymo RNA Clean & Concentrator-5 columns. Indexed libraries were prepared starting from 1000 ng of total RNA according to Illumina Stranded Total RNA prep Ligation with Ribo-Zero Plus kit. Final libraries were sequenced at a concentration of 0,6 pM/lane on the Illumina Novaseq 6000 using S4 flowcell and v1.5 reagents. The current study was focused on the investigation of molecular mechanisms underlying the antiproliferative effect of BRPF1 inhibition or silencing in ovarian cancer. To this end, transcriptome changes induced by GSK6853 treatment in chemotherapy-resistant PEO4 and OVCAR-3 cells and BRPF1 silencing in OVCAR-3 cells were analysed.

INSTRUMENT(S): server unisa, Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Domenico Memoli

PROVIDER: E-MTAB-13663 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Extensive Differential DNA Methylation in Bovine Tuberculosis Skin Test Positive and Skin Test Negative Cattle

Project description:Bovine tuberculosis (bTB), caused by Mycobacterium bovis, represents a significant issue for the global agriculture industry as well as for human health. Epigenetic modifications can alter the course of the immune response and differentially methylated regions (DMRs) could contribute to the failure of current generation tests to detect all TB-infected cattle. Whole Genome Bisulphite Sequencing (WGBS) was used to profile DNA methylation levels from peripheral blood of cattle naturally infected with M. bovis (positive for the single intradermal comparative tuberculin test (SICTT) and/or the interferon-γ release assay (IGRA) compared to negative controls [n=8/group, total of 16 WGBS libraries]. Although overall methylation profiles were similar across the genome, 224 DMRs and 159 Differentially Methylated Promoter Gene (DMPGs) were identified between groups with an excess of hypermethylated sites in bTB+ infected cattle (threshold >15% differential methylation). Genes located within these DMRs included the Interleukin 1 receptor (IL1R1) and MHC related genes (BOLA and BOLA-DQB) which may influence effective immunity. KEGG pathway analysis identified enrichment of genes involved in Calcium and MAPK signalling, as well as metabolism pathways. Analysis of DMRs in a subset of SICTT- cattle (n=4 group) which were IGRA+, and thereby potentially represent a risk for disease recurrence on farms, showed differential methylation of genes including Interleukin 10 Receptor, alpha (IL10RA), Interleukin 17F (IL17F) and host defence peptides (DEFB and BDEF109). This study has identified a number of immune gene loci at which differential methylation could impact on the host immune response and the ability of cattle to clear infection. Differential methylation of immune gene loci is an informative avenue to improve our understanding of the regulation of host immunity as well as the role of methylation on diagnostic test performance.

2024-06-26 | E-MTAB-13487 | biostudies-arrayexpress

RNA-Seq of human epithelial follicular cell line Nthy-ori 3-1 treated for 24 hours with benzo[a]pyrene or DMSO solvent control and mouse embryonic stem cell-derived thyroid follicles treated for 24 hours with DMSO solvent control.

Project description:The human epithelial follicular cell line Nthy-ori 3-1 was treated with 10 uM or 1 uM benzo[a]pyrene in 0.5% DMSO or with 0.5% DMSO only for 24 hours. Thyroid follicles were differentiated from a recombinant mESC line (A2LoxNkx2-1-Pax8) and treated with 0.5% DMSO for 24 hours. For Nthy-ori 3-1 samples, total RNA was extracted and used to prepare combined mRNA/miRNA libraries, poly(A) libraries and small RNA libraries. For thyroid follicles samples, total RNA was extracted and used to prepare combined mRNA/miRNA libraries.

2022-12-14 | E-MTAB-12078 | biostudies-arrayexpress

RNA-seq from human peripheral blood isolated and CRISPR/Cas9-mediated BCL11B depleted alpha-beta CD8+ T cells and corresponding not transfected (nt) and mock (mock gRNA transfected) controls.

Project description:B-cell lymphoma/leukemia (BCL) 11B represents a major regulator of vital processes in post-thymic lymphocytes as well as of lymphocyte differentiation by blocking NK cell and promoting T cell development and is thus considered a \\"guardian of T cell fate\\". Interestingly, on the one hand, NK cell maturation correlates with increased expression of BCL11B, on the other hand, native or induced T cell populations characterized by multiple NK cell features showed reduced BCL11B expression. Both NK cells or T cells display unique and desired features for cellular therapies. NK cells are able to efficiently lyse cancerous or virally infected cells but can only be poorly expanded in vitro. In contrast, T cell cytotoxic activity is limited by T cell receptor (TCR) but in vitro expansion is easily achievable. We show that from buffy coats of healthy donors isolated and CRISPR/Cas9-mediated BCL11B knock-out CD8+ T cells stimulated with IL-15 acquired remarkable innate characteristics and combine spontaneous and antibody-dependent NK cell cytotoxicity with T cell capability for rapid in vitro expansion. The observed features of the induced innate CD8+ (iiT8) cells make them an interesting and promising tool for cellular therapy.

2022-12-07 | E-MTAB-12064 | biostudies-arrayexpress

RNAseq analysis of tumours from GEMMS animals to determine the effect of different aPDL1 combinations on lung tumours in situ

Project description:This study aims to identify combination treatments capable of inducing improved IO responses in lung tumours and thus, help guide decisions on the next combination arms for the HUDSON trial (post-IO). For that purpose, a lung tumour GEMM model was treated with either vehicle, PD-L1, ATR, ATR/PD-L1; Cisplatin/PD-L1/Ctla4 or VEGFR/PD-L1 and tumours collected for transcriptional profiling.

2024-01-29 | E-MTAB-13704 | biostudies-arrayexpress

scRNA-seq of mouse immune compartment from tumours treated with ATRi ceralasertib (AZD6738)

Project description:Mice implanted with CT26 tumour cells were divided into two experimental groups (vehicle and ceralasertib) with the aim of assessing changes in intra-tumour T cells (CD3+) after 7 days of treatment with ceralasertib, and 7 days off. At the end of the treatment course, tumour tissue was isolated, chopped and enzymatically digested to generate a single-cell suspension. Cells sorted on CD3 were then processed using Chromium Next GEM Single Cell 5' Kit v2.

2024-02-05 | E-MTAB-13713 | biostudies-arrayexpress

Essential gene screening identifies the Bromodomain-Containing Protein BRPF1 as a new therapeutic target for endocrine therapy-resistant breast cancer

Project description:Exploring epigenetic gene essentiality identifying key regulators of cell survival represents a promising way to exploit new targets to overcome resistance to current pharmacological regimens. In breast cancer (BC), endocrine therapy (ET) resistance arises from aberrant Estrogen Receptor alpha (ERα) signaling and targeting cancer cell vulnerability within the ERα pathway represents a rationale for development of effective new drugs against this disease. By combining bioinformatics analysis of genome-wide ‘drop-out’ screenings and siRNA-mediated gene knock-down (kd) we identified a set of essential genes that includes, as the most effective, the bromodomain containing protein BRPF1. BRPF1 belongs to a family of epigenetic readers acting as chromatin remodelers to control gene transcription. To gather mechanistic insight into the role of this epienzyme in BC, we applied chromatin and transcriptome profiling, gene ablation and specific pharmacological inhibition followed by cellular and functional assays. Experimental evidences indicate that BRPF1 associates with ERa in MCF-7 cells chromatin and its blockade inhibits cell cycle progression, reduces cell proliferation and mediates transcriptome changes through modulation of chromatin accessibility. This results in a widespread inhibition of ER-dependent hormonal signaling obtained by ERa gene silencing in AE-sensitive and -resistant BC cells and pre-clinical patient-derived models (PDO). The characterization of functional interplays between ERα and BRPF1 revealed a new master regulator of BC survival, providing a rationale for a BRPF1 targeted cancer diagnosis and highlighting a new therapeutic vulnerability for the treatment of these aggressive tumors.

2024-10-03 | E-MTAB-13885 | biostudies-arrayexpress

RNASeq analysis of solid tumours from CT26 syngeneic mice to study the role of T-cells and tumour intrinsic pathways (STING/IFN) for driving ceralasertib (AZD6738) efficacy

Project description:Understanding MoA of ceralasertib (AZD6738) in driving efficacy through immune regulation via T-cells and tumour intrinsic pathways (STING/IFN) for AZD6738 driven efficacy.

2024-01-29 | E-MTAB-13703 | biostudies-arrayexpress

Capture Hi-C (HiCap) experiments performed on LUHMES cell line differentiated in three (D3) and six days (D6). We fragmented the genome using DpnII. HiCap experiments at each time point (D1, D3 and D6) are performed in two replicates

Project description:LUHMES cells are non-tumorigenic model of human dopaminergic neurons. Their physiology and phenotypic changes upon differentiation can provide clues into the pathology of neurological diseases such as dyslexia, autism, schizophrenia.

2024-01-14 | E-MTAB-13665 | biostudies-arrayexpress

RNA-seq mouse intestines from PN, Germ-free, SPF and Antibiotics-treated mice

Project description:We hypothesized that there were genes involved in the maintenance of intestinal tolerance to commensal bacteria. These genes should meet the following criteria: expressed in intestines, upregulated in the presence of commensal bacteria and downregulated in absence of microbes. To find these genes, we collected small intestines from postnatal mice that neither affected by the bacteria nor by the food, adult mice bred in germ-free or specific pathogen-free conditions, and adult SPF mice treated with antibiotics. We therefore performed bulk RNA sequencing using these cells.

2023-01-01 | E-MTAB-12215 | biostudies-arrayexpress

Effect of 20-Hete and dietary restriction on murine kidneys

Project description:Transcriptomic dataset of 15 murine kidneys of 14-week-old male C57Bl6 mice. Mice were divided into 3 treatment groups four weeks prior to nephrectomy and 5 mice had ad libitum (AL) access to food and water, while another 10 mice received 30% food restriction (CR). Calorically restricted mice either received intraperitoneal supplementation of 20-HETE (HETE) or vehicle (Veh, EtOH in sodiumchloride 0.9%) for 8 days on a daily basis prior to nephrectomy. Ad libitum fed mice received vehicle injections for 8 days on a daily basis prior to nephrectomy.

2022-05-10 | E-MTAB-11428 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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