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Species

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Gene

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Platform

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Channel

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HiPlex Channel

  • T1 (85058) Apply T1 filter
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  • T11 (85039) Apply T11 filter
  • T9 (82563) Apply T9 filter
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  • S1 (32) Apply S1 filter
  • 8 (17) Apply 8 filter
  • 1 (1) Apply 1 filter
  • 10 (1) Apply 10 filter
  • 6 (1) Apply 6 filter

Product

  • RNAscope Multiplex Fluorescent Assay (1035) Apply RNAscope Multiplex Fluorescent Assay filter
  • RNAscope (998) Apply RNAscope filter
  • RNAscope Fluorescent Multiplex Assay (732) Apply RNAscope Fluorescent Multiplex Assay filter
  • RNAscope 2.5 HD Red assay (704) Apply RNAscope 2.5 HD Red assay filter
  • RNAscope 2.0 Assay (497) Apply RNAscope 2.0 Assay filter
  • RNAscope 2.5 HD Brown Assay (293) Apply RNAscope 2.5 HD Brown Assay filter
  • TBD (193) Apply TBD filter
  • RNAscope 2.5 LS Assay (191) Apply RNAscope 2.5 LS Assay filter
  • RNAscope 2.5 HD Duplex (160) Apply RNAscope 2.5 HD Duplex filter
  • RNAscope 2.5 HD Reagent Kit - BROWN (108) Apply RNAscope 2.5 HD Reagent Kit - BROWN filter
  • RNAscope Multiplex Fluorescent v2 (97) Apply RNAscope Multiplex Fluorescent v2 filter
  • BASEscope Assay RED (91) Apply BASEscope Assay RED filter
  • RNAscope 2.5 VS Assay (85) Apply RNAscope 2.5 VS Assay filter
  • Basescope (53) Apply Basescope filter
  • RNAscope HiPlex v2 assay (30) Apply RNAscope HiPlex v2 assay filter
  • miRNAscope (26) Apply miRNAscope filter
  • DNAscope HD Duplex Reagent Kit (15) Apply DNAscope HD Duplex Reagent Kit filter
  • RNAscope 2.5 HD duplex reagent kit (13) Apply RNAscope 2.5 HD duplex reagent kit filter
  • BaseScope Duplex Assay (12) Apply BaseScope Duplex Assay filter
  • RNAscope Multiplex fluorescent reagent kit v2 (6) Apply RNAscope Multiplex fluorescent reagent kit v2 filter
  • RNAscope Fluorescent Multiplex Reagent kit (5) Apply RNAscope Fluorescent Multiplex Reagent kit filter
  • RNAscope ISH Probe High Risk HPV (5) Apply RNAscope ISH Probe High Risk HPV filter
  • CTCscope (4) Apply CTCscope filter
  • RNAscope 2.5 HD Reagent Kit (4) Apply RNAscope 2.5 HD Reagent Kit filter
  • RNAscope HiPlex12 Reagents Kit (3) Apply RNAscope HiPlex12 Reagents Kit filter
  • DNAscope Duplex Assay (2) Apply DNAscope Duplex Assay filter
  • RNAscope 2.5 HD Assay (2) Apply RNAscope 2.5 HD Assay filter
  • RNAscope 2.5 LS Assay - RED (2) Apply RNAscope 2.5 LS Assay - RED filter
  • RNAscope Multiplex Fluorescent Assay v2 (2) Apply RNAscope Multiplex Fluorescent Assay v2 filter
  • BOND RNAscope Brown Detection (1) Apply BOND RNAscope Brown Detection filter
  • HybEZ Hybridization System (1) Apply HybEZ Hybridization System filter
  • miRNAscope Assay Red (1) Apply miRNAscope Assay Red filter
  • RNA-Protein CO-Detection Ancillary Kit (1) Apply RNA-Protein CO-Detection Ancillary Kit filter
  • RNAscope 2.0 HD Assay - Chromogenic (1) Apply RNAscope 2.0 HD Assay - Chromogenic filter
  • RNAscope 2.5 HD- Red (1) Apply RNAscope 2.5 HD- Red filter
  • RNAscope 2.5 LS Reagent Kits (1) Apply RNAscope 2.5 LS Reagent Kits filter
  • RNAScope HiPlex assay (1) Apply RNAScope HiPlex assay filter
  • RNAscope HiPlex Image Registration Software (1) Apply RNAscope HiPlex Image Registration Software filter
  • RNAscope LS Multiplex Fluorescent Assay (1) Apply RNAscope LS Multiplex Fluorescent Assay filter
  • RNAscope Multiplex Fluorescent Reagent Kit V3 (1) Apply RNAscope Multiplex Fluorescent Reagent Kit V3 filter
  • RNAscope Multiplex Fluorescent Reagent Kit v4 (1) Apply RNAscope Multiplex Fluorescent Reagent Kit v4 filter
  • RNAscope Multiplex Fluorescent v1 (1) Apply RNAscope Multiplex Fluorescent v1 filter
  • RNAscope Target Retrieval Reagents (1) Apply RNAscope Target Retrieval Reagents filter

Research area

  • Neuroscience (1849) Apply Neuroscience filter
  • Cancer (1385) Apply Cancer filter
  • Development (509) Apply Development filter
  • Inflammation (472) Apply Inflammation filter
  • Infectious Disease (410) Apply Infectious Disease filter
  • Other (406) Apply Other filter
  • Stem Cells (258) Apply Stem Cells filter
  • Covid (237) Apply Covid filter
  • Infectious (220) Apply Infectious filter
  • HPV (187) Apply HPV filter
  • lncRNA (135) Apply lncRNA filter
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  • Immunotherapy (72) Apply Immunotherapy filter
  • Other: Methods (67) Apply Other: Methods filter
  • HIV (64) Apply HIV filter
  • CGT (62) Apply CGT filter
  • Pain (62) Apply Pain filter
  • diabetes (57) Apply diabetes filter
  • LncRNAs (46) Apply LncRNAs filter
  • Aging (43) Apply Aging filter
  • Other: Heart (40) Apply Other: Heart filter
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  • Obesity (29) Apply Obesity filter
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  • Behavior (27) Apply Behavior filter
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  • Other: Kidney (27) Apply Other: Kidney filter
  • Alzheimer's Disease (26) Apply Alzheimer's Disease filter
  • Bone (24) Apply Bone filter
  • Stress (21) Apply Stress filter
  • Other: Zoological Disease (20) Apply Other: Zoological Disease filter
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  • Fibrosis (17) Apply Fibrosis filter
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  • Other: Endocrinology (16) Apply Other: Endocrinology filter
  • Other: Skin (16) Apply Other: Skin filter
  • Injury (15) Apply Injury filter
  • Anxiety (14) Apply Anxiety filter
  • Memory (14) Apply Memory filter
  • Reproductive Biology (14) Apply Reproductive Biology filter

Product sub type

  • Target Probes (256568) Apply Target Probes filter
  • Control Probe - Automated Leica (409) Apply Control Probe - Automated Leica filter
  • Control Probe - Automated Leica Multiplex (284) Apply Control Probe - Automated Leica Multiplex filter
  • Control Probe - Automated Leica Duplex (168) Apply Control Probe - Automated Leica Duplex filter
  • Control Probe- Manual RNAscope Multiplex (148) Apply Control Probe- Manual RNAscope Multiplex filter
  • Control Probe - Automated Ventana (143) Apply Control Probe - Automated Ventana filter
  • Control Probe - Manual RNAscope Singleplex (142) Apply Control Probe - Manual RNAscope Singleplex filter
  • Control Probe - Manual RNAscope Duplex (137) Apply Control Probe - Manual RNAscope Duplex filter
  • Control Probe (73) Apply Control Probe filter
  • Control Probe - Manual BaseScope Singleplex (51) Apply Control Probe - Manual BaseScope Singleplex filter
  • Control Probe - VS BaseScope Singleplex (41) Apply Control Probe - VS BaseScope Singleplex filter
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  • L-HBsAG (15) Apply L-HBsAG filter
  • Cancer (13) Apply Cancer filter
  • Automated Assay 2.5: Leica System (8) Apply Automated Assay 2.5: Leica System filter
  • Control Probe- Manual BaseScope Duplex (8) Apply Control Probe- Manual BaseScope Duplex filter
  • 1765 (8) Apply 1765 filter
  • 1379 (8) Apply 1379 filter
  • 2184 (8) Apply 2184 filter
  • 38322 (8) Apply 38322 filter
  • Manual Assay 2.5: Pretreatment Reagents (5) Apply Manual Assay 2.5: Pretreatment Reagents filter
  • Controls: Manual Probes (5) Apply Controls: Manual Probes filter
  • Control Probe- Manual RNAscope HiPlex (5) Apply Control Probe- Manual RNAscope HiPlex filter
  • Manual Assay RNAscope Brown (4) Apply Manual Assay RNAscope Brown filter
  • Manual Assay RNAscope Duplex (4) Apply Manual Assay RNAscope Duplex filter
  • Manual Assay RNAscope Multiplex (4) Apply Manual Assay RNAscope Multiplex filter
  • Manual Assay BaseScope Red (4) Apply Manual Assay BaseScope Red filter
  • IA: Other (4) Apply IA: Other filter
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  • Manual Assay miRNAscope Red (4) Apply Manual Assay miRNAscope Red filter
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  • Control Probe - Automated Ventana Duplex (3) Apply Control Probe - Automated Ventana Duplex filter
  • Manual Assay BaseScope Duplex (3) Apply Manual Assay BaseScope Duplex filter
  • Manual Assay RNAscope Red (2) Apply Manual Assay RNAscope Red filter
  • Controls: Control Slides (2) Apply Controls: Control Slides filter
  • Control Probe- Manual BaseScope Singleplex (2) Apply Control Probe- Manual BaseScope Singleplex filter
  • Control Probe - Manual BaseScope™Singleplex (2) Apply Control Probe - Manual BaseScope™Singleplex filter
  • Manual Assay: Accessory Reagent (1) Apply Manual Assay: Accessory Reagent filter
  • Accessory Reagent (1) Apply Accessory Reagent filter
  • Controls: Manual RNAscope Multiplex (1) Apply Controls: Manual RNAscope Multiplex filter
  • IA: HybEZ (1) Apply IA: HybEZ filter
  • Automated Assay BaseScope: LS (1) Apply Automated Assay BaseScope: LS filter
  • Automated Assay BaseScope: VS (1) Apply Automated Assay BaseScope: VS filter
  • Software: RNAscope HiPlex Image Registration (1) Apply Software: RNAscope HiPlex Image Registration filter
  • miRNAscope Automated Assay: Leica System (1) Apply miRNAscope Automated Assay: Leica System filter
  • Automated Assay: VS (1) Apply Automated Assay: VS filter
  • Control Probe - VS BaseScope™Singleplex (1) Apply Control Probe - VS BaseScope™Singleplex filter
  • Controls:2.5VS Probes (1) Apply Controls:2.5VS Probes filter
  • Control Probe - Manual RNAscope Multiplex (1) Apply Control Probe - Manual RNAscope Multiplex filter

Sample Compatibility

  • Cell pellets (49) Apply Cell pellets filter
  • FFPE (41) Apply FFPE filter
  • Fixed frozen tissue (31) Apply Fixed frozen tissue filter
  • TMA (31) Apply TMA filter
  • Adherent cells (26) Apply Adherent cells filter
  • Freshfrozen tissue (18) Apply Freshfrozen tissue filter
  • Fresh frozen tissue (13) Apply Fresh frozen tissue filter
  • Cell Cultures (12) Apply Cell Cultures filter
  • TMA(Tissue Microarray) (9) Apply TMA(Tissue Microarray) filter
  • FFPE,Freshfrozen tissue,Fixed frozen tissue,TMA,Cell pellets,Adherent cells (7) Apply FFPE,Freshfrozen tissue,Fixed frozen tissue,TMA,Cell pellets,Adherent cells filter
  • CTC (4) Apply CTC filter
  • PBMC's (4) Apply PBMC's filter
  • Adherent or Cultured Cells (1) Apply Adherent or Cultured Cells filter
  • Fixed frozen (1) Apply Fixed frozen filter
  • FFPE,TMA (1) Apply FFPE,TMA filter
  • Fixed frozen tissues (for chromogenic assays) (1) Apply Fixed frozen tissues (for chromogenic assays) filter

Category

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Application

  • Cancer (139875) Apply Cancer filter
  • Neuroscience (51010) Apply Neuroscience filter
  • Cancer, Neuroscience (32227) Apply Cancer, Neuroscience filter
  • Non-coding RNA (24365) Apply Non-coding RNA filter
  • Cancer, Inflammation (16436) Apply Cancer, Inflammation filter
  • Cancer, Inflammation, Neuroscience (12591) Apply Cancer, Inflammation, Neuroscience filter
  • Inflammation (9879) Apply Inflammation filter
  • Cancer, Stem Cell (7932) Apply Cancer, Stem Cell filter
  • Cancer, Neuroscience, Stem Cell (7028) Apply Cancer, Neuroscience, Stem Cell filter
  • Cancer, Immunotherapy, Inflammation, Neuroscience, Stem Cell (6854) Apply Cancer, Immunotherapy, Inflammation, Neuroscience, Stem Cell filter
  • Cancer, Inflammation, Neuroscience, Stem Cell (5424) Apply Cancer, Inflammation, Neuroscience, Stem Cell filter
  • Immunotherapy (5368) Apply Immunotherapy filter
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  • Cancer, Immunotherapy, Inflammation (2844) Apply Cancer, Immunotherapy, Inflammation filter
  • Cancer, Immunotherapy, Inflammation, Neuroscience (1878) Apply Cancer, Immunotherapy, Inflammation, Neuroscience filter
  • Cancer, Immunotherapy, Neuroscience (1786) Apply Cancer, Immunotherapy, Neuroscience filter
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High protein and mRNA expression levels of TUBB3 (class III ß-tubulin) are associated with aggressive tumor features in esophageal adenocarcinomas.

Oncotarget.

2017 Dec 11

Loeser H, Schallenberg S, von Winterfeld M, Tharun L, Alakus H, Hölscher A, Bollschweiler E, Buettner R, Zander T, Quaas A.
PMID: 29383151 | DOI: 10.18632/oncotarget.23112

Abstract

BACKGROUND:

Esophageal adenocarcinomas show an increasing incidence in the Western world and their overall survival remains low. Microtubules are multifunctional cytoskeletal proteins involved in crucial cellular roles, including maintenance of cell shape, intracellular transport, meiosis, and mitosis. Microtubulus-TUBB3 was found overexpressed in several carcinomas suggesting a significant role in cancer development. High levels of TUBB3 expression were also described to be associated with poor clinical outcome in various cancers. It was shown that overexpression of TUBB3 could be related to reduced efficiency of taxane-based targeting anticancer drugs in several cancer types.

RESULTS:

There is a statistically significant association between high TUBB3 protein and TUBB3 mRNA expression and shortened survival (p<0,0001). Prognostic impact of TUBB3 expression is seen in patients with and without multimodal treatment. Multivariate analysis revealed a strong TUBB3 expression to be an independent prognosis factor. Validation of protein expression by mRNA in situ hybridization underlines the credibility of the immunohistochemical results.

DISCUSSION:

Our study emphasized the significant importance of TUBB3 in esophageal adenocarcinoma. TUBB3 serves as an independent prognostic marker and may be a valuable biomarker for routine application in esophageal adenocarcinoma especially to address the need for adjuvant treatment in individuals following neoadjuvant therapy and surgery. Future prospective studies are needed which include the results of TUBB3 in preoperative biopsy material to proof the prognostic impact of TUBB3.

MATERIALS AND METHODS:

280 esophageal adenocarcinomas that underwent primary surgical resection or resection after neoadjuvant therapy were analyzed by mRNA-in-situ-hybridization (RNAscope™) and by immunohistochemistry (TUBB3 rabbit monoclonal antibody; Epitomics).

Nitrergic signaling via interstitial cells of Cajal and smooth muscle cells influences circular smooth muscle contractility in murine colon

Neurogastroenterol Motil.

2018 Jan 29

Beck K, Friebe A, Voussen B.
PMID: 29377328 | DOI: 10.1111/nmo.13300

Abstract

BACKGROUND:

Regulation of gastrointestinal motility involves excitatory and inhibitory neurotransmission. Nitric oxide (NO), the major inhibitory neurotransmitter, acts via its receptor NO-sensitive guanylyl cyclase (NO-GC). In the GI tract, NO-GC is expressed in several cell types such as smooth muscle cells (SMC) and interstitial cells of Cajal (ICC). Using cell-specific knockout mice, we have previously shown that NO-GC modulates spontaneous contractions in colonic longitudinal smooth muscle. However, its detailed role in the colonic circular smooth muscle is still unclear.

METHODS:

Myography was performed to evaluate spontaneous contractions in rings of proximal colon (2.5 mm) from global (GCKO) and cell-specific knockout mice for NO-GC. Immunohistochemistry and in situ hybridization were used to specify NO-GC expression.

KEY RESULTS:

Colonic circular smooth muscle showed three different contraction patterns: high-frequency ripples, slow phasic contractions, and large contractions. Ripples formed independently of NO-GC. Slow phasic contractions occurred intermittently in WT, SMC-GCKO, and ICC-GCKO tissue, whereas they were more prominent and prolonged in GCKO and SMC/ICC-GCKO tissue. Tetrodotoxin and the NO-GC inhibitor ODQ transformed slow phasic contractions of WT and single cell-specific knockout into GCKO-like contractions. ODQ increased the frequency of large contractions in WT and ICC-GCKO colon but not in GCKO, SMC-GCKO, and SMC/ICC-GCKO preparations. Tetrodotoxin and hexamethonium abolished large contractions.

CONCLUSIONS AND INFERENCES:

We conclude that short rings of murine colon can be effectively used to record spontaneous contractions. Although NO-GC in SMC determines smooth muscle tone, concerted action of NO-GC in both SMC and ICC modulates slow phasic contractions and large contractions.

Transcription Factor GATA6: A Novel Marker and Putative Inducer of Ductal Metaplasia in Biliary Atresia.

Am J Physiol Gastrointest Liver Physiol.

2018 Feb 01

Soini T, Pihlajoki M, Andersson N, Lohi J, Huppert KA, Rudnick DA, Huppert SS, Wilson DB, Pakarinen MP, Heikinheimo M.
PMID: 29388792 | DOI: 10.1152/ajpgi.00362.2017

Biliary atresia (BA), a neonatal liver disease, is characterized by obstruction of extrahepatic bile ducts with subsequent cholestasis, inflammation, and progressive liver fibrosis. To gain insights into the pathophysiology of BA, we focused attention on GATA6, a transcription factor implicated in biliary development. Early in fetal development GATA6 expression is evident in cholangiocytes and hepatocytes, but by late gestation it is extinguished in hepatocytes. Utilizing a unique set of BA liver samples collected before and after successful portoenterostomy (PE), we found that GATA6 expression is markedly upregulated in hepatocytes of patients with BA compared to healthy and cholestatic disease controls. This upregulation is recapitulated in two murine models simulating bile duct obstruction and intrahepatic bile ductule expansion. GATA6 expression in BA livers correlates with two established negative prognostic indicators (age at PE, degree of intrahepatic bile ductule expansion) and decreases after normalization of serum bilirubin by PE. GATA6 expression in BA livers correlates with expression of known regulators of cholangiocyte differentiation ( JAGGED1, HNF1β, and HNF6). These same genes are upregulated after enforced expression of GATA6 in human hepatocyte cell models. In conclusion, GATA6 is a novel marker and a putative driver of hepatocyte-cholangiocyte metaplasia in BA and its expression in hepatocytes is downregulated after successful PE.

Creation of a long-acting nanoformulated dolutegravir

Nat Commun.

2018 Feb 06

Sillman B, Bade AN, Dash PK, Bhargavan B, Kocher T, Mathews S, Su H, Kanmogne GD, Poluektova LY, Gorantla S, McMillan J, Gautam N, Alnouti Y, Edagwa B, Gendelman HE.
PMID: 29402886 | DOI: 10.1038/s41467-018-02885-x

Potent antiretroviral activities and a barrier to viral resistance characterize the human immunodeficiency virus type one (HIV-1) integrase strand transfer inhibitor dolutegravir (DTG). Herein, a long-acting parenteral DTG was created through chemical modification to improve treatment outcomes. A hydrophobic and lipophilic modified DTG prodrug is encapsulated into poloxamer nanoformulations (NMDTG) and characterized by size, shape, polydispersity, and stability. Retained intracytoplasmic NMDTG particles release drug from macrophages and attenuate viral replication and spread of virus to CD4+ T cells. Pharmacokinetic tests in Balb/cJ mice show blood DTG levels at, or above, its inhibitory concentration90 of 64 ng/mL for 56 days, and tissue DTG levels for 28 days. NMDTG protects humanized mice from parenteral challenge of the HIV-1ADA strain for two weeks. These results are a first step towards producing a long-acting DTG for human use by affecting drug apparent half-life, cell and tissue drug penetration, and antiretroviral potency.

The Strength of Mechanical Forces Determines the Differentiation of Alveolar Epithelial Cells

Dev Cell.

2018 Feb 05

Li J, Wang Z, Chu Q, Jiang K, Li J, Tang N.
PMID: 29408236 | DOI: 10.1016/j.devcel.2018.01.008

The differentiation of alveolar epithelial type I (AT1) and type II (AT2) cells is essential for the lung gas exchange function. Disruption of this process results in neonatal death or in severe lung diseases that last into adulthood. We developed live imaging techniques to characterize the mechanisms that control alveolar epithelial cell differentiation. We discovered that mechanical forces generated from the inhalation of amniotic fluid by fetal breathing movements are essential for AT1 cell differentiation. We found that a large subset of alveolar progenitor cells is able to protrude from the airway epithelium toward the mesenchyme in an FGF10/FGFR2 signaling-dependent manner. The cell protrusion process results in enrichment of myosin in the apical region of protruded cells; this myosin prevents these cells from being flattened by mechanical forces, thereby ensuring their AT2 cell fate. Our study demonstrates that mechanical forces and local growth factors synergistically control alveolar epithelial cell differentiation.

Feasibility Evaluation of Myocardial Cannabinoid Type 1 Receptor Imaging in Obesity: A Translational Approach

JACC Cardiovasc Imaging.

2018 Feb 05

Valenta I, Varga ZV, Valentine H, Cinar R, Horti A, Mathews WB, Dannals RF, Steele K, Kunos G, Wahl RL, Pomper MG, Wong DF, Pacher P, Schindler TH.
PMID: 29413441 | DOI: 10.1016/j.jcmg.2017.11.019

Abstract

OBJECTIVES:

The aim of this study was to evaluate the feasibility of targeted imaging of myocardial cannabinoid type 1 receptor (CB1-R) and its potential up-regulation in obese mice with translation to humans using [11C]-OMAR and positron emission tomography (PET)/computed tomography (CT).

BACKGROUND:

Activation of myocardial CB1-R by endocannabinoids has been implicated in cardiac dysfunction in diabetic mice. Obesity may lead to an up-regulation of myocardial CB1-R, potentially providing a mechanistic link between obesity and the initiation and/or progression of cardiomyopathy.

METHODS:

Binding specificity of [11C]-OMAR to CB1-R was investigated by blocking studies with rimonabant in mice. The heart was harvested from each mouse, and its radioactivity was determined by γ-counter. Furthermore, [11C]-OMAR dynamic micro-PET/CT was carried out in obese and normal-weight mice. Ex vivo validation was performed by droplet digital polymerase chain reaction (absolute quantification) and RNAscope Technology (an in situ ribonucleic acid analysis platform). Subsequently, myocardial CB1-R expression was probed noninvasively with intravenous injection of CB1-R ligand [11C]-OMAR and PET/CT in humans with advanced obesity and normal-weight human control subjects, respectively.

RESULTS:

Rimonabant significantly blocked OMAR uptake in the heart muscle compared with vehicle, signifying specific binding of OMAR to the CB1-R in the myocardium. The myocardial OMAR retention quantified by micro-PET/CT in mice was significantly higher in obese compared with normal-weight mice. Absolute quantification of CB1-R gene expression with droplet digital polymerase chain reaction and in situ hybridization confirmed CB1-R up-regulation in all major myocardial cell types (e.g., cardiomyocytes, endothelium, vascular smooth muscle cells, and fibroblasts) of obese mice. Obese mice also had elevated myocardial levels of endocannabinoids anandamide and 2-arachidonoylglycerol compared with lean mice. Translation to humans revealed higher myocardial OMAR retention in advanced obesity compared with normal-weight subjects.

CONCLUSIONS:

Noninvasive imaging of cardiac CB1-R expression in obesity is feasible applying [11C]-OMAR and PET/CT. These results may provide a rationale for further clinical testing of CB1-R-targeted molecular imaging in cardiometabolic diseases.

Normal aging induces A1-like astrocyte reactivity

PNAS 2018

2018 Feb 07

Clarke LE, Liddelow SA, Chakraborty C, Münch AE, Heiman M, Barres BA.
PMID: - | DOI: 10.1073/pnas.1800165115

The decline of cognitive function occurs with aging, but the mechanisms responsible are unknown. Astrocytes instruct the formation, maturation, and elimination of synapses, and impairment of these functions has been implicated in many diseases. These findings raise the question of whether astrocyte dysfunction could contribute to cognitive decline in aging. We used the Bac-Trap method to perform RNA sequencing of astrocytes from different brain regions across the lifespan of the mouse. We found that astrocytes have region-specific transcriptional identities that change with age in a region-dependent manner. We validated our findings using fluorescence in situ hybridization and quantitative PCR. Detailed analysis of the differentially expressed genes in aging revealed that aged astrocytes take on a reactive phenotype of neuroinflammatory A1-like reactive astrocytes. Hippocampal and striatal astrocytes up-regulated a greater number of reactive astrocyte genes compared with cortical astrocytes. Moreover, aged brains formed many more A1 reactive astrocytes in response to the neuroinflammation inducer lipopolysaccharide. We found that the aging-induced up-regulation of reactive astrocyte genes was significantly reduced in mice lacking the microglial-secreted cytokines (IL-1α, TNF, and C1q) known to induce A1 reactive astrocyte formation, indicating that microglia promote astrocyte activation in aging. Since A1 reactive astrocytes lose the ability to carry out their normal functions, produce complement components, and release a toxic factor which kills neurons and oligodendrocytes, the aging-induced up-regulation of reactive genes by astrocytes could contribute to the cognitive decline in vulnerable brain regions in normal aging and contribute to the greater vulnerability of the aged brain to injury.

Notch signaling regulates Hey2 expression in a spatiotemporal dependent manner during cardiac morphogenesis and trabecular specification.

Sci Rep.

2018 Feb 08

Miao L, Li J, Li J, Tian X, Lu Y, Hu S, Shieh D, Kanai R, Zhou BY, Zhou B, Liu J, Firulli AB, Martin JF, Singer H, Zhou B, Xin H, Wu M.
PMID: 29422515 | DOI: 10.1038/s41598-018-20917-w

Hey2 gene mutations in both humans and mice have been associated with multiple cardiac defects. However, the currently reported localization of Hey2 in the ventricular compact zone cannot explain the wide variety of cardiac defects. Furthermore, it was reported that, in contrast to other organs, Notch doesn't regulate Hey2 in the heart. To determine the expression pattern and the regulation of Hey2, we used novel methods including RNAscope and a Hey2 CreERT2 knockin line to precisely determine the spatiotemporal expression pattern and level of Hey2 during cardiac development. We found that Hey2 is expressed in the endocardial cells of the atrioventricular canal and the outflow tract, as well as at the base of trabeculae, in addition to the reported expression in the ventricular compact myocardium. By disrupting several signaling pathways that regulate trabeculation and/or compaction, we found that, in contrast to previous reports, Notch signaling and Nrg1/ErbB2 regulate Hey2 expression level in myocardium and/or endocardium, but not its expression pattern: weak expression in trabecular myocardium and strong expression in compact myocardium. Instead, we found that FGF signaling regulates the expression pattern of Hey2 in the early myocardium, and regulates the expression level of Hey2 in a Notch1 dependent manner.

Notum attenuates Wnt/βcatenin signaling to promote tracheal cartilage patterning

Dev Biol.

2018 Feb 09

Gerhardt B, Leesman L, Burra K, Snowball J, Rosenzweig R, Guzman N, Ambalavanan M, Sinner D.
PMID: 29428562 | DOI: 10.1016/j.ydbio.2018.02.002

Tracheobronchomalacia (TBM) is a common congenital disorder in which the cartilaginous rings of the trachea are weakened or missing. Despite the high prevalence and clinical issues associated with TBM, the etiology is largely unknown. Our previous studies demonstrated that Wntless (Wls) and its associated Wnt pathways are critical for patterning of the upper airways. Deletion of Wls in respiratory endoderm caused TBM and ectopic trachealis muscle. To understand mechanisms by which Wls mediates tracheal patterning, we performed RNA sequencing in prechondrogenic tracheal tissue of Wlsf/f;ShhCre/wt embryos. Chondrogenic Bmp4, and Sox9 were decreased, while expression of myogenic genes was increased. We identified Notum, a deacylase that inactivates Wnt ligands, as a target of Wls induced Wnt signaling. Notum's mesenchymal ventral expression in prechondrogenic trachea overlaps with expression of Axin2, a Wnt/β-catenin target and inhibitor. Notum is induced by Wnt/β-catenin in developing trachea. Deletion of Notum activated mesenchymal Wnt/β-catenin and caused tracheal mispatternning of trachealis muscle and cartilage as well as tracheal stenosis. Notum is required for tracheal morphogenesis, influencing mesenchymal condensations critical for patterning of tracheal cartilage and muscle. We propose that Notum influences mesenchymal cell differentiation by generating a barrier for Wnt ligands produced and secreted by airway epithelial cells to attenuate Wnt signaling.

Comparison of clinical, radiological and morphological features including the distribution of HPV E6/E7 oncogenes in resection specimens of oropharyngeal squamous cell carcinoma

Oral Oncology

2018 Feb 06

Channir HI, Kiss K, Rubek N, Andersen J, Georgsen JB, Rathje GS, Charabi BW, von Buchwald C, Lajer CB.
PMID: - | DOI: 10.1016/j.oraloncology.2018.01.029

Abstract

Background

Human papillomavirus (HPV)-driven oropharyngeal squamous cell carcinoma (OPSCC) represents a distinct tumour entity in comparison to HPV-negative OPSCC. The clinical, radiological, morphological features and distribution of HPV E6/E7 mRNA were investigated in resected specimens of OPSCC.

Methods

We retrieved formalin-fixed, paraffin-embedded whole section slides from 24 p16/HPV-DNA positive and 18 p16/HPV-DNA negative primary tumours and 16 corresponding metastases in patients with early-stage OPSCC who underwent planned curative or diagnostic primary transoral robotic surgery. A detailed clinicoradiological and histopathological investigation of the tumours was performed along with detection of HPV E6/E7 mRNA by in situ hybridisation.

Results

HPV-driven OPSCC was characterised by non-keratinising morphology and was dominated by a cohesive invasion pattern at the leading edge of the tumour. Dysplastic zones of the squamous epithelium were strictly located in the tonsillar crypts in contrast to HPV-negative OPSCC which predominantly arised from the dysplastic surface epithelium. Thirteen HPV-driven OPSCC invaded through the tonsillar lymphoid compartment and into soft tissue, causing a stromal desmoplastic reaction. HPV mRNA was consistently but inhomogenously expressed in the entire tumour area and in the dysplastic squamous epithelium. There was no HPV expression in the adjacent normal epithelium and in the non-neoplastic tissues.

