Evaluation of the sensitivity of two triple-negative breast cancer cell lines (HCC1806, HCC70) to a collection of dual mTOR and PI3K-like kinase (PIKK) inhibitors. Dataset 1 of 2: GR values.
Project description:We explored potential bypass mechanisms to PI3K/mTOR-directed therapy in KRAS mutant CRC models, utilizing genetically engineered mouse models (GEMM) to generate acquired resistance to the targeted dual PI3K/mTOR small molecule inhibitor PF-04691502. Transcriptomic analysis revealed a dynamic stem-like progenitor signature which was increased in the presence of drug pressure.
Project description:Phosphatidylinositol-3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway activation contributes to mantle cell lymphoma (MCL) pathogenesis and drug resistance. However, the use of mTOR inhibitors as single agents have shown limited clinical efficacy in relation with drug activation of feedback loops. Selective PI3K inhibition or dual PI3K/mTOR catalytic inhibition are different therapeutic approaches developed to achieve effective pathway blockage. Here, we evaluated the antitumor activity of a mTOR inhibitor, a pan-PI3K inhibitor and a dual PI3K/mTOR inhibitor in primary MCL cells. We found that dual PI3K/mTOR inhibitor modulated angiogenesis, tumor invasiveness and cytokine signaling compared to a mTOR inhibitor and a pan-PI3K inhibitor in MCL. We used microarrays to compare the effect of these three compounds in MCL and identified distinct classes of down-regulated genes modulated by each compound. Global RNA expression in primary cells from two MCL patients treated with a mTOR inhibitor, a pan-PI3K inhibitor and a dual PI3K/mTOR inhibitor for 8 hours
Project description:Treatment-naive HIV, HCV mono-/co-infected individuals with CD4+ T cell counts >300/uL were recruited, and the global gene expression profiles of CD4+ T cells were analyzed.Equal amount of CD4+ T cells isolated from each individual were pooled to form three replicative groups. Total RNA was isolated and analyzed by Affymetrix GeneChip Array. Differentially expressed genes were identified and further confirmed by qRT-PCR. To further understand the biological meanings underlying the transcriptome data the Gene Set Enrichment Analysis was used.
Project description:The aim of the project was to characterize changes in gene expression that are associated with induced autophagic flux. We engineered HeLa, HEK 293 and SH-SY5Y cell lines to express tandem-fluorecent LC3 (tf-LC3). The ratio of the red and green fluorophores indicated how much of the LC3 is in the acidic interior of lysosomes, which was a proxy measure for autophagic flux. RNA sequencing was performed for the cell lines at baseline and 1h, 15h and 30h after treatments. Additional untreated samples were also sequenced at some but not all time points. Autophagy was induced by amino acid starvation or mTOR inhibition (AZD8055).
Project description:Autophagy is a lysosomal-mediated catabolic process that degrades cytoplasmic components to help maintain cellular homeostasis and cell survival during exposure to stress. Lysine acetylation is a reversible post-translational modification that plays an important role in the regulation of diverse cellular processes. In this study, by using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics analysis, we explored lysine acetylomics in response to rapamycin-induced autophagy in HeLa cells. In total, we identified 1,808 acetylation sites on 944 proteins, among which, significant changes of lysine acetylation on 533 sites on 397 proteins were observed. The identified lysine acetylated proteins were mainly distributed in the cytoplasm, nucleus and mitochondria. FxK*, K*xxxxK and KxxxxK* were shown to be potential autophagy-related lysine acetylated motifs. Gene Ontology enrichment analysis showed that all of the significantly acetylated proteins were involved in diverse transcription-dependent and independent pathways. Further analysis found that acetylation was significantly enriched in three major metabolic processes. Moreover, Several protein complexes, such as ribosomes, RNA spliceosomes and the ubiquitin-proteasome complex, were also significantly acetylated. Moreover, as expected, significant changes of variations were observed in the acetylation levels of lysine acetylation in acetyltransferases and deacetylases, such as KAT7 and p300, were observed in response to rapamycin-induced autophagy. Taken together, our data are the first to these data reveal that the lysine acetylation associates acetylome associated with autophagy, and therefore to provide new insights into exploring the mechanism of autophagy.
Project description:In this study, Genome-wide transcriptomes of CD8+ T cells from HCV/HIV co-infected or mono-infected treatment-naive individuals were analyzed by using microarray assays. Pairwise comparisons were performed and differentially expressed genes were identified followed by quantitative real time PCR (qRT-PCR) validation. To identify the important functional categories, Directed Acyclic Graphs (DAG) from Web-based Gene SeT AnaLysis Toolkit (WebGestalt) was used to find out Gene Ontology (GO) categories with significantly enriched gene numbers. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were also obtained by using the similar methods in the same website.
Project description:In this study, treatment-naive HIV, HCV mono-/co-infected individuals with CD4+ T cell counts >300/?l were recruited and their global gene expression profiles were investigated. By gene set enrichment analysis (GSEA), we revealed that gene sets of cell cycle progression, innate immune response and some transcription factors in CD4+ T cells were affected mainly by HIV; while genes associated with extracellular matrix (ECM), Beta cell development and insulin synthesis and secretion were the major targets of HCV. For metabolic pathways, it was modulated by both viruses. Besides, for the first time, our data uncovered the importance of GPCR signaling pathway during HCV, HIV infections. These data for the first time offer genetic basis for HCV/HIV mono-/co- infections, which will facilitate the understanding of the interaction of HCV/HIV in vivo and how they subvert the human gene machinery at the individual cell type level.