Project description:Lipidomic LC/MS of neurons and lipid droplets isolated from mouse. Extracted using MTBE and run on an Agilent 1290 Infinity II LC with MS acquisition on an Agilent QToF 6546.
Project description:Metabolic profiling of serum samples were performed on an Agilent 1290 infinity system (Agilent technologies, Santa-Clara, California, USA) coupled to an AB SCIEX Triple TOF 6600 System (AB SCIEX, Framingham, MA, USA) with an electrospray ion (ESI) source in both positive and negative ion modes. There were 30 differential metabolites under positive ion mode and 23 differential metabolites under negative ion mode, respectively.
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:Metastatic castration-resistant prostate cancer (mCRPC) is a lethal stage of disease for which current biomarkers have modest predictive power. Liquid biopsies have emerged as a minimally invasive approach but may be inaccessible to patients with limited access to clinical facilities. Here we evaluate small-volume dried capillary blood as a biospecimen for liquid biopsies that stabilizes biomarkers for use in decentralized clinical scenarios. We focus on exosomal microRNAs miR-1290 and miR-375 that in venous blood draws predict overall progression and survival in mCRPC. Using a combination of RNA sequencing (RNA-seq) and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in matched plasma and dried blood samples from 62 mCRPC patients, microRNA recovery was optimized to exceed 50% for abundant microRNAs (miR-16-5p) but was more variable (30–70%) for lower-abundance targets (miR-1290, miR-30a-5p, miR-375). For predictive biomarkers, RT-qPCR consistently measured miR-1290 but was insufficiently sensitive to consistently detect less abundant miR-375 which was selectively depleted from DBS samples relative to plasma. Normalization by abundant, stable miRs was necessary to reduce systematic bias for correlation between plasma and dried blood extracts. Kaplan-Meier analysis showed that high miR-1290/miR-16-5p ratios from dried blood predicted poor survival with a hazard ratio of 3.29 (95% CI = 1.64–6.62, p = 0.0013), performing comparably to PSA. These findings indicate that small-volume dried capillary blood may be a valid biospecimen for decentralized liquid biopsies applying microRNA profiling, and may enhance the flexibility of prognostic testing in mCRPC.
Project description:The extracted MRM peaks from LC-MS/MS experiments were integrated using Agilent MassHunter Quantitative Data Analysis software. Data extraction for GC-MS experiments was performed using Agilent MassHunter Profinder software.
Project description:Methanococcus maripaludis is a methanogenic archaeon. Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). The S40 and S2 strains were grown in 14N and 15N media with acetate separately. A biological replicate was made by switching the media. Mass spectrometry based quantitative proteomics were done on the mixtures to investigate the differences in expression patterns between S40 and S2. Keywords: isotope labeling mass spectrometry, quantitative proteomics