Conclusions

This study enhances the current understanding of HPV-driven OPSCC. Only tumours that invade through the lymphoid compartment induce a stromal desmoplastic reaction. A consistent but inhomogenous expression of E6 and E7 mRNA was found in tumour and dysplastic areas, emphasizing that the E6/E7 oncogenes are the driving factors in HPV-driven OPSCC.

Targeting p53-dependent stem cell loss for intestinal chemoprotection

Sci. Transl. Med.

2018 Feb 07

Leibowitz BJ, Yang L, Wei L, Buchanan ME, Rachid M, Parise RA, Beumer JH, Eiseman JL, Schoen RE, Zhang L, Yu J.
PMID: 29437148 | DOI: 10.1126/scitranslmed.aam7610

The gastrointestinal (GI) epithelium is the fastest renewing adult tissue and is maintained by tissue-specific stem cells. Treatment-induced GI side effects are a major dose-limiting factor for chemotherapy and abdominal radiotherapy and can decrease the quality of life in cancer patients and survivors. p53 is a key regulator of the DNA damage response, and its activation results in stimulus- and cell type-specific outcomes via distinct effectors. We demonstrate that p53-dependent PUMA induction mediates chemotherapy-induced intestinal injury in mice. Genetic ablation of Puma, but not of p53, protects against chemotherapy-induced lethal GI injury. Blocking chemotherapy-induced loss of LGR5+ stem cells by Puma KO or a small-molecule PUMA inhibitor (PUMAi) prevents perturbation of the stem cell niche, rapid activation of WNT and NOTCH signaling, and stem cell exhaustion during repeated exposures. PUMAi also protects human and mouse colonic organoids against chemotherapy-induced apoptosis and damage but does not protect cancer cells in vitro or in vivo. Therefore, targeting PUMA is a promising strategy for normal intestinal chemoprotection because it selectively blocks p53-dependent stem cell loss but leaves p53-dependent protective effects intact.

Indirect presentation in the thymus limits naïve and regulatory T cell differentiation by promoting deletion of self-reactive thymocytes

Immunology.

2018 Feb 07

Yap JY, Wirasinha RC, Chan A, Howard DR, Goodnow CC, Daley SR.
PMID: 29411880 | DOI: 10.1111/imm.12904

Acquisition of T cell central tolerance involves distinct pathways of self-antigen presentation to thymocytes. One pathway termed indirect presentation requires a self-antigen transfer step from thymic epithelial cells (TECs) to bone marrow (BM)-derived cells before the self-antigen is presented to thymocytes. The role of indirect presentation in central tolerance is context-dependent, potentially due to variation in self-antigen expression, processing and presentation in the thymus. Here, we report experiments in mice in which TECs expressed a membrane-bound transgenic self-antigen, hen egg lysozyme (HEL), from either the insulin (insHEL) or thyroglobulin (thyroHEL) promoter. Intrathymic HEL expression was less abundant and more confined to the medulla in insHEL mice compared to thyroHEL mice. When indirect presentation was impaired by generating mice lacking MHCII expression in BM-APCs, insHEL-mediated thymocyte deletion was abolished, whereas thyroHEL-mediated deletion occurred at a later stage of thymocyte development and Foxp3+ T-regulatory cell differentiation increased. Indirect presentation increased the strength of TCR signalling that both self-antigens induced in thymocytes, as assessed by Helios expression. Thus, indirect presentation limits the differentiation of naïve and regulatory T cells by promoting deletion of self-reactive thymocytes.

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Description
sense
Example: Hs-LAG3-sense
Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron#
Example: Mm-Htt-intron2
Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan
Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)
A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp
Example: Hs-PDGFB-No-XMm
Does not cross detect with the species (Sp)
XSp
Example: Rn-Pde9a-XMm
designed to cross detect with the species (Sp)
O#
Example: Mm-Islr-O1
Alternative design targeting different regions of the same transcript or isoforms
CDS
Example: Hs-SLC31A-CDS
Probe targets the protein-coding sequence only
EnEmProbe targets exons n and m
En-EmProbe targets region from exon n to exon m
Retired Nomenclature
tvn
Example: Hs-LEPR-tv1
Designed to target transcript variant n
ORF
Example: Hs-ACVRL1-ORF
Probe targets open reading frame
UTR
Example: Hs-HTT-UTR-C3
Probe targets the untranslated region (non-protein-coding region) only
5UTR
Example: Hs-GNRHR-5UTR
Probe targets the 5' untranslated region only
3UTR
Example: Rn-Npy1r-3UTR
Probe targets the 3' untranslated region only
Pan
Example: Pool
A mixture of multiple probe sets targeting multiple genes or transcripts

Enabling research, drug development (CDx) and diagnostics

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