The statsitcal model, latent pathway identification analysis (LPIA), was implemented for the analysis of A549 lung carcinoma cells treated with geldanamycin. Control and treated samples were assayed with Affymetrix HG_U133_plus_2 arrays and analyzed using LPIA. LPIA looks for statistically signcant evidence of dysregulation in a network of pathways constructed in a manner that explicitly links pathways through their common function in the cell. Geldanamycin (geld) is known to inhibit the molecular chaperone protein, Hsp90, and plays a role in preventing the malignant transformation and proliferation of healthy cells during oncogenesis. LPIA successfully identified pathways specific to geldanamycin effects at the gene transcription level.
Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis.
Specimen part, Cell line, TimeView Samples
We report a transcriptome comparison of HEK293 cells modified at the DPYSL2 gene promoter dinucleotide repeat (chr8:26,435,510-26,435,534) by CRISPR/Cas9 to change from the common 11 repeats to the more rare 13 repeats Overall design: 11/11 repeat HEK 293 cells were modified by CRISPR/Cas 9. Cell were flow sorted by the co-transfected GFP and single cells were expanded. From those we selected 4 modified and 8 unmodified clones for RNA seq. RNA was extracted at 80% confluency
The DPYSL2 gene connects mTOR and schizophrenia.
Specimen part, Cell line, SubjectView Samples
The MYB gene family encodes transcription factors with a diverse range of functions in Arabidopsis. This study demonstrated that MYB5, which is expressed in trichomes and seeds, plays a central role in trichome and seed development. A microarray analysis of myb5 seeds identified other members of the MYB5 regulatory network.
The Arabidopsis MYB5 transcription factor regulates mucilage synthesis, seed coat development, and trichome morphogenesis.
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Background: In malaria, parasites of the genus Plasmodium elicit robust host expansion of macrophages and monocytes, but the underlying mechanisms remain unclear. In a microarray analysis of pooled, activated CD4+ T cells from mice infected with P. chabaudi, we detected inducible expression of Csf1, which promotes macrophage proliferation. To better characterize Csf1-producing T cells, single-cell RNA-Seq was performed. Results: Robust Csf1 expression was detected in a subset of sampled CD4+ T cells (n = 14/35), whereas the remainder of cells had no detectable Csf1. Further, we identified ~ 400 genes that were differentially expressed between Csf1+ and Csf1- T cells. Conclusions: This work defines the transcriptional landscape of a subset of activated CD4+ T cells that produce the cytokine Csf1. These cells are expected to be important in infections with intracellular pathogens such as Plasmodium. Overall design: Antigen-experienced (CD11a+ CD49d+) CD4+ T cells were isolated by double-sorting from the blood of C57BL/6 adult female mice 6 days post-infection with Plasmodium chabaudi. Single cells were isolated and processed for RNA sequencing using a Fluidigm C1 integrated fluidic circuit chip. 35 biological replicates were analyzed.
Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection.
Sex, Specimen part, Subject, TimeView Samples
Analysis of gene expression in prostatic tissue from BPH patients with and without SRD5A2 gene methylation. The hypothesis is that BPH patients with DNA methylation of the SRD5A2 gene promoter have impaired conversion of testosterone to dihydrotestosterone, and therefore may use an alternative signaling pathway for prostatic tissue growth. Here, we compare gene expression profiles of SRD5A2-methylated vs. unmethylated prostatic tissue to nominate alternative biological pathways relevant in each molecular subtype of BPH.
Androgenic to oestrogenic switch in the human adult prostate gland is regulated by epigenetic silencing of steroid 5α-reductase 2.
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Despite the fact that clinically relevant infectious agents such as human immunodeficiency virus enter through the intestinal mucosa, the intestinal T cell response to infection remains understudied. Listeria monocytogenes (LM) has been used as a model organism for studying T cell responses and the normal route of infection for LM and a potential route for use of LM as a vaccine are through ingestion. Nevertheless, the vast majority of LM immunological studies utilize inoculation routes other than oral. Moreover in the bacterial strains used the internalin. A protein binds human E-cadherin with high affinity but poorly binds mouse E-cadherin. This receptor-ligand pairing is required for entry of LM into intestinal epithelial cells. The oral infection studies proposed here utilize a recombinant LM that expresses an internalin A protein with high affinity for mouse E-cadherin. Thus, the physiologic route and entry point of LM is recapitulated in our studies. Our preliminary studies revealed a remarkable mucosal TCR gd T cell response to oral LM infection, whose kinetics mimic an adaptive T cell response. Most importantly, this phenotypically and functionally distinct subset of mucosal TCR gd T cells are retained long-term and undergo a recall response upon challenge. The hypothesis to be tested in this proposal is that this specialized subset of putative memory TCR gd T cells is important for protection against LM infection and also regulates the long-term protective CD8 TCR ab response. This hypothesis will be tested in the following specific aims: Aim 1. To test whether a subset of TCR gd represent bona fide mucosal memory cells. A detailed kinetic, phenotypic and functional analysis of the primary and secondary TCR gd cell response to oral LM infection will be undertaken. Aim 2. To determine the requirements for mucosal TCRgd activation in response to LM infection. Here we will test the role of dendritic cells, cosfimulation and cytokines in mounting primary and secondary TCR gd cell responses. Aim 3. To visualize the mucosal TCR gd cell response to oral LM infection. The oral infection system provides an exceptional opportunity to examine the anatomy of the mucosal TCR gd cell response.
γδ T cells exhibit multifunctional and protective memory in intestinal tissues.
Sex, Age, Specimen part, Cell lineView Samples
Gene expression, histone modification, DNA methylation, and DNA hydroxymethylation from normal, cirrhotic, and HCC livers Overall design: 10 total samples (2 normal, 4 cirrhosis, 4 HCC). Cirrhosis and HCC are from the same four patients.
Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma.
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PP2A regulates inflammatory cytokine/chemokine gene expression by dephosphorylating protein kinases at multiple signaling pathways from stimulated cells. In this dataset, Affymetrix mouse Gene ST 2.1 Array was used to assay total RNA extracted from LPS-treated PP2AC knockout BMDM (PP2ACfl/fl;lyM-Cre) and the control BMDM (PP2ACfl/fl)
Myeloid-Specific Gene Deletion of Protein Phosphatase 2A Magnifies MyD88- and TRIF-Dependent Inflammation following Endotoxin Challenge.
Specimen partView Samples
The goal of this study is to elucidate the influence of treadmill training on transcriptome of the upper lumbar spinal cord after thoracic spinal cord hemisection. mRNA profiles of spinal cords at 23 days-post injury with/without treadmill training were generated. The expression levels of 650 genes in the trained animal were increased ( > 2-fold) compared to untrained animals. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion after treadmill training, with biologic replicates, generated by RNA-seq technology. Overall design: The effect of training after spinal cord injury (T9) on the transcriptome of intact upper spinal cord was investigated.
Locomotor Training Increases Synaptic Structure With High NGL-2 Expression After Spinal Cord Hemisection.
Specimen part, Cell line, SubjectView Samples
The dendritic cell (DC) is a master regulator of immune responses. Pathogenic viruses subvert normal immune function in DCs through the expression of immune antagonists. Understanding how these antagonists interact with the host immune system requires knowledge of the underlying genetic regulatory network that operates during an uninhibited antiviral response. In order to isolate and identify this network, we studied DCs infected with Newcastle Disease Virus (NDV), which is able to stimulate innate immunity and DC maturation through activation of RIG-I signaling, but lacks the ability to evade the human interferon response. To analyze this experimental model, we developed a new approach integrating genome-wide expression kinetics and time-dependent promoter analysis. We found that the genetic program underlying the antiviral cell state transition during the first 18-hours post-infection could be explained by a single regulatory network. Gene expression changes were driven by a step-wise multi-factor cascading control mechanism, where the specific transcription factors controlling expression changed over time. Within this network, most individual genes are regulated by multiple factors, indicating robustness against virus-encoded immune evasion genes. In addition to effectively recapitulating current biological knowledge, we predicted, and validated experimentally, antiviral roles for several novel transcription factors. More generally, our results show how a genetic program can be temporally controlled through a single regulatory network to achieve the large-scale genetic reprogramming characteristic of cell state transitions.
Antiviral response dictated by choreographed cascade of transcription factors.
Specimen part, SubjectView Samples