Comparison of transcription profile of allogenic immune response generated in MLR and Humanzied mouse model
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ABSTRACT: This experiment was carried out to demonstrate the efficacy of our novel humanized mouse model for identifying the best potential donor for the recipient. We performed a transcriptome analysis comparing the allogeneic immune response in MLR and the Hu-NSG-PBMC model. We identified several clinically relevant markers of graft rejection, such as GZMB, PRF1, and IL2, were significantly up regulated in one of the related donors only observed in the allogeneic response generated in the humanized mouse model.
Project description:MicroRNAs are small non-coding RNA molecules that regulate the post-transcriptional expression of target genes. In addition to being involved in many biologic processes including development, cell differentiation, proliferation, and apoptosis, microRNAs are important regulators in innate and adaptive immune responses. Distinct sets of expressed miRNAs are found in different cell types and tissues and aberrant expression of microRNAs is associated with many disease states. MicroRNA expression was examined in a model of heterotopic heart transplantation by microarray analyses and a unique profile was detected in rejecting allogeneic transplants (BALB/C to C57BL/6) as compared to syngeneic transplants (C57BL/6 to C57BL/6). The microRNA miR-182 was significantly increased in rejecting cardiac allografts and in mononuclear cells that infiltrate the grafts. Forkhead Box (FOX) proteins are a family of important transcription factors and FOXO1 is a target of miR-182. As miR-182 increases after transplant, there is a concomitant post-transcriptional decrease in FOXO1 expression in heart allografts that is localized to both the cardiomyocytes and CD3+ T cells. The microRNA miR-182 is significantly increased in both PBMC and plasma during graft rejection suggesting potential as a biomarker of graft status. Our results identify microRNAs that may regulate alloimmune responses and graft outcomes. In total 14 microRNA microarrays data. For heart graft: each sample column corresponds to the expression profile of 3 pooled syngeneic or 3 pooled allogeneic heart grafts or 3 pooled normal heart. For graft infiltrating lymphocytes (GILs): each sample column corresponds to the expression profile of 3 pooled syngeneic or 3 pooled allogeneic GILs or 3 pooled normal PBMC.
Project description:Sarcoidosis and tuberculosis share similarities in clinical manifestations and histopathological features. We aimed to identify the microRNA (miRNA) profiles of the lymph nodes of individuals with sarcoidosis and of those with tuberculous lymphadenitis to investigate the value of miRNAs in the differential diagnosis of sarcoidosis and tuberculous lymphadenitis. The miRNA profiles of the lymph nodes of individuals with sarcoidosis, those with tuberculous lymphadenitis (TBLN) and controls were detected by miRNA microarray analysis in the age- and sex-matched development group of the controls (n=3), patients with TBLN (n=3) and patients with sarcoidosis (n=3), and the results were validated by quantitative real-time polymerase chain reaction in the validation group of the controls (n=30), TBLN (n=30) and patients with sarcoidosis (n=31). The relationship between miRNA expression and the clinical parameters of sarcoidosis was analyzed.
Project description:LMO2 overexpressing transgenic mouse models suggest an accumulation of immature T-cell progenitors in the thymus as main pre-leukemic event. The effects of LMO2 overexpression on human T-cell development in vivo, however, are unknown. Here we report studies of a humanized mouse model transplanted with LMO2 transduced human hematopoietic stem and progenitor cells. The effects of LMO2 overexpression were confined to the T-cell lineage although initially multipotent cells were transduced. Three effects of LMO2 on human T-cell development were observed: 1) a block at the DN/ISP stage, 2) an accumulation of CD4+CD8+ double positive CD3- cells and 3) an altered CD8/CD4 ratio with enhanced peripheral T lymphocytes Single stranded cDNA was synthesized from 1000 pg total RNA using the Ovation Pico WTA System V2 Module (NuGEN Technologies Inc, Leek, The Netherlands) in combination with the Encore Biotin Module (NuGEN Technologies Inc) according to the instructions of the manufacturer. Biotin labeling and fragmentation was performed and fragmented cDNA was hybridized onto Affymetrix Gene Atlas human U219 arrays.
Project description:The goal is to identify new molecules implicated in tolerance, to determine the implication of these molecules in immune responses to transplantation by gene expression comparison of 27,088 individual rat genes between tolerated kidney allotransplant and syngeneic kidney transplant. In this study 27,088 individual rat genes expression from total mRNA of 3 tolerated allogeneic kidney transplants by anti-classII, were compared to 3 syngeneic kidney transplants at day 100 post transplantation.
Project description:This experiment focused on the miRNA expressions within the tissues specific niches of mice afflicted with melanoma, compared to littermates without malignancy. BRafCA/ PtenloxP/ Tyr::CreERT2 or genetically matched littermates without Cre recombinase were treated with 2µl 4-hydroxytamoxifen (5mM), every other day, for on days 0, 2, and 4, on the shaved right flank of the abdomen of the animal. Mice slowly grow melanoma at the treated site, and some metastases distal to treatment location (eg. Ear or opposite side of abdomen). Endpoint criteria was designated as a Samples were taken when tumors reached 1.5mm diameter. Total RNA was isolated from tumors or tamoxifen treated healthy skin, skin adjacent to the treatment site, or the ear ( representing a metastatic site). Total RNA was prepared with FLAG-TAG kit and miRNA microarray 4.0 was performed.
Project description:In order to assess the impact of PTCy on T cells in our humanized mouse GVHD model, we performed single cell RNA-sequencing on human T cells isolated from spleen of control and PTCy-treated mice on day 6 after hPBMC injection
Project description:Peripheral blood samples of patients with acute myocardial infarction were matched with those of control patients to identify possible differences in corresponding gene expression profiles. The controls were matched to cases based on gender, age, status of diabetes mellitus and smoking status. Six months cardiovascular survival status of the cases was used to identify two distinct subgroups among the cases. Linear models for microarray data (M-bM-^@M-^XlimmaM-bM-^@M-^Y) were employed to identify differential gene expression. Shrunken centroids technique helped in identifying the subsets of differentially expressed genes with predictive properties in independent samples. Predictive properties were evaluated using bootstrap sampling. Using the limma modeling with the log-fold change threshold of one (clinical significance) and StoreyM-bM-^@M-^Ys q-value approach (statistical significance), sixty transcripts were found to be both clinically and statistically differentially expressed among the cases not surviving the follow-up period relative to controls, while no such transcripts were observed among other surviving cases. The two subgroups of cases exhibited fourteen differentially expressed transcripts. Predictive modeling indicated sixteen out of sixty transcripts to best discriminate between the controls and cases who died during the follow-up period from cardiovascular causes, while for the surviving cases the already non-significant set of transcripts could not be further reduced. Eleven out of fourteen transcripts were found to best discriminate between the two groups of cases using shrunken centroids. The study identified genes, which were differentially expressed during the acute myocardial infarction, including those associated with short-term fatality of the cases. The genome-wide study used matched case-control design, with 97 samples of 90 patients in three disease groups. Matched control samples were used and several (7) technical replicates were performed.
Project description:Background: Exercising is know to have an effect on exercising skeletal muscle, but unkown is the effect on non-exercising skeletal muscle. Gene expression changes in the non-exercising skeletal muscle would point to a signalling role of skeletal muscle 9 healthy middle-aged men performed 1 hour of one-legged exercise, before and afterwards muscle biopsies were taken from both legs. Skeletal muscle biopsies were analyzed by microarray.
Project description:Rationale: Obstructive sleep apnea (OSA) has been associated with a number of chronic disorders that may improve with effective therapy. However, the molecular pathways affected by continuous positive airway pressure (CPAP) treatment are largely unknown. We sought to assess the system-wide consequences of CPAP therapy by transcriptionally profiling peripheral blood leukocytes (PBLs). Methods: Subjects diagnosed with severe OSA were treated with CPAP, and whole-genome expression measurement of PBLs was performed at baseline and following therapy. We used Gene Set Enrichment Analysis (GSEA) to identify gene sets that were differentially enriched. Network analysis was then applied to identify key drivers of pathways influenced by CPAP. Results: 18 subjects with severe OSA (apnea hypopnea index ≥ 30 events/hour) underwent CPAP therapy and microarray analysis of their PBLs. Treatment with CPAP improved AHI, daytime sleepiness and blood pressure but did not affect anthropometric measures. GSEA revealed a number of enriched gene sets, many of which were involved in neoplastic processes and displayed down-regulated expression patterns in response to CPAP. Network analysis identified several densely connected genes that are important modulators of cancer and tumor growth. Conclusions: Effective therapy of OSA with CPAP is associated with alterations in circulating leukocyte gene expression. Functional enrichment and network analyses highlighted transcriptional suppression in cancer-related pathways suggesting potentially novel mechanisms linking OSA with neoplastic signatures. Total RNA from peripheral blood leukocytes of 18 subjects with severe sleep apnea at baseline and after effective CPAP therapy was hybridized to 36 Affymetrix Genechip Human Gene 1.0 ST microarrays