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Species

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Gene

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Platform

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  • Manual Assay miRNAscope (5159) Apply Manual Assay miRNAscope filter
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  • T3 (3) Apply T3 filter
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Channel

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HiPlex Channel

  • T1 (85619) Apply T1 filter
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  • T12 (85613) Apply T12 filter
  • T11 (85602) Apply T11 filter
  • T9 (83134) Apply T9 filter
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  • T3 (83117) Apply T3 filter
  • T6 (83117) Apply T6 filter
  • T5 (83111) Apply T5 filter
  • 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
  • Metabolism (91) Apply Metabolism filter
  • Developmental (83) Apply Developmental filter
  • Stem cell (78) Apply Stem cell filter
  • 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
  • Reproduction (38) Apply Reproduction filter
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  • Obesity (29) Apply Obesity filter
  • Other: Lung (29) Apply Other: Lung filter
  • Behavior (27) Apply Behavior filter
  • Kidney (27) Apply Kidney filter
  • 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
  • Regeneration (20) Apply Regeneration filter
  • Skin (20) Apply Skin filter
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  • Fibrosis (17) Apply Fibrosis filter
  • Other: Liver (17) Apply Other: Liver filter
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  • behavioral (16) Apply behavioral filter
  • 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 (256875) Apply Target Probes filter
  • Control Probe - Automated Leica (411) Apply Control Probe - Automated Leica filter
  • Control Probe - Automated Leica Multiplex (286) Apply Control Probe - Automated Leica Multiplex filter
  • Control Probe - Automated Leica Duplex (169) Apply Control Probe - Automated Leica Duplex filter
  • Control Probe- Manual RNAscope Multiplex (149) 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 (138) 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
  • Control Probe - LS BaseScope Singleplex (40) Apply Control Probe - LS BaseScope Singleplex filter
  • 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
  • Control Probe - Manual BaseScope Duplex (4) Apply Control Probe - Manual BaseScope Duplex filter
  • Manual Assay miRNAscope Red (4) Apply Manual Assay miRNAscope Red filter
  • Automated Assay 2.5: Ventana System (3) Apply Automated Assay 2.5: Ventana System 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

  • Publications (7110) Apply Publications filter

Application

  • Cancer (141121) Apply Cancer filter
  • Neuroscience (51506) Apply Neuroscience filter
  • Cancer, Neuroscience (32649) Apply Cancer, Neuroscience filter
  • Non-coding RNA (24489) Apply Non-coding RNA filter
  • Cancer, Inflammation (16566) Apply Cancer, Inflammation filter
  • Cancer, Inflammation, Neuroscience (12901) Apply Cancer, Inflammation, Neuroscience filter
  • Inflammation (9888) Apply Inflammation filter
  • Cancer, Stem Cell (8008) Apply Cancer, Stem Cell filter
  • Cancer, Neuroscience, Stem Cell (7076) Apply Cancer, Neuroscience, Stem Cell filter
  • Cancer, Immunotherapy, Inflammation, Neuroscience, Stem Cell (6865) Apply Cancer, Immunotherapy, Inflammation, Neuroscience, Stem Cell filter
  • Cancer, Inflammation, Neuroscience, Stem Cell (5437) Apply Cancer, Inflammation, Neuroscience, Stem Cell filter
  • Immunotherapy (5368) Apply Immunotherapy filter
  • Cancer, Immunotherapy (3902) Apply Cancer, Immunotherapy filter
  • Stem Cell (3396) Apply Stem Cell filter
  • Cancer, Immunotherapy, Neuroscience, Stem Cell (3058) Apply Cancer, Immunotherapy, Neuroscience, Stem Cell filter
  • Cancer, Immunotherapy, Inflammation (2852) Apply Cancer, Immunotherapy, Inflammation filter
  • Cancer, Immunotherapy, Inflammation, Neuroscience (1878) Apply Cancer, Immunotherapy, Inflammation, Neuroscience filter
  • Cancer, Immunotherapy, Neuroscience (1822) Apply Cancer, Immunotherapy, Neuroscience filter
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E2F1 controls germ cell apoptosis during the first wave of spermatogenesis

Andrology. 2015 Sep;3(5):1000-14.

Rotgers E, Nurmio M, Pietilä E, Cisneros-Montalvo S, Toppari J.
PMID: 26311345 | DOI: 10.1111/andr.12090.

Cell cycle control during spermatogenesis is a highly complex process owing to the control of the mitotic expansion of the spermatogonial cell population and following meiosis, induction of DNA breaks during meiosis and the high levels of physiological germ-cell apoptosis. We set out to study how E2F1, a key controller of cell cycle, apoptosis, and DNA damage responses, functions in the developing and adult testis. We first analyzed the expression pattern of E2f1 during post-natal testis development using RNA in situ hybridization, which showed a differential expression pattern of E2f1 in the adult and juvenile mouse testes. To study the function of E2f1, we took advantage of the E2F1(-/-) mouse line, which was back-crossed to C57Bl/6J genetic background. E2f1 loss led to a severe progressive testicular atrophy beginning at the age of 20 days. Spermatogonial apoptosis during the first wave of spermatogenesis was decreased. However, already in the first wave of spermatogenesis an extensive apoptosis of spermatocytes was observed. In the adult E2F1(-/-) testes, the atrophy due to loss of spermatocytes was further exacerbated by loss of spermatogonial stem cells. Surprisingly, only subtle changes in global gene expression array profiling were observed in E2F1(-/-) testis at PND20. To dissect the changes in each testicular cell type, an additional comparative analysis of the array data was performed making use of previously published data on transcriptomes of the individual testicular cell types. Taken together, our data indicate that E2F1 has a differential role during first wave of spermatogenesis and in the adult testis, which emphasizes the complex nature of cell cycle control in the developing testis.
TMBIM6 (transmembrane BAX inhibitor motif containing 6) Enhances Autophagy and Reduces Renal Dysfunction in a Cyclosporine A-induced nephrotoxicity model.

Autophagy. 2015 Aug 25:0.

Yadav RK, Lee GH, Lee HY, Li B, Jung HE, Rashid HO, Choi MK, Yadav BK, Kim WH, Kim KW, Park BH, Kim W, Lee YC, Kim HR, Chae HJ.
PMID: 26305401

Cyclosporine A (CsA) is widely used as an immunosuppressor in transplantation. Previous studies reported that CsA induces autophagy and that chronic treatment with CsA results in accumulation of autophagosomes and reduced autophagic clearance. Autophagy is a prosurvival process that promotes recovery from acute kidney injury by degrading misfolded proteins produced in the kidney. In the present study, we used TMBIM6-expressing HK-2, human kidney tubular cells (TMBIM6 cells) and Tmbim6 knockout (tmbim6-/-) mice. When exposed to CsA, the TMBIM6 cells maintained autophagy activity by preventing autophagosome accumulation. With regard to signaling, PRKKA/AMPK phosphorylation and mechanistic target of rapamycin (serine/threonine kinase) complex 1 (MTORC1) expression and its downstream target TFEB (transcription factor EB), a lysosome biogenesis factor, were regulated in the TMBIM6 cells. Lysosomal activity was highly increased or stably maintained in the presence of TMBIM6. In addition, treatment of tmbim6-/- mice with CsA resulted in increased autophagosome formation and decreased lysosome formation and activity. We also found that tmbim6-/- mice were susceptible to CsA-induced kidney injury. Taken together, these results indicate that TMBIM6 protects against CsA-induced nephrotoxicity both in vitro and in vivo by inducing autophagy and activating lysosomes.
Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity.

Nat Cell Biol. 2015 Sep;17(9):1145-57.

Kourtidis A, Ngok SP, Pulimeno P, Feathers RW, Carpio LR, Baker TR, Carr JM, Yan IK, Borges S, Perez EA, Storz P, Copland JA, Patel T, Thompson EA, Citi S, Anastasiadis PZ.
PMID: 26302406 | DOI: 10.1038/ncb3227

E-cadherin and p120 catenin (p120) are essential for epithelial homeostasis, but can also exert pro-tumorigenic activities. Here, we resolve this apparent paradox by identifying two spatially and functionally distinct junctional complexes in non-transformed polarized epithelial cells: one growth suppressing at the apical zonula adherens (ZA), defined by the p120 partner PLEKHA7 and a non-nuclear subset of the core microprocessor components DROSHA and DGCR8, and one growth promoting at basolateral areas of cell-cell contact containing tyrosine-phosphorylated p120 and active Src. Recruitment of DROSHA and DGCR8 to the ZA is PLEKHA7 dependent. The PLEKHA7-microprocessor complex co-precipitates with primary microRNAs (pri-miRNAs) and possesses pri-miRNA processing activity. PLEKHA7 regulates the levels of select miRNAs, in particular processing of miR-30b, to suppress expression of cell transforming markers promoted by the basolateral complex, including SNAI1, MYC and CCND1. Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.
Reporter mouse strain provides a novel look at angiotensin type-2 receptor distribution in the central nervous system.

Brain Struct Funct. 2014 Nov 27.

de Kloet AD, Wang L, Ludin JA, Smith JA, Pioquinto DJ, Hiller H, Steckelings UM, Scheuer DA, Sumners C, Krause EG.
PMID: 25427952

Angiotensin-II acts at its type-1 receptor (AT1R) in the brain to regulate body fluid homeostasis, sympathetic outflow and blood pressure. However, the role of the angiotensin type-2 receptor (AT2R) in the neural control of these processes has received far less attention, largely because of limited ability to effectively localize these receptors at a cellular level in the brain. The present studies combine the use of a bacterial artificial chromosome transgenic AT2R-enhanced green fluorescent protein (eGFP) reporter mouse with recent advances in in situ hybridization (ISH) to circumvent this obstacle. Dual immunohistochemistry (IHC)/ISH studies conducted in AT2R-eGFP reporter mice found that eGFP and AT2R mRNA were highly co-localized within the brain. Qualitative analysis of eGFP immunoreactivity in the brain then revealed localization to neurons within nuclei that regulate blood pressure, metabolism, and fluid balance (e.g., NTS and median preoptic nucleus [MnPO]), as well as limbic and cortical areas known to impact stress responding and mood. Subsequently, dual IHC/ISH studies uncovered the phenotype of specific populations of AT2R-eGFP cells. For example, within the NTS, AT2R-eGFP neurons primarily express glutamic acid decarboxylase-1 (80.3 ± 2.8 %), while a smaller subset express vesicular glutamate transporter-2 (18.2 ± 2.9 %) or AT1R (8.7 ± 1.0 %). No co-localization was observed with tyrosine hydroxylase in the NTS. Although AT2R-eGFP neurons were not observed within the paraventricular nucleus (PVN) of the hypothalamus, eGFP immunoreactivity is localized to efferents terminating in the PVN and within GABAergic neurons surrounding this nucleus. These studies demonstrate that central AT2R are positioned to regulate blood pressure, metabolism, and stress responses.
Neuroimmune Regulation of GABAergic Neurons Within the Ventral Tegmental Area During Withdrawal from Chronic Morphine.

Neuropsychopharmacology. 2015 Jul 23.

Taylor AM, Castonguay A, Ghogha A, Vayssiere P, Pradhan AA, Xue L, Mehrabani S, Wu J, Levitt P, Olmstead MC, De Koninck Y, Evans CJ, Cahill CM.
PMID: 26202104 | DOI: 10.1038/npp.2015.221.

Opioid dependence is accompanied by neuroplastic changes in reward circuitry leading to a negative affective state contributing to addictive behaviors and risk of relapse. The current study presents a neuroimmune mechanism through which chronic opioids disrupt the ventral tegmental area (VTA) dopaminergic circuitry that contributes to impaired reward behavior. Opioid dependence was induced in rodents by treatment with escalating doses of morphine. Microglial activation was observed in the VTA following spontaneous withdrawal from chronic morphine treatment. Opioid-induced microglial activation resulted in an increase in brain-derived neurotrophic factor (BDNF) expression and a reduction in the expression and function of the K+Cl- co-transporter KCC2 within VTA GABAergic neurons. Inhibition of microglial activation or interfering with BDNF signaling prevented the loss of Cl- extrusion capacity and restored the rewarding effects of cocaine in opioid-dependent animals. Consistent with a microglial-derived BDNF-induced disruption of reward, intra-VTA injection of BDNF or a KCC2 inhibitor resulted in a loss of cocaine-induced place preference in opioid-naïve animals. The loss of the extracellular Cl- gradient undermines GABAA-mediated inhibition, and represents a mechanism by which chronic opioid treatments can result in blunted reward circuitry. This study directly implicates microglial-derived BDNF as a negative regulator of reward in opioid-dependent states, identifying new therapeutic targets for opiate addictive behaviors.
Nucleoporin 35 regulates cardiomyocyte pH homeostasis by controlling Na+-H+ exchanger-1 expression.

J Mol Cell Biol. 2015 Aug 10.

Xu L, Pan L, Li J, Huang B, Feng J, Li C, Wang S, The E, Liu Y, Yuan T, Zhen L, Liang D, Liu Y, Li L, Cui Y, Jiang X, Peng L, Chen YH.
PMID: 26260029 | DOI: mjv054.

The mammalian nuclear pore complex is comprised of ∼30 different nucleoporins (Nups). It governs the nuclear import of gene expression modulators and the export of mRNAs. In cardiomyocytes, Na+-H+ exchanger-1 (NHE1) is an integral membrane protein that exclusively regulates intracellular pH (pHi) by exchanging one intracellular H+ for one extracellular Na+. However, the role of Nups in cardiac NHE1 expression remains unknown. We herein report that Nup35 regulates cardiomyocyte NHE1 expression by controlling the nucleo-cytoplasmic trafficking of nhe1 mRNA. The N-terminal domain of Nup35 determines nhe1 mRNA nuclear export by targeting the 5'-UTR (-412--213 nt) of nhe1 mRNA. Nup35 ablation weakens the resistance of cardiomyocytes to an acid challenge by depressing NHE1 expression. Moreover, we identify that Nup35 and NHE1 are simultaneously downregulated in ischemic cardiomyocytes both in vivo and in vitro. Enforced expression of Nup35 effectively counteracts the anoxia-induced intracellular acidification. We conclude that Nup35 selectively regulates cardiomyocyte pHi homeostasis by posttranscriptionally controlling NHE1 expression. This finding reveals a novel regulatory mechanism of cardiomyocyte pHi, and may provide insight into the therapeutic strategy for ischemic cardiac diseases.
Kinesin-1 interacts with Bucky ball to form germ cells and is required to pattern the zebrafish body axis.

Development. 2015 Aug 7.

Campbell PD, Heim AE, Smith MZ, Marlow FL.
PMID: 26253407 | DOI: dev.124586.

In animals, specification of the primordial germ cells (PGCs), the stem cells of the germline, is required to transmit genetic information from one generation to the next. Bucky ball (Buc) is essential for germ plasm (GP) assembly in oocytes and its overexpression results in excess PGCs in zebrafish embryos. However, the mechanistic basis for the excess PGCs in response to Buc overexpression, and whether endogenous Buc functions during embryogenesis are unknown. Here we show that endogenous Buc, like GP and overexpressed Buc-GFP, accumulates at embryonic cleavage furrows. Furthermore, we show that the maternally expressed zebrafish Kinesin-1 Kif5Ba is a binding partner of Buc and that maternal kif5Ba (Mkif5Ba) plays an essential role in germline specification in vivo. Specifically, Mkif5Ba is required to recruit GP to cleavage furrows and thereby specifies PGCs. Moreover, Mkif5Ba is required to enrich Buc at cleavage furrows and for Buc's ability to promote excess PGCs, providing mechanistic insight into how Buc functions to assemble embryonic GP. In addition, we show that Mkif5Ba is also essential for dorsoventral (DV) patterning. Specifically, Mkif5Ba promotes formation of the parallel vegetal microtubule array required to asymmetrically position dorsal determinants (DDs) towards the prospective dorsal side. Interestingly, while Syntabulin and wnt8a translocation depend on kif5Ba, grip2a translocation does not, providing evidence for two distinct mechanisms by which DDs may be asymmetrically distributed. These studies identify essential roles for maternal Kif5Ba in PGC specification and DV patterning and provide mechanistic insight into Buc functions during early embryogenesis.
An Nfic-Hedgehog Signaling Cascade Regulates Tooth Root Development

Liu Y, Feng J, Li J, Zhao H, Ho TV, Chai Y.
PMID: 26293299

Coordination between the Hertwig’s Epithelial Root Sheath (HERS) and apical papilla (AP) is crucial for proper tooth root development. The Hedgehog (Hh) signaling pathway and Nfic are both involved in tooth root development, however their relationship has yet to be elucidated. Here we establish a time course of mouse molar root development by histological staining of sections and demonstrate that Hh signaling is active before and during root development in the AP and HERS using Gli1 reporter mice. The proper pattern of Hh signaling activity in the AP is critical for the proliferation of dental mesenchymal cells, because either inhibition with Hh inhibitors or constitutive activation of Hh signaling activity in transgenic mice leads to decreased proliferation in the AP and shorter roots. Moreover, Hh activity is elevated in Nfic-/- mice, a root defect model, whereas RNA sequencing and in situ hybridization show that Hh attenuator Hhip is down-regulated. ChIP and RNAscope analyses suggest that Nfic binds to the promoter region of Hhip. Treatment of Nfic-/- mice with Hh inhibitor partially restores cell proliferation, AP growth and root development. Taken together, our results demonstrate that an Nfic-Hhip-Hh signaling pathway is critical for apical papilla growth and proper root formation. This discovery provides insight into the molecular mechanisms regulating tooth root development.
FGFR1 and FGFR2 in Fibrolamellar Carcinoma

Histopathology. 2015 Aug 11.

Graham RP, Garcia JJ, Greipp PT, Barr Fritcher EG, Kipp BR, Torbenson MS.
PMID: 26259677 | DOI: 10.1111/his.12799.

Abstract AIMS: Fibrolamellar carcinoma is characterized by a recurrent DNAJB1-PRKACA chimeric transcript. The functional properties of the fusion are unknown but are believed to include PRKACA upregulation. PRKCA is a subunit of protein kinase A. The downstream targets of protein kinase A are unknown, but may include interactions with fibroblast growth factor (FGFR) pathways. In addition, inhibitors for FGFR proteins have recently been developed. METHODS AND RESULTS: 19 histologically confirmed fibrolamellar carcinomas were studied. All showed the characteristic DNAJB1-PRKACA transcript by RT-PCR. Immunohistochemistry for FGFR1 was negative in 19/19 cases using a monoclonal antibody, while a polyclonal antibody showed no expression (n=11) or weak and focal expression (n=8). RNA in situ hybridization was 2+ in two cases, 1+ in four cases and negative in four cases. FGFR1 fluorescence in situ hybridization (FISH) revealed polysomy of chromosome 8 in 17/19 cases. Break apart FISH for FGFR2 was negative for rearrangements in 12/12 informative cases. CONCLUSIONS: Fibrolamellar carcinomas show polysomy of chromosome 8 and the FGFR1 locus, only modest mRNA expression and weak or absent expression at the protein level. FGFR2 rearrangement was not detected. These data reduce the likelihood that FGFR inhibitors will be effective in the treatment of most fibrolamellar carcinomas.
The Role of LOX and LOXL2 in the Pathogenesis of an Experimental Model of Choroidal Neovascularization.

Invest Ophthalmol Vis Sci. 2015 Aug 1;56(9):5280-9.

Van Bergen T, Spangler R, Marshall D, Hollanders K, Van de Veire S, Vandewalle E, Moons L, Herman J, Smith V, Stalmans I.
PMID: 26258612 | DOI: 10.1167/iovs.14-15513.

Abstract PURPOSE: We investigated whether lysyl oxidase (LOX) and lysyl oxidase-like 2 (LOXL2) play a role in an experimental model of choroidal neovascularization (CNV). The therapeutic potential of antibodies against LOX (M64) and LOXL2 (AB0023) was evaluated in a murine laser-induced CNV model. METHODS: Expression of LOX and LOXL2 in the posterior eye cups (including retina, retinal pigment epithelium, choroid, and sclera) was studied by qRT-PCR and immunohistochemistry. In the murine model of CNV, both antibodies were administered intraperitoneally every other day until the day killed. On different time points after laser, treatment outcome was studied by immunohistochemical analysis of inflammation, angiogenesis and fibrosis, and by transcript analysis of different cytokines. RESULTS: Levels of LOX and LOXL2 in the posterior eye cups were increased after CNV-induction at different time points after laser. At day 35, their protein expression patterns appeared to correlate with retinal glial cells and endothelial cells, respectively. Both antibodies significantly inhibited fibrosis, whereas AB0023 also significantly reduced angiogenesis and inflammation. Transcript levels of α-1 type I collagen (COL1A1) in the posterior eye cups were significantly decreased in lasered mice treated with either M64 or AB0023. Vascular endothelial growth factor expression was also reduced only after AB0023 treatment, whereas activated fibroblast marker α-smooth muscle actin (αSMA) levels were not significantly changed. CONCLUSIONS: This study suggests that LOX and LOXL2 may play an important role in the pathogenesis of AMD. Targeting LOXL2 could have a broader efficacy than targeting LOX, by reducing angiogenesis and inflammation, as well as fibrosis.
Correlation of p16 immunohistochemistry in FNA biopsies with corresponding tissue specimens in HPV-related squamous cell carcinomas of the oropharynx.

Cancer Cytopathol. 2015 Aug 4.

Jalaly JB, Lewis JS Jr, Collins BT, Wu X, Ma XJ, Luo Y, Bernadt CT.
PMID: 26242494 | DOI: 10.1002/cncy.21600.

Abstract BACKGROUND: Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (SCC) is a unique form of carcinoma that is important to identify for prognosis and treatment. Immunohistochemistry (IHC) for p16 (also known as cyclin-dependent kinase inhibitor 2A, multiple tumor suppressor 1) is used as a surrogate marker for transcriptionally active, high-risk HPV. The primary objective of this study was to correlate p16 IHC of cell blocks from fine-needle aspirations (FNAs) with surgical pathology specimens of HPV-related oropharyngeal SCC. METHODS: In total, 48 patients who had a diagnosis of oropharyngeal or nonoropharyngeal SCC and also had an FNA that demonstrated metastatic SCC with available cell block material were identified. IHC for p16 was evaluated on both FNA cell blocks and surgical pathology specimens. In situ hybridization for high-risk HPV messenger RNA was performed on 31 of the FNA cell blocks. RESULTS: Although partial p16 staining was observed in the majority of cell blocks, there was concordance in 47 of 48 FNAs (98%) with surgical pathology specimens when strong positive p16 staining of at least 15% of tumor cells in FNA cell block material was present. In addition, high-risk HPV RNA in situ hybridization demonstrated a high correlation with p16 staining in surgical pathology specimens (96%) and FNAs (93%). CONCLUSIONS: There was excellent correlation between p16 IHC of FNA cell blocks and surgical pathology specimens using a cutoff of at least 15% positive staining in cell blocks. The recommended threshold (70% positive staining) for surgical pathology specimens may yield a high rate of false-negative results if applied to FNA cell blocks.
ETV1 mRNA is specifically expressed in gastrointestinal stromal tumors

Virchows Arch. 2015 Aug 5.

Jang BG, Lee HE, Kim WH.
PMID: 26243012

Gastrointestinal stromal tumors (GISTs) develop from interstitial cells of Cajal (ICCs) mainly by activating mutations in the KIT or PDGFRA genes. Immunohistochemical analysis for KIT, DOG1, and PKC-θ is used for the diagnosis of GIST. Recently, ETV1 has been shown to be a lineage survival factor for ICCs and required for tumorigenesis of GIST. We investigated the diagnostic value of ETV1expression in GIST. On fresh-frozen tissue samples, RT-PCR analysis showed that ETV1 as well as KIT, DOG1, and PKC-θ are highly expressed in GISTs. On tissue microarrays containing 407 GISTs and 120 non-GIST mesenchymal tumors of GI tract, we performed RNA in situ hybridization (ISH) for ETV1 together with immunohistochemical analysis for KIT, DOG1, PKC-θ, CD133, and CD44. Overall, 387 (95 %) of GISTs were positive for ETV1, while KIT and DOG1 were positive in 381 (94 %) and 392 (96 %) cases, respectively, showing nearly identical overall sensitivity of ETV1, KIT, and DOG1 for GISTs. In addition, ETV1 expression was positively correlated with that of KIT. Notably, ETV1 was positive in 15 of 26 (58 %) KIT-negative GISTs and even positive in 2 cases of GIST negative for KIT and DOG1, whereas only 6 (5 %) non-GIST mesenchymal GI tumors expressed ETV1. We conclude that ETV1 is specifically expressed in the majority of GISTs, even in some KIT-negative cases, suggesting that ETV1 may be useful as ancillary marker in diagnostically difficult select cases of GIST.

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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

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