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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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Human papillomavirus infection and its biomarkers' expressions in laryngeal basaloid squamous cell carcinoma.

J Int J Clin Exp Pathol (2018)

2018 Nov 15

Cui L, Qu C, Liu H.
| DOI: ISSN:1936-2625/IJCEP0085220

Abstract: Aims: To investigate the frequency and transcriptional activity of HPV and its correlation to p16 and p21 expression in basaloid squamous cell carcinoma (BSCC) of the larynx. Methods: We evaluated tissues from 29 patients with BSCC of the larynx for the expressions of p16 and p21 proteins by immunohistochemistry (IHC) and for HPV E6 and E7 mRNA by RNA in situ hybridization (ISH). The presence of genotype-specific HPV DNA was evaluated using PCR-RDB in formalin-fixed paraffin-embedded tissues. P16 and p21 expression and HPV DNA status were correlated with clinicopathological features. Results: HPV DNA was detected in 8 of 29 (27.59%) patients, with HPV-16 being the predominant genotype. P16 and p21-positivity were observed in 7/29 (24.14%) and 8/29 (27.59%) patients, respectively. HPV was not correlated with p16 expression (P > 0.05). However, p21 expression was significantly higher in HPV-positive tumors than in HPV-negative tumors (P < 0.05). No cases exhibited transcriptionally active HPV in our series. Conclusion: Our findings suggest that a small fraction of BSCC of the larynx is HPV DNA-positive in this Chinese population, p21 expression was significantly higher in HPV-positive tumors, and no cases were HPV transcriptionally active in this small cohort. Further research of HPV and its role in BSCC of the larynx are warranted.
Endogenous Notch Signaling in Adult Kidneys Maintains Segment-Specific Epithelial Cell Types of the Distal Tubules and Collecting Ducts to Ensure Water Homeostasis.

J Am Soc Nephrol. 2018 Dec 4.

2018 Dec 01

Mukherjee M, deRiso J, Otterpohl K, Ratnayake I, Kota D, Ahrenkiel P, Chandrasekar I, Surendran K.
PMID: 30514723 | DOI: 10.1681/ASN.2018040440

Abstract Background Notch signaling is required during kidney development for nephron formation and principal cell fate selection within the collecting ducts. Whether Notch signaling is required in the adult kidney to maintain epithelial diversity, or whether its loss can trigger principal cell transdifferentiation (which could explain acquired diabetes insipidus in patients receiving lithium) is unclear. Methods To investigate whether loss of Notch signaling can trigger principal cells to lose their identity, we genetically inactivated Notch1 and Notch2, inactivated the Notch signaling target Hes1, or induced expression of a Notch signaling inhibitor in all of the nephron segments and collecting ducts in mice after kidney development. We examined renal function and cell type composition of control littermates and mice with conditional Notch signaling inactivation in adult renal epithelia. In addition, we traced the fate of genetically labeled adult kidney collecting duct principal cells after Hes1 inactivation or lithium treatment. Results Notch signaling was required for maintenance of Aqp2-expressing cells in distal nephron and collecting duct segments in adult kidneys. Fate tracing revealed mature principal cells in the inner stripe of the outer medulla converted to intercalated cells after genetic inactivation of Hes1 and, to a lesser extent, lithium treatment. Hes1 ensured repression of Foxi1 to prevent the intercalated cell program from turning on in mature Aqp2+ cell types. Conclusions Notch signaling via Hes1 regulates maintenance of mature renal epithelial cell states. Loss of Notch signaling or use of lithium can trigger transdifferentiation of mature principal cells to intercalated cells in adult kidneys.

Distribution of bile acid receptor TGR5 in the gastrointestinal tract of dogs.

Histol Histopathol. 2018 Jul 12:18025.

2018 Jul 12

Giaretta PR, Suchodolski JS, Blick AK, Steiner JM, Lidbury JA, Rech RR.
PMID: 29999170 | DOI: 10.14670/HH-18-025

Takeda-G-protein-receptor-5 (TGR5) is a receptor for bile acids and its expression has been described in a variety of tissues and species. Characterization of TGR5 distribution and function has been investigated in drug discovery for the treatment of metabolic diseases in humans. Because dogs are one of the species used in biomedical research and share some similarities with human gastrointestinal diseases, the objective of this study was to characterize the distribution of TGR5 receptor in the canine species. This study characterizes the distribution of TGR5 receptor in the gastrointestinal tract, liver, gallbladder, and pancreas of 8 dogs. The distribution of TGR5 antigen and mRNA expression was investigated using immunohistochemistry and RNA in situ hybridization, respectively. TGR5 immunolabeling was located in the cell membrane or in the cell membrane and cytoplasm. TGR5 immunolabeling was broadly distributed in macrophages, endothelial cells, ganglion cells, and leiomyocytes throughout all the examined tissues. Epithelial cells from tongue, stomach to rectum, as well as from gallbladder, biliary and pancreatic ducts demonstrated TGR5 immunolabeling. In endocrine cells, TGR5 immunolabeling was observed in intestinal enteroendocrine cells and islets of Langerhans in the pancreas. The hepatocytes had a unique pattern of immunolabeling located on the canalicular surface of the cell membrane. TGR5 mRNA expression was located mainly in the nucleus and the only negative cells throughout all examined tissues were striated muscle from tongue and esophagus, muscularis mucosae, esophageal glands, and hepatic sinusoids. These findings indicate that the bile acid receptor TGR5 is ubiquitously distributed in the canine gastrointestinal tract.
Epacadostat Plus Pembrolizumab in Patients With Advanced Solid Tumors: Phase I Results From a Multicenter, Open-Label Phase I/II Trial (ECHO-202/KEYNOTE-037).

J Clin Oncol. 2018 Sep 28:JCO2018789602.

2018 Sep 28

Mitchell TC, Hamid O, Smith DC, Bauer TM, Wasser JS, Olszanski AJ, Luke JJ, Balmanoukian AS, Schmidt EV, Zhao Y, Gong X, Maleski J, Leopold L, Gajewski TF.
PMID: 30265610 | DOI: 10.1200/JCO.2018.78.9602

Abstract PURPOSE: Tumors may evade immunosurveillance through upregulation of the indoleamine 2,3-dioxygenase 1 (IDO1) enzyme. Epacadostat is a potent and highly selective IDO1 enzyme inhibitor. The open-label phase I/II ECHO-202/KEYNOTE-037 trial evaluated epacadostat plus pembrolizumab, a programmed death protein 1 inhibitor, in patients with advanced solid tumors. Phase I results on maximum tolerated dose, safety, tolerability, preliminary antitumor activity, and pharmacokinetics are reported. PATIENTS AND METHODS: Patients received escalating doses of oral epacadostat (25, 50, 100, or 300 mg) twice per day plus intravenous pembrolizumab 2 mg/kg or 200 mg every 3 weeks. During the safety expansion, patients received epacadostat (50, 100, or 300 mg) twice per day plus pembrolizumab 200 mg every 3 weeks. RESULTS: Sixty-two patients were enrolled and received one or more doses of study treatment. The maximum tolerated dose of epacadostat in combination with pembrolizumab was not reached. Fifty-two patients (84%) experienced treatment-related adverse events (TRAEs), with fatigue (36%), rash (36%), arthralgia (24%), pruritus (23%), and nausea (21%) occurring in ≥ 20%. Grade 3/4 TRAEs were reported in 24% of patients. Seven patients (11%) discontinued study treatment because of TRAEs. No TRAEs led to death. Epacadostat 100 mg twice per day plus pembrolizumab 200 mg every 3 weeks was recommended for phase II evaluation. Objective responses (per Response Evaluation Criteria in Solid Tumors [RECIST] version 1.1) occurred in 12 (55%) of 22 patients with melanoma and in patients with non-small-cell lung cancer, renal cell carcinoma, endometrial adenocarcinoma, urothelial carcinoma, and squamous cell carcinoma of the head and neck. The pharmacokinetics of epacadostat and pembrolizumab and antidrug antibody rate were comparable to historical controls for monotherapies. CONCLUSION: Epacadostat in combination with pembrolizumab generally was well tolerated and had encouraging antitumor activity in multiple advanced solid tumors.
Autocrine regulation of mesenchymal progenitor cell fates orchestrates tooth eruption.

Proc Natl Acad Sci U S A. 2018 Dec 3.

2018 Dec 03

Takahashi A, Nagata M, Gupta A, Matsushita Y, Yamaguchi T, Mizuhashi K, Maki K, Ruellas AC, Cevidanes LS, Kronenberg HM, Ono N, Ono W.
PMID: 30509999 | DOI: 10.1073/pnas.1810200115

Formation of functional skeletal tissues requires highly organized steps of mesenchymal progenitor cell differentiation. The dental follicle (DF) surrounding the developing tooth harbors mesenchymal progenitor cells for various differentiated cells constituting the tooth root–bone interface and coordinates tooth eruption in a manner dependent on signaling by parathyroid hormone-related peptide (PTHrP) and the PTH/PTHrP receptor (PPR). However, the identity of mesenchymal progenitor cells in the DF and how they are regulated by PTHrP-PPR signaling remain unknown. Here, we show that the PTHrP-PPR autocrine signal maintains physiological cell fates of DF mesenchymal progenitor cells to establish the functional periodontal attachment apparatus and orchestrates tooth eruption. A single-cell RNA-seq analysis revealed cellular heterogeneity of PTHrP+ cells, wherein PTHrP+ DF subpopulations abundantly express PPR. Cell lineage analysis using tamoxifen-inducible PTHrP-creER mice revealed that PTHrP+ DF cells differentiate into cementoblasts on the acellular cementum, periodontal ligament cells, and alveolar cryptal bone osteoblasts during tooth root formation. PPR deficiency induced a cell fate shift of PTHrP+ DF mesenchymal progenitor cells to nonphysiological cementoblast-like cells precociously forming the cellular cementum on the root surface associated with up-regulation of Mef2c and matