Browsing by Author "Department of Cellular & Integrative Physiology, School of Medicine"

Now showing 1 - 5 of 5
  • Thumbnail Image
    Item
    BioVLAB-MMIA-NGS: MicroRNA-mRNA Integrated Analysis using High Throughput Sequencing Data
    (Oxford, 2015-09) Chae, Heejoon; Rhee, Sungmin; Nephew, Kenneth P.; Kim, Sun; Department of Cellular & Integrative Physiology, School of Medicine
    Motivation: It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence-specific manner, and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA–mRNA analysis remains a major computational challenge, requiring powerful informatics systems and bioinformatics expertise. Results: The objective of this study was to modify our widely recognized Web server for the integrated mRNA–miRNA analysis (MMIA) and its subsequent deployment on the Amazon cloud (BioVLAB-MMIA) to be compatible with high-throughput platforms, including next-generation sequencing (NGS) data (e.g. RNA-seq). We developed a new version called the BioVLAB-MMIA-NGS, deployed on both Amazon cloud and on a high-performance publicly available server called MAHA. By using NGS data and integrating various bioinformatics tools and databases, BioVLAB-MMIA-NGS offers several advantages. First, sequencing data is more accurate than array-based methods for determining miRNA expression levels. Second, potential novel miRNAs can be detected by using various computational methods for characterizing miRNAs. Third, because miRNA-mediated gene regulation is due to hybridization of an miRNA to its target mRNA, sequencing data can be used to identify many-to-many relationship between miRNAs and target genes with high accuracy.
  • Thumbnail Image
    Item
    CARDIOVASCULAR AND HEMODYNAMIC EFFECTS OF GLUCAGON-LIKE PEPTIDE-1
    (Springer US, 2014-09) Goodwill, Adam G.; Mather, Kieren J.; Conteh, Abass M.; Sassoon, Daniel; Noblet, Jillian N.; Tune, Johnathan D.; Department of Cellular & Integrative Physiology, School of Medicine
    Glucagon-like peptide-1 (GLP-1) is an incretin hormone that has been shown to have hemodynamic and cardioprotective capacity in addition to its better characterized glucoregulatory actions. Because of this, emerging research has focused on the ability of GLP-1 based therapies to drive myocardial substrate selection, enhance cardiac performance and regulate heart rate, blood pressure and vascular tone. These studies have produced consistent and reproducible results amongst numerous laboratories. However, there are obvious disparities in findings obtained in small animal models versus those of higher mammals. This species dependent discrepancy calls to question, the translational value of individual findings. Moreover, few studies of GLP-1 mediated cardiovascular action have been performed in the presence of a pre-existing comorbidities (e.g. obesity/diabetes) which limits interpretation of the effectiveness of incretin-based therapies in the setting of disease. This review addresses cardiovascular and hemodynamic potential of GLP-1 based therapies with attention to species specific effects as well as the interaction between therapies and disease.
  • Thumbnail Image
    Item
    Label-free quantitative imaging of cholesterol in intact tissues by hyperspectral stimulated Raman scattering microscopy
    (Wiley, 2013-12) Wang, Ping; Li, Junjie; Wang, Pu; Hu, Chun-Rui; Zhang, Delong; Sturek, Michael; Cheng, Ji-Xin; Department of Cellular & Integrative Physiology, School of Medicine
    A finger on the pulse: Current molecular analysis of cells and tissues routinely relies on separation, enrichment, and subsequent measurements by various assays. Now, a platform of hyperspectral stimulated Raman scattering microscopy has been developed for the fast, quantitative, and label-free imaging of biomolecules in intact tissues using spectroscopic fingerprints as the contrast mechanism.
  • Thumbnail Image
    Item
    microRNA regulation of mammalian target of rapamycin expression and activity controls estrogen receptor function and RAD001 sensitivity
    (BioMed Central, 2014-10-06) Martin, Elizabeth C.; Rhodes, Lyndsay V.; Elliott, Steven; Krebs, Adrienne E.; Nephew, Kenneth P.; Flemington, Erik K.; Collins-Burow, Bridgette M.; Burow, Matthew E.; Department of Cellular & Integrative Physiology, School of Medicine
    Background: The AKT/mammalian target of rapamycin (mTOR) signaling pathway is regulated by 17 α -estradiol (E2) signaling and mediates E2-induced proliferation and progesterone receptor (PgR) expression in breast cancer. Methods and results: Here we use deep sequencing analysis of previously published data from The Cancer Genome Atlas to demonstrate that expression of a key component of mTOR signaling, rapamycin-insensitive companion of mTOR (Rictor), positively correlated with an estrogen receptor- α positive (ER α + ) breast tumor signature. Through increased microRNA-155 (miR-155) expression in the ER α + breast cancer cells we demonstrate repression of Rictor enhanced activation of mTOR complex 1 (mTORC1) signaling with both qPCR and western blot. miR-155-mediated mTOR signaling resulted in deregulated ER α signalingbothinculturedcells in vitro and in xenografts in vivo in addition to repressed PgR expression and act ivity.FurthermoreweobservedthatmiR-155 enhanced mTORC1 signaling (observed through western blot for increased phosphorylation on mTOR S2448) and induced inhibition of mTORC2 signaling (evident through repressed Rictor and tuberous sclerosis 1 (TSC1) gene expression). mTORC1 induced deregulation of E2 signaling was confirmed using qPCR and the mTORC1-specific inhibitor RAD001. Co-treatment of MCF7 breast cancer cells stably overexpressing miR-155 with RAD001 and E2 restored E2-induced PgR gene expression. RAD001 treatment of SCID/CB17 mice inhibited E2-induced tumorigenesis of the MCF7 miR-155 overexpressing cell line. Finally we demonstrated a strong positive correlation between Rictor and PgR expression and a negative correlation with Raptor expression in Luminal B breast cancer samples, a breast cancer histological subtype known for having an altered ER α -signaling pathway. Conclusions: miRNA mediated alterations in mTOR and ER α signaling establishes a new mechanism for altered estrogen responses independent of growth factor stimulation.
  • Thumbnail Image
    Item
    Previously differentiated medial vascular smooth muscle cells contribute to neointima formation following vascular injury
    (BioMed Central, 2014-10-01) Herring, Brian Paul; Hoggatt, April M.; Burlak, Christopher; Offermanns, Stefan; Department of Cellular & Integrative Physiology, School of Medicine
    Background The origins of neointimal smooth muscle cells that arise following vascular injury remains controversial. Studies have suggested that these cells may arise from previously differentiated medial vascular smooth muscle cells, resident stem cells or blood born progenitors. In the current study we examined the contribution of the previously differentiated vascular smooth muscle cells to the neointima that forms following carotid artery ligation. Methods We utilized transgenic mice harboring a cre recombinase-dependent reporter gene (mTmG). These mice express membrane targeted tandem dimer Tomato (mTomato) prior to cre-mediated excision and membrane targeted EGFP (mEGFP) following excision. The mTmG mice were crossed with transgenic mice expressing either smooth muscle myosin heavy chain (Myh11) or smooth muscle α-actin (Acta2) driven tamoxifen regulated cre recombinase. Following treatment of adult mice with tamoxifen these mice express mEGFP exclusively in differentiated smooth muscle cells. Subsequently vascular injury was induced in the mice by carotid artery ligation and the contribution of mEGFP positive cells to the neointima determined. Results Analysis of the cellular composition of the neointima that forms following injury revealed that mEGFP positive cells derived from either Mhy11 or Acta2 tagged medial vascular smooth muscle cells contribute to the majority of neointima formation (79 ± 17% and 81 ± 12%, respectively). Conclusion These data demonstrate that the majority of the neointima that forms following carotid ligation is derived from previously differentiated medial vascular smooth muscle cells.