Project description:Analyses of gene expression profiling in sinonasal sarcoma (SNS) harboring PAX3-MAML3 fusion gene or PAX3 rearrangement and other types of tumors without having such fusion or rearrangement. The results provide important information for further investigations of the PAX3-MAML3 fusion functions in SNS. Total RNA was obtained from FFPE tissues of 41 tumors including 8 SNS (6 with PAX3-MAML3 fusion and 2 with PAX3 rearrangement only) and 33 cases from other 10 different types of tumors. Gene expression profiling of fusion group including 8 SNA vs.non-fusion group including 33 control tumors were analyszed.
Project description:Analyses of gene expression profiling in Nodular fasciitis tumors harboring USP6 fusions Total RNA was obtained from FFPE tissues tumors and profiled using Illumina expression arrays
Project description:Listeria monocytogenes (Lm) kills up to 60% of infected newborns and adults >60 years of age but is asymptomic is most young adults. Monocytes are central to effective host defense against Lm. We hypothesize that age-dependent, pathway-specific differences in the ability of the monocyte to respond to Lm explain the increased risk of the newborn and older adult to severely suffer or die from Lm infection. To delineate age-dependent differences in innate responses that lead to differential infectious outcome, monocytes were isolated from cord blood (newborn) and peripheral blood (young and older adults) and infected with Lm. RNA was collected to determine age-dependent transcriptomic changes upon infection. Total RNA was isolated from purified human monocytes from 6 adult, 6 cord , 6 older adult blood donors that were infected with wild-type Listeria monocytogenes at a multiplicity of infected (MOI)=5 for 2 and 6 hr.
Project description:Human monocyte-derived dendritic cells (moDCs) have been used as an in vitro model for studying tolerance and immunity. However, the underlying metabolic states of tolerogenic (dexamethasone and vitamin D3-treated), immature and immunogenic (mature, LPS-treated) moDCs have not been completely characterized. Through transcriptomic analyses, we determined that tolerogenic moDCs exhibit augmented catabolic pathways with respect to oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO) and glycolysis. Functionally, tolerogenic moDCs showed the highest mitochondrial membrane potential, production of reactive oxygen species and superoxide, and increased mitochondrial spare respiratory capacity. Tolerogenic and mature moDCs manifested differential FAO gene expression with FAO activity being significantly higher in tolerogenic and immature moDCs than in mature. In addition, tolerogenic and mature moDCs demonstrated similar levels of glycolytic rate, but not glycolytic capacity and reserve, which were more pronounced in tolerogenic and immature moDCs. Finally, tolerogenic and immature moDCs, but not mature moDCs, showed high plasticity to compensate the intracellular ATP content after inhibition of different energetic metabolic pathways. Overall, tolerogenic moDCs exhibit a metabolic signature of increased, stable OXPHOS programing and high plasticity for metabolic adaptation. These findings provide a framework for future research of metabolic properties of human DCs. Total RNA of sixteen samples from four moDC types (tolerogenic, LPS-tolerogenic, immature and mature) were extracted by Trizol (Invitrogen) followed by a clean-up procedure using RNeasy Micro Kit (Qiagen). All RNA samples had an integrity number ≥9.6 assessed by Agilent Bioanalyzer. Total RNA samples were amplified using TargetAmp™ and the biotinilated cRNA was prepared by Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre). After the hybridization to the Illumina Human HT-12 v4 Beadchips for 17 h at 58°C, the arrays were washed, stained (Illumina Wash Protocol) and then scanned using BeadArray Scanner 500GX. Array data were extracted at the probe level without background correction using Illumina GenomeStudio software. These raw data were quantile normalized and log2 transformed. Technical replicates were obtained from the hybridization in duplicate of three samples. Pearson correlation analysis showed high correlation between the technical replicates (r>0.99). Differentially expressed genes (DEGs) were identified using Limma16 with Benjamini-Hochberg multiple testing correction (p<0.05). DEGs were further clustered into different groups according to the patterns of expression change among the different moDC types using STEM software17. The analysis was performed in R v.2.12.2 (http://www.R-project.org) with Bioconductor 2.12 (http://www.bioconductor.org) and enabled by Pipeline Pilot (www.accelrys.com).
Project description:Human abdominal adipose tissue was obtained with informed consent from a 33-year old Caucasian female (BMI = 32.96 Kg/m2) undergoing lipoaspiration. Adipose stromal cells (hASCs) were isolated and differentiated into adipocytes in vitro. Two technical replicates from 9 time points relative to induction of adipogenesis (day 0). Also, one sample from pre-adipocytes (day -2) grown without FGF.
Project description:We recently reported the scalable in vitro production of functional stem cell-derived β cells. Here we extend this approach to generate SC-β cells from Type 1 diabetic patients (T1D), a cell type that is destroyed during disease progression and has not been possible to extensively study. These cells express β cell markers, respond to glucose both in vitro and in vivo, prevent alloxan-induced diabetes in mice, and respond to anti-diabetic drugs. Furthermore, we use an in vitro disease model to demonstrate the cells respond to different forms of β cell stress. Using these assays, we find no major differences in T1D SC-β cells compared to SC-β cells derived from non-diabetic patients (ND). These results show that T1D SC-β cells can be used for the treatment of diabetes, drug screening, and the study of β cell biology. Differentiated cells were sorted and processed for RNA isolation using the MARIS protocol published previously (PMID: 24516164.) Human induced pluripotent stem cell (hiPSC) line were differentiated into SC-beta cells or dysfunctional, polyhormonal cells (PH). Four biological replicates were assessed with differentiation to both SC-beta and PH cells. Those data were normalized together with and compared to existing, previously published data from Hrvatin et al. (PMID: 24516164) and Pagliuca et al. (PMID: 25303535) from human islet-derived insulin+ cells, undifferentiated HUES8 hES cells, SC-beta cells derived from HUES8 and PH cells derived from HUES8 according to previously published protocols.
Project description:Evaluation of microRNAs that are downstream of apelin/APJ signaling in the pulmonary artery endothelial cells. Triplicates per group, subjected to: 1) control siRNA, 2) apelin siRNA, 3) APJ siRNA, 4) apelin + APJ siRNA
Project description:Study investigating the role of miRNAs in breast cancer detection miRNA extracted from plasma on 20 breast cancer patients, 20 controls, 20 post-resection breast cancer patients and 10 lung/colorectal cancer patients, miRNA quanitification using Illumina microarray
Project description:To seek effects of inflammatory status and 5-aminosalicylic acid (5-ASA, mesalazine) exposure ex vivo on mRNA levels within rectal mucosal biopsies from patients with ulcerative colitis. A total of 12 biopsies were analysed, 3 biological replicates in each of 4 categories (inflamed with or without 5-ASA, non-inflamed with or without 5-ASA).