Project description:The PPARD ligand response (agonist and inverse agonist) in monocyte derived macrophages from 3 healthy donors was assesed via RNAseq.
Project description:The transcriptome of serous ovarian cancer tumor associated macrophages was characterized. Additionally, their transcription response to PPARD agonists and inverse agonists in cell culture was analyzed.
Project description:Monocyte-derived dendritic cells (DC) and macrophages (MΦ) generated in vitro from the same individual blood donors were exposed to five different pathogens, and gene expression profiles were assessed by microarray analysis. Responses to Mycobacterium tuberculosis and to phylogenetically distinct protozoan (Leishmania major, L. donovani, Toxoplasma gondii) and helminth (Brugia malayi) parasites were examined, each of which produces chronic infections in humans yet vary considerably in the nature of the immune responses they trigger.<br><br>Note that the following pairs of files as imported from GEO are identical: GSM5135.txt and GSM5144.txt; GSM5137.txt and GSM5138.txt; GSM5143.txt and GSM5150.txt; GSM5148.txt and GSM5155.txt
Project description:To identify the functional non-coding RNAs in human DC development, we explored the gene expression profiles during DC development from peripheral monocytes. Using RNA-seq, we identified many annotated lncRNAs with markedly altered expressions during human DC differentiation and maturation. RNA samples from human peripheral blood monocytes and monocyte-derived DCs were collected. RNAs from 3 donors were pooled together to form monocyte sample or DC sample and then these two samples were subjected to RNA-seq and analysis.
Project description:About 40% of patients with myelodysplastic syndromes (MDS) present with a normal karyotype and they are facing different courses of disease. To advance the biological understanding and find molecular prognostic markers we performed a high resolution oligonucleotide array study of 107 MDS patients (FAB) with a normal karyotype. Recurrent hidden deletions overlapping with known cytogenetic aberrations or sites of known tumor associated genes were identified in 4q24 (TET2, 2x), 5q31.2 (2x), 7q22.1 (3x) and 21q22.12 (RUNX1, 2x). One patient with a 7q22.1 had an additional 5q31.2 deletion of the AML/MDS region; the smallest deletion identified so far and includes the putative tumor suppressor (ts) genes EGR1 and CTNNA1. One TET2 deletion was homozygous and one heterozygous, with a missense mutation in the remaining allele, further supporting its role as ts gene. Besides these recurrent alterations, additional individual imbalances were found in 34 cases; in total 42/107 (39%) cases had genomic imbalances, deletions were more frequent than gains. These patients had an inferior survival as compared with the rest of the patients (P=0.002). This study emphasizes the heterogeneity of MDS but points to interesting genes which may have diagnostic and prognostic impact. Array CGH experiment, MDS tumor cells vs. control DNA. Total of 107 tumors.
Project description:scRNAseq of monocytes from in vitro Trained immunity experiments stimulated by β-glucan (BG), uric acid (UA), muramyl dipeptide (MDP), oxidized low-density lipoprotein (oxLDL), or RPMI-Control, and respective samples restimulated with Lipopolysaccharide (LPS).
Project description:Background: Many tools used to analyze microarrays in different conditions have been described. However, the integration of the deregulated genes within coherent metabolic pathways is lacking. Currently no objective selection criterion, based on biological functions exists, to determine a threshold demonstrating that a gene is indeed differentially expressed. Methodology/Principal Findings: To improve transcriptomic analysis of microarrays, we propose a new statistical approach, which takes into account biological parameters. We present an iterative method to optimise the selection of differentially expressed gene in two experimental conditions. The stringency level of gene selection was associated simultaneously with the p-value of expression variation and the occurrence rate parameter, which is associated with the percentage of donors whose transcriptomic profile is similar. Our method intertwines stringency level settings, biological data and a knowledge database to highlight molecular interactions using networks and pathways. Analysis performed during iterations helped us select the optimal threshold required for the most pertinent selection of differently expressed genes. Conclusions/significance: We have applied this approach to the well documented mechanism of human macrophage response to lipopolysaccharide stimulation. For example, we thus verified that our method was able to determine with the highest degree of accuracy the best threshold for selecting genes, which are truly differentially expressed. Macrophages isolated from six heathy donnor was/or not stimulated. Paired data, i.e. LPS stimulated macrophages versus unstimulated macrophages from the same donor have been compared (eg, Donor1_LPS vs Donor1_NT; see processed data file linked below). The six comparaisons have been globaly analyse using two parameters, i.e. threshod and occurency, associated with a request of a database knowledge. Both parameters has been tune to define the best setting allowing to optimize the selection of differentially expressed genes
Project description:Tissue response following implantation determines the success of the healing process. This response is not only dependent on the chemical properties of the implant surface but also by the surface topography or its roughness. Although in vitro and in vivo studies show improved results with rough- and fluoride-modified implants, the mechanisms behind these findings are still unknown. Here, we have used a two step procedure to identify novel genes related to the early cell response of primary human osteoblasts to roughness and fluoride-modified titanium implants. 217 genes were identified by microarray analysis as response genes to roughness and 198 genes as response genes to fluoride. 11 of these identified genes have been related to bone and mineralization and were further investigated by real-time RT-PCR. After one day of culture, TLR3, ANKH, DCN, OC and RUNX2 were classified as responsive genes to roughness; DLX2 and TUFT1 as responsive genes to fluoride treatment. COLL-I, PTHLH, HES1, FST, ENPP1 and THRA as responsive genes to both, roughness and fluoride treatment. In conclusion, our strategy was useful for identifying novel genes that might be involved in the early response of osteoblasts to roughness and fluoride treatment of titanium implants. Tissue response following implantation determines the success of the healing process. This response is not only dependent on the chemical properties of the implant surface but also by the surface topography or its roughness. Although in vitro and in vivo studies show improved results with rough- and fluoride-modified implants, the mechanisms behind these findings are still unknown. Here, we have used a two step procedure to identify novel genes related to the early cell response of primary human osteoblasts to roughness and fluoride-modified titanium implants. 217 genes were identified by microarray analysis as response genes to roughness and 198 genes as response genes to fluoride. 11 of these identified genes have been related to bone and mineralization and were further investigated by real-time RT-PCR. After one day of culture, TLR3, ANKH, DCN, OC and RUNX2 were classified as responsive genes to roughness; DLX2 and TUFT1 as responsive genes to fluoride treatment. COLL-I, PTHLH, HES1, FST, ENPP1 and THRA as responsive genes to both, roughness and fluoride treatment. In conclusion, our strategy was useful for identifying novel genes that might be involved in the early response of osteoblasts to roughness and fluoride treatment of titanium implants. Human osteoblasts were cultured for 24 hours on titanium disks modified either with polished surfaces (P), grit-blasted surfaces (GB), or grit-blasted High Fluor treated surfaces (GB-HF). After 24 hours of culture RNA was isolated. 3 arrays were hybridized, one with the isolated RNA from cells cultured on titanium polished surfaces (P), one with the isolated RNA from cells cultured on titanium grit-blasted surfaces (GB) and one with the isolated RNA from cells cultured on titanium grit-blasted HF treated surfaces (GB-HF).
Project description:Unstimulated (M0), M1-polarized (GM-CSF, LPS, IFNγ-stimulated), and M2-polarized (M-CSF, IL-4-stimulated) canine blood-derived macrophages were generated in vitro and investigated for differences in their transcriptome to create a basis for future investigations upon the role of macrophage polarization in dogs, a species, which has emerging importance for translational research.