Project description:Metastasis accounts for almost 90% of breast cancer-related fatalities, making it frequent malignancy and the main reason of tumor mortality globally among women. A key player in breast cancer is the histone demethylase lysine-specific demethylase 1 (LSD1). We used LSD1 knockdown MCF7 and T47D cell exosomes to treat breast cancer cells for greatly increasing the invasion and migration of breast cancer cells for evaluating the impact of LSD1 on breast cancer invasion and migration. miR-1290 expression was downregulated in LSD1 knockdown MCF7 exosomes. Furthermore, miR-1290 could control NAT1 expression by looking through the database of miR-1290 target genes. These data provide fresh insights into the biology of breast cancer therapy by demonstrating how the epigenetic factor LSD1 stimulates the breast cancer cells’ invasion and migration via controlling exosomal miRNA.
Project description:Comparative genomic hybridization analysis for detection of copy number variation for cancer genes in breast cancer mestastatic brain tumors DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled reference Agilent (female) reference DNA
Project description:Probe electrospray ionization mass spectrometry (PESI-MS) is an ambient ionization-based mass spectrometry method that surpasses the original electrospray ionization technique in features such as the rapidity of analysis, simplicity of the equipment and procedure, and lower cost. This study found that the PESI-MS system with machine learning has the potential to establish a lipid-based diagnosis of breast cancer with higher accuracy, using a simpler approach. Rapid mass spectrometry for breast cancer.
Project description:Lipid composition in cell membrane is closely associated with cell characteristics. Here, matrix-assisted laser desorption/ionization- Fourier transform ion cyclotron resonance mass spectrometry was employed to in situ determine membrane components of human mammary epithelial cells (MCF-10 A) and six different breast cancer cell lines (i.e., BT-20, MCF-7, SK-BR-3, MDA-MB-231, MDA-MB-157, and MDA-MB-361) without any lipid extraction and separation. Partial least-square discriminant analysis indicated that changes in the levels of these membrane lipids were closely correlated with the types of breast cell lines. Elevated levels of polyunsaturated lipids in MCF-10 A cells relative to six breast cancer cells and in BT-20 cells relative to other breast cancer cell lines were detected. The Western blotting assays indicated that the expression of five lipogenesis-related enzymes (i.e., fatty acid synthase 1(FASN1), stearoyl-CoA desaturase 1 (SCD1), stearoyl-CoA desaturase 5 (SCD5), choline kinase α (CKα), and sphingomyelin synthase 1) was associated with the types of the breast cells, and that the SCD1 level in MCF-7 cells was significantly increased relative to other breast cell lines. Our findings suggest that elevated expression levels of FASN1, SCD1, SCD5, and CKα may closely correlated with enhanced levels of saturated and monounsaturated lipids in breast cancer cell lines.
Project description:Mice were euthanized at 20 weeks of age, and various tissues were obtained for metabolomic analyses including whole bone, bone marrow, and isolated cortical bone. Metabolites were extracted and underwent LC-MS analysis using an Agilent LC 1290 coupled to an Agilent 6538 QTOF
Project description:Purpose: We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer. This report makes these data publicly available in raw and processed forms, as a resource to the community. Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens. Experimental design: Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast). Cases and controls were rigorously paired to avoid bias. Results: In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate â¤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively. Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue. Conclusions and clinical relevance: These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for MRM-MS. The availability of these datasets will contribute positively to clinical proteomics. Custom Agilent 44K whole mouse genome expression oligonucleotide microarrays were used to profile breast tumors from three Her2/Neu mice compared to normal breast epithelium from two control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice. All samples were laser-capture microdissected and total RNA isolated and amplified prior to hybridization against a reference pool of normal adult mouse tissues.
Project description:In this project we used the strain E. coli BW25113 ΔfrmA::frt (Δ(araD-araB)567, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, hsdR514, ΔfrmA(::frt)) from the Keio collection (Baba et al. 2006). The plasmid {pSEVA424_mdh-das} (Low-copy-number, lacIq/Ptrc promoter, RK2 ori, SmR) from Silva-Rocha et al. 2013 was integrated in the strain to express mdh (Methanol dehydrogenase) and das (Dihydroxyacetone synthase) respectively from Acinetobacter gerneri and Pichia angusta. In this experiment, we inoculated 50 mL of M9 minimal medium with 15 mM xylose and with or without 0.15 M methanol, in baffled flasks at 30°C, 150 rpm. At D600=1 and D600=2, 12mL of each culture were centrifuged 1’30 at 14000 rpm before discarding the supernatant and freezing the pellets for 15 sec in liquid nitrogen. RNA extraction were carried out using a RNeasy Midi Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol and the transcriptomic experiments were run at the GeT-Biopuces Platform (Toulouse, France). Prior to the experiment, the quality of the RNA extracted was analyzed by Nanodrop and Cell Bio Analyser (Agilent Technologies, California, USA). The labelling with Cy3, hybridation on the Agilent chip and wash were carried out accordingly to the Agilent protocol and kits. We used the scanner NimbleGen MS 200 (Roche, Bâle, Suisse) with the following parameters: autogain, 5micros resolution, 532nm scan. The Agilent Feature Extraction software was used to extract the data.
Project description:Plasma and tissue from breast cancer patients are valuable for diagnostic/prognostic purposes and are accessible by multiple mass spectrometry (MS) tools. Liquid chromatography-mass spectrometry (LC-MS) and ambient mass spectrometry imaging (MSI) were shown to be robust and reproducible technologies for breast cancer diagnosis. Here, we investigated whether there is a correspondence between lipid cancer features observed by desorption electrospray ionization (DESI)-MSI in tissue and those detected by LC-MS in plasma samples. The study included 28 tissues and 20 plasma samples from 24 women with ductal breast carcinomas of both special and no special type (NST) along with 22 plasma samples from healthy women. The comparison of plasma and tissue lipid signatures revealed that each one of the studied matrices (i.e., blood or tumor) has its own specific molecular signature and the full interposition of their discriminant ions is not possible. This comparison also revealed that the molecular indicators of tissue injury, characteristic of the breast cancer tissue profile obtained by DESI-MSI, do not persist as cancer discriminators in peripheral blood even though some of them could be found in plasma samples.
Project description:Mice were euthanized at 20 weeks of age, and humeri were obtained for metabolomic analyses. Once obtained, marrow was flushed in some humeri resulting in 3 sample types including whole bone, bone marrow, and isolated cortical bone. Metabolites were extracted and underwent LC-MS analysis using an Agilent LC 1290 coupled to an Agilent 6538 QTOF