4T1 multi-omics characterization
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB36287 | ENA |
REPOSITORIES: ENA
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2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress
Project description:Whole Genome Sequencing of the murine breast cancer cell line 4T1 and of the murine melanoma cell line B16-ova was carried out with the aim of identifying somatic mutations. We also ran deep Mass Spectrometry proteomics analysis on the same cell lines, aiming to determine which somatic mutations carry over to the protein expression level. Further, we tested these cancer specific protein epitopes (putative neoantigens) for immunogenicity using mouse models. Finally, the putative neoantigens that showed good immunogenic potential were used in tumor growth control experiments with mice engrafted with the two tumor cell lines. In these experiments we tested whether cancer vaccines based on individual neoantigen peptides (MHC-I) restricted the growth of the tumor compared to adequate controls. The overall aim of the project is to validate the ability of our multi-omics/bioinformatics pipeline to identify and deliver neoantigens that can be used to suppress tumor growth. File names Sample names P10859_101_S1_L001_R1_001_BHKWV3CCXY 4T1_S1_L001_R1_001_BHKWV3CCXY P10859_101_S1_L001_R2_001_BHKWV3CCXY 4T1_S1_L001_R2_001_BHKWV3CCXY P10859_101_S1_L002_R1_001_BHKWV3CCXY 4T1_S1_L002_R1_001_BHKWV3CCXY P10859_101_S1_L002_R2_001_BHKWV3CCXY 4T1_S1_L002_R2_001_BHKWV3CCXY P10859_102_S2_L003_R1_001_BHKWV3CCXY B16-OVA_S2_L003_R1_001_BHKWV3CCXY P10859_102_S2_L003_R2_001_BHKWV3CCXY B16-OVA_S2_L003_R2_001_BHKWV3CCXY P10859_102_S2_L004_R1_001_BHKWV3CCXY B16-OVA_S2_L004_R1_001_BHKWV3CCXY P10859_102_S2_L004_R2_001_BHKWV3CCXY B16-OVA_S2_L004_R2_001_BHKWV3CCXY
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Project description:In this project, 4T1 parental cells (4T1/WT) were exposed to increasing concentrations of epirubicin (EPB) to establish a novel multi-drug resistant CSC-like breast cancer cell line (4T1/EPB). The ubiquitinated proteins were enriched from 4T1/WT or 4T1/EPB derived cell lysate using a-Al2O3-Vx3 nanoparticles to produce the covalently linked product UPs nanovaccine. Label-free LC-MS/MS mass spectrometry was used to detect the type and amount of enriched proteins of UPs from the 4T1/WT cells and the 4T1/EPB cells.
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Project description:Multi-omics molecular profiling was performed on post-radical prostatectomy material from a cohort of 132 patients with localized prostate adenocarcinoma. Unsupervised classification techniques were used to build a comprehensive classification of prostate tumours based on three molecular levels: DNA copy number, DNA methylation, and mRNA expression.
2018-06-24 | E-MTAB-6128 | biostudies-arrayexpress
Project description:Multi-omics molecular profiling was performed on post-radical prostatectomy material from a cohort of 132 patients with localized prostate adenocarcinoma. Unsupervised classification techniques were used to build a comprehensive classification of prostate tumours based on three molecular levels: DNA copy number, DNA methylation, and mRNA expression.
2018-06-24 | E-MTAB-6126 | biostudies-arrayexpress