ABSTRACT: The plasmacytoid dendritic cell (pDC) is vital to the coordinated action of innate and adaptive immunity. pDC development has not been unequivocally traced, nor has its transcriptional regulatory network been fully clarified. Here we confirm an essential requirement for the BCL11A transcription factor in fetal pDC development, and demonstrate this lineage-specific requirement in the adult organism. Furthermore, we identify BCL11A gene targets and provide a molecular mechanism for its action in pDC commitment. Embryonic germ-line deletion of Bcl11a revealed an absolute cellular, molecular, and functional absence of pDCs in fetal mice. In adults, deletion of Bcl11a in hematopoietic stem cells resulted in perturbed yet continued generation of progenitors, loss of downstream pDC and B-cell lineages, and persisting myeloid, conventional dendritic, and T-cell lineages. Challenge with virus resulted in a marked reduction of antiviral response in conditionally deleted adults. Genome-wide analyses of BCL11A DNA binding and expression revealed that BCL11A regulates transcription of E2-2 and other pDC differentiation modulators, including ID2 and MTG16. Our results identify BCL11A as an essential, lineage- specific factor that regulates pDC development, supporting a model wherein differentiation into pDCs represents a primed "default" pathway for common dendritic cell progenitors. Raji cells were infected with retroviruses containing pXY-PURO (negative control vector) or pXY-BCL11A-XS. BJAB cells were infected with retroviruses containing pXY-PURO (negative control vector) or pXY-BCL11A-XL. Two arrays measured Raji BCL11A-XS expression and two arrays measured BJAB BCL11A-XL expression.
Project description:The variability in the prognosis of hepatocellular carcinoma (HCC) patients suggests that HCC may comprise several distinctive biological phenotypes. These phenotypes may result from different neoplastic pathways during the tumorigenesis and/or from a different cell of origin. Here we address if the transcriptional characteristics of the HCC would provide insight into the cellular origin of the tumors. We integrated gene expression data from rat fetal hepatoblasts and adult hepatocytes, HCC from mouse models, and human HCC. The HCC patients who shared gene expression patterns with fetal hepatoblasts showed extremely poor prognosis when compared with those lacking the hepatoblast signature. The gene expression program that distinguishes this novel subtype from the rest of HCC includes well known markers of hepatic oval cells, suggesting that HCC in this subtype may arise from hepatic progenitor cells. Two independent gene network analyses of the gene expression signature characteristic for the tumors sharing the hepatoblast expression patterns revealed that activation of AP-1 transcription factors might play key roles in tumor development in the newly identified HCC subtype. In addition, by applying hepatoblast-specific and genome-wide global signatures, HCC patients were further stratified into three distinct subgroups with a significant association with overall survival and recurrence. Total RNAs from 19 normal livers were pooled and used as the reference for all microarray experiments. To obtain gene expression profile data from 49 human HCC, 20 µg of total RNAs from tissues were used to drive fluorescently (Cy-5 or Cy-3) labeled cDNA. At least two hybridizations were carried out for each tissue using a dye-swap strategy to eliminate dye labeling bias.
Project description:The mechanism whereby IL-9 stimulated monocytes, promote proliferation of co-cultured ATL cells remains undefined. To obtain preliminary clues concerning this contribution, transcription profiles were obtained between monocytes derived from ATL patients and those derived from healthy donors as assessed by cDNA microarray. Keywords: disease state design The experiment included 3 biological replicate ATL samples and 3 biological replicate normal samples. The Stratagene Universal Human RNA Reference sample was used as a control.
Project description:To identify the prognostic subtypes of hepatocellular carcinoma with potential progenitor cell origin. Keywords: disease state design We used our in-house oligonucleotide microarray data of 238 HBV-positive HCC cases.
Project description:To identify HGF/Met regulated genes, we performed expression microarray analysis after inducible activation of Met receptor in primary cultures of hepatocytes established from wild-type control (Alb-Cre +/-) and Met conditional knockout mice (Alb-Cre +/-; Met Fl/Fl). Total RNA was isolated from untreated hepatocyte cultures as well as from cultures treated with 50 ng/ml of HGF for 0.5, 2, 12 or 24 hours. RNA collected from these experiments was converted to fluorescently labeled cDNA and used for hybridizations of oligonucleotide microarrays. All experiments were repeated in triplicates. Total RNA from pooled wild-type mouse hepatocytes was used as universal reference and all hybridizations were repeated following a reverse flourescing.
Project description:We determined the gene expression profiles of murine melan-a melanocytes treated with ASP or alpha-MSH over a 4 days time course using genome-wide oligonucleotide microarrays. As expected, the gene expression patterns emphasized the opposing effects of the 2 ligands, and there were significant reductions in expression of numerous melanogenic proteins elicited by ASP, which correlates with its inhibition of pigmentation. However, ASP also unexpectidly modulated the expression of genes involved in various other cellular pathways, including glutathione synthesis and redox metabolism. Many genes up-regulated by ASP are involved in morphogenesis, cell adhesion and ECM-receptor interactions. Treatment with ASP or alpha-MSH was performed for 3 hr, 1 day, 2 days, 3 days and 4 days, in triplicate. Each biological replicate was submitted to a direct hybridization (treated/untreated samples) after coupling with Cy5 or Cy3 and to a reverse dye-swap, leading to 2 replicated hybridization for each biological sample. A total of 6 hybridized arrays was used for each of the 5 time points, for each drug.
Project description:To explore the effects on the NF-kB transcriptome after knockdown of RPS3 in stimulated T cells, we performed microarray assays comparing RPS3-silenced versus NS-treated samples on the same chip. p65-silenced versus NS-treated samples were used as a control. Keywords: time series design Jurkat cells transfected with control siRNA versus RPS3 or p65-siRNA were stimuated with TCR for 1, 3, or 6 hours for a total of 6 arrays.
Project description:To identify c-myc target genes by siRNA transfection in a lymphoma cell line. Keywords: time series design OCI-Ly10 cells were transfected with c-myc siRNA pool versus control siRNA or buffer for a total of 4 microarrays.
Project description:The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma Keywords: lymphochip; MCL; untreated Tumor biopsies from 71 untreated patients with mantle cell lymphoma
Project description:Gene expression profiles reflect unique aspects of individual biologic phenotypes and may characterize the heterogeneity of solid tumors. Using previously-described methodologies that employ DNA microarray data, a 50-gene expression profile (metagene) that predicts risk of recurrence in early stage colon carcinoma was identified. This analysis used an initial discovery cohort of 52 patients. The performance of the 50-gene predictor was evaluated in an independent validation cohort of 73 patients. Using a connectivity map analysis of the 50-gene model, we identified candidate agents and then tested the in vitro efficacy of these compounds in colon cancer cell lines. 73 samples that had patient recurrence data with stage information were used in the analysis. Keywords: Disease state analysis A total of 73 samples were spotted on microarray slides. No replicates are included in the study.