Project description:We derived gene set signature for GSEA investigation study from primary cell culture derived from healthy patients. Cells were exposed or not to cytokine for 24H before RNA collection and microarray analysis
Project description:Natural functions of the amyloid beta (Aβ) peptide are incompletely understood. We studied the effects nanomolar concentrations of Aβ in combination with known pro-inflammatory cytokines on primary human astrocytes, a cell type increasingly implicated in neurodegeneration. RNA-seq was performed to profile changes in astrocyte transcriptomes in response to high and low concentration Aβ alone, as well as low concentration Aβ and/or the cytokines C1q, TNF-α and IL-1α. Experiments were performed in triplicate within cells from one donor/supplier, and in triplicate using cells from three different donors/suppliers (to identify conserved biological responses).
Project description:The clinical features of psoriasis, characterized by sharply demarcated scaly erythematous plaques, are typically so distinctive that a diagnosis can easily be made on these grounds alone. However, there is great variability in treatment response between individual patients, and this may reflect heterogeneity of inflammatory networks driving the disease. In this study, whole-genome transcriptional profiling was used to characterize inflammatory and cytokine networks in 62 lesional skin samples obtained from patients with stable chronic plaque psoriasis. We were able to stratify lesions according to their inflammatory gene expression signatures, identifying those associated with strong (37% of patients), moderate (39%) and weak inflammatory infiltrates (24%). Additionally, we identified differences in cytokine signatures with heightened cytokine-response patterns in one sub-group of lesions (IL-13-strong; 50%) and attenuation of these patterns in a second sub-group (IL-13-weak; 50%). These sub-groups correlated with the composition of the inflammatory infiltrate, but were only weakly associated with increased risk allele frequency at some psoriasis susceptibility loci (e.g., REL, TRAF3IP2 and NOS2). Our findings highlight variable points in the inflammatory and cytokine networks known to drive chronic plaque psoriasis. Such heterogeneous aspects may shape clinical course and treatment responses, and can provide avenues for development of personalized treatments. We used Affymetrix microarrays to evaluate genome-wide expression in primary human keratinocytes exposed to cytokines. Cytokine activity signatures were used to interpret the shifts in gene expression that occur in psoriasis plaques relative to normal uninvolved skin. Primary keratinocytes from three donors (subjects 1, 2, and 3) were obtained and were either untreated (control) or exposed to cytokines (IL-4, IL-13, IFN-alpha, IFN-gamma and TNF). For the IL17A samples, primary keratinocytes were obtained from six donors, with cells derived from three donors treated with IL-17A and cells derived from the other three donors left untreated (i.e., unpaired control samples).
Project description:To determine the different gene signatures between primary tumor and tumor-derived exosomes, we have employed RNA-sequencing as a discovery platform to identify gene signatures of tumor-derived exosomes, taking the original tumors as a control. We subcutaneously inoculated C57BL/6 mice with Lewis lung carcinoma (LLC). Three weeks later, tumor tissues were cut and tumor-derived exosomes were isolated as described in the "treatment protocol". Then, both exosomal RNA and tumor RNA were extracted and sequenced. From sequencing, we found that exosomal RNAs showed quite different transcript profiles from tumor RNAs. Examination of different gene signatures between primary tumor and tumor-derived exosomes. 2 replicates each.