Ontology highlight
ABSTRACT:
PROVIDER: PRJNA545487 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9161240.fastq.gz | Fastqsanger.gz | |||
| SRR9161250.fastq.gz | Fastqsanger.gz | |||
| SRR9161241.fastq.gz | Fastqsanger.gz | |||
| SRR9161251.fastq.gz | Fastqsanger.gz | |||
| SRR9161242.fastq.gz | Fastqsanger.gz |
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Project description:To enable successful SLC function deorphanization we aimed to select a minimal number of cell lines covering expression of as many SLCs as possible. Based on a publicly available RNA-Seq dataset of 675 cell lines (Klijn C. et al, Nat. Biotechnol. 2015) we selected a set of 6 adherent human cell lines (HCT 116, Huh 7, LS180, MDA MB 468, SK MEL 28, 1321N1) cumulatively covering expression (TPM>1) of about 80% of all human SLCs. These cell lines will be used to generate SLC-knockout and SLC-overexpressing single cell clones. Additionally, Jump-In T-REx HEK293 cells will be used for generating SLC-overexpression cell lines. In order to characterize the expressed proteome of these parental cell lines, we performed extensive proteomic profiling using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Mass spectra were acquired on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific) in data-dependent acquisition (DDA) mode. Instrument performance was monitored by a quality control routine using BSA- and HeLa digest standards. Data was analyzed using Thermo Proteome Discoverer 2.3 software. This data release consist of (1) RAW mass spectrometry data files generated by the instrument per fraction, (2) ProteomeDiscoverer result files containing all Peptide-Spectrum-Matches (PSMs), peptide and protein grouping, scoring and confidence values, as well as abundance values from label-free-quantitation (LFQ). As RESOLUTE will generate a significant number of protein-protein interaction data sets (AP-MS and BioID), the presented whole proteome profiling data set can serve as a reference core proteome data set, providing I) technical information on detected and expressed tryptic peptides and proteins; and II) provide valuable information on quantitative distribution of i.e. bait and prey proteins in the different cell lines. In conjunction with the other Omics data sets, like the previously published transcriptomics data, the characterization of the proteome will complement and enable valuable insight into the biological state of the investigated cell lines under default culturing conditions. Furthermore, members of the research community might apply advanced analyses with a focus out of the scope of the RESOLUTE project (e.g. PTM analysis).
2024-04-29 | PXD051747 | Pride
Project description:Background: Radiotherapy plays an important role in the multimodal treatment of breast cancer. The response of a breast tumour to radiation depends not only on its innate radiosensitivity but also on tumour repopulation by cells that have developed radioresistance. Development of effective cancer treatments will require further molecular dissection of the processes that contribute to resistance. Methods: Radioresistant cell lines were established by exposing MDA-MB-231, MCF-7 and ZR-751 parental cells to increasing weekly doses of radiation. The development of radioresistance was evaluated through proliferation and colony formation assays. Phenotypic characterisation included migration and invasion assays and immunohistochemistry. Intrinsic differences and changes in response to radiation between parental and radioresistant cells were investigated by whole-transcriptome gene expression analysis. Gene enrichment and pathway-focused analyses identified signalling networks differentially activated in radioresistant cells, which were confirmed by western blotting. Results: Proliferation and colony formation assays confirmed radioresistance. Radioresistant cells exhibited enhanced migration and invasion, with evidence of epithelial-to-mesenchymal-transition, and limited activation of DNA damage and apoptotic pathways in response to 2 Gy ionising radiation. Significantly, acquisition of radioresistance in MCF-7 and ZR-751 cell lines resulted in a loss of expression of both ERα and PgR and an increase in EGFR expression; based on gene analysis they changed subtype classification from their parental luminal A to HER2-overexpressing (MCF-7 RR) and normal-like (ZR-751 RR) subtypes, indicating the extent of phenotypic changes and cellular plasticity involved in this process. Whole-transcriptome gene expression analysis identified down-regulation of ER signalling genes and up-regulation of genes associated with PI3K, MAPK and WNT pathway activity in radioresistant cell lines derived from ER+ cells; this was confirmed by western blot, which showed increased p-AKT and p-ERK expression following radiation. Conclusions: This is the first study to date that extensively describes the development and characterisation of three novel radioresistant breast cancer cell lines through both genetic and phenotypic analysis. More changes were identified between parental cells and their radioresistant derivatives in the ER+ (MCF-7 and ZR-751) compared with the ER- cell line (MDA-MB-231) model; however, multiple and likely interrelated mechanisms were identified that may contribute to the development of acquired resistance to radiotherapy.
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