Project description:Triple-negative breast cancer (TNBC) presents a significant challenge in women’s health due to its aggressive phenotype and the absence of targeted therapeutic options. β-Elemene, a sesquiterpene isolated from Curcuma wenyujin, has demonstrated clinical benefits against TNBC; however, its mechanisms of action, particularly with respect to the immune and metabolic tumor microenvironment, remain poorly characterized. In this study, we employed single-cell RNA sequencing and untargeted metabolomics to investigate how β-elemene reshapes the cellular and metabolic landscape of TNBC using a 4T1 orthotopic mouse model. Our findings are expected to provide the first comprehensive elucidation of β-elemene’s dual immunomodulatory and metabolic effects in TNBC, highlighting the potential of natural compounds to enhance antitumor immunity.
Project description:Multi-omics integration is highly effective for the holistic characterization of biological systems. However, current bioinformatics tools face limitations when incorporating metabolomics data, particularly for handling untargeted annotation, and when providing alternatives to predefined knowledge bases. Advanced algorithms required for multi-omics integration typically demand programming skills and statistical background, restricting their use to specialized users. Here, we introduce TurbOmics, a user-friendly web-based platform that enables researchers with diverse backgrounds to analyze metabolomics, proteomics, and transcriptomics data using an integrative workflow that includes advanced algorithms for multi-omics integration, while addressing key challenges associated with metabolomics data. The platform is available at https://proteomics.cnic.es/TurboPutative/TurbOmicsApp.html.
Project description:Human iPSCs and NSCs were engineered by AAVS1 and/or C13 safe-harbor TALENs which mediated targeted integration of various reporter genes at single or dual safe-harbor loci. Multiple clones of targeted human iPSCs were used to compare with parental untargeted NCRM5 iPSCs. Polyclonal targeted human NSCs were used to compare with their parental untargeted NCRM1NSCs or H9NSCs. Total RNA obtained from targeted human iPSCs or NSCs compared to untargeted control iPSCs or NSCs.
Project description:Our previous studies identified an increase in the levels of the metabolite 1,5-anhydroglucitol (1,5-AG) in the plasma of patients with newly diagnosed B-ALL by untargeted metabolomics detection.Except for the direct influence of 1,5-AG on leukemia cells, the effect on macrophages is still unclear.We reported the application of RNA sequencing to determine the transcriptional response of murine macrophage Raw 264.7 cells in response to stimulate with 1,5-AG conditions.
Project description:A novel one-dimensional on-line pH gradient-eluted strong cation exchange (SCX)-nano-ESI-MS/MS method was developed for protein identification and tested with mixture of six standard proteins, total lysate of HuH7 and N2a cells, as well as membrane fraction of N2a cells. This method utilized an on-line nano-flow SCX column in a nano-LC system coupled with a nano-electrospray high-resolution mass spectrometer. Protein digests were separated on a nano-flow SCX column with a pH gradient and directly introduced into a mass spectrometer through nano-electrospray ionization. SCXLC-MS/MS showed identification capability for higher proportion of basic peptides compared to RPLC-MS/MS method, especially for histidine-containing peptides. Our SCXLC-MS/MS method is an excellent alternative method to the RPLC-MS/MS method for analysis of standard proteins, total cell and membrane proteomes.