Project description:We report a 29-gene diagnostic signature, which distinguishes individuals with NSCLC from controls with non-malignant lung disease with 91% Sensitivity, 79% Specificity and a ROC AUC of 92%. Accuracy on an independent set of 18 NSCLC samples from the same location was 79%. Samples from an independent location including 12 stage 1 NSCLC and 15 controls, achieved an accuracy of 74%. A study of 18 paired samples taken pre and post surgery shows that the PBMC associated “cancer” signature is significantly reduced after tumor removal, supporting the hypothesis that the signature detected in pre-surgery samples is a response to the presence of the tumor.
Project description:Gene expression (by Affymetrix GeneChip Human 1.0ST) profiling of biopsy samples from recurrent, platinum resistant epithelial ovarian cancer patients before and after treatment of decitabine in combination with carboplatin. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in PBMC (14 paired samples), tumor (8 paired samples) and ascites (6 paired samples) (GSE31826).
Project description:Genome wide DNA methylation profiling of blood and biopsy samples from recurrent, platinum resistant epithelial ovarian cancer patients before and after treatment of decitabine in combination with carboplatin. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in PBMC (14 paired samples), tumor (8 paired samples) and ascites (6 paired samples).
Project description:CD14+ monocytes were separated from human peripheral blood and exposed to IL-4 for 12 or 72 hours then subjected to microarray analysis We used Affymetrix miRNA1.0 microarray to obtain global miRNA expression data of human monocytes, unstimulated and IL-4-stimulated differentiating macrophages.
Project description:Genome wide DNA methylation profiling of 12 paired monozygotic twin samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 12 paired monozygotic twin samples.
Project description:IL-2 mutant (F42K) is a variant of IL-2 that binds preferentially to the lower affinity IL-2Rβγ and has minimal binding to CD25, on Tregs, effector NK and T-cell subsets. Our recent study has uncovered that in contrast to WT IL-2, F42K did not efficiently induce the expansion of highly suppressive ICOS+ Tregs in PBMC from healthy controls and melanoma patients whereas it did promote the expansion of NK cells. We used microarray to study the differences of gene profiles induced by wild-type (WT) IL-2, F42K and IL-15 when treated on freshly isolated human peripheral blood mononuclear cells (PBMC) from healthy control.
Project description:Genome wide DNA methylation profiling of paired adjacent and hepatocellular samples and 8 non-diseased liver samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 12 paired adjacent and 12 hepatocellular samples.
Project description:Purpose: We analyzed RNA-seq from peripheral blood mononuclear cells (PBMC) in DMARDs-naïve RA patients and healthy subjects. Our goal was to evaluate the transcriptional profiles of ST2825-treated PBMC to identify its therapeutic potential. Methods: We analyzed bulk RNA-seq from peripheral blood mononuclear cells (PBMC) in DMARDs-naïve RA patients after stimulation with LPS and IL-1β, PBMC were treated with the MyD88 chemical inhibitor, ST2825. Collection of RNA was performed after 24 h of treatment and samples were sequenced to determine transcriptional changes and regulated processes in treated PBMC. Results: paired-end reads were mapped to the hg19 human genome assembly. RNA levels were normalized using DESeq. We identified 796 differentially expressed (DE) genes by 2-fold change (p<0.05) between RA patients and healthy subjects. Our analysis revealed 631 DE genes between DMARDs-naïve RA patients before and after ST2825 treatment. We identified 471 DE genes between LPS-stimulated RA PBMC and LPS-stimulated RA PBMC treated with ST2825. Conclusion: Our study provides comprehensive evidence supporting the potential application of the MyD88 inhibitor, ST2825, as a modulator of gene expression signtaures involved in pathogenic processes in PBMC from DMARDs-naïve RA patients. Our indepth analysis of RNA-seq data will serve as a valuable resource containing the inflammatory gene expression signatures by MyD88.
Project description:IL-2 mutant (F42K) is a variant of IL-2 that binds preferentially to the lower affinity IL-2Rβγ and has minimal binding to CD25, on Tregs, effector NK and T-cell subsets. Our recent study has uncovered that in contrast to WT IL-2, F42K did not efficiently induce the expansion of highly suppressive ICOS+ Tregs in PBMC from healthy controls and melanoma patients whereas it did promote the expansion of NK cells. We used microarray to study the differences of gene profiles induced by wild-type (WT) IL-2, F42K and IL-15 when treated on freshly isolated human peripheral blood mononuclear cells (PBMC) from healthy control. Human peripheral blood mononuclear cells (PBMC) were isolated from buffy coat and were stimulated with 0.4nM WT IL-2, F42K or IL-15 for 24 hr. Total RNA was extracted from each WT IL-2, F42K and IL-15 treated PBMCs and Sense RNA was reverse-transcribed via RT reaction into DNA and labeled with biotin using Affymetrix labeling kits and hybridized on human Affymetrix microarray chip.
Project description:Aim: To discovery biomarkers in JIA base on gene expression from RNA sequencing on PBMC Method: Paired-end Ilumina sequencing to capture gene expression of PBMC from JIA individuals and healthy controls Results:sample heterogeneity makes RNA sequencing on PBMC unsuitable as a first-step method for screening biomarker candidates in JIA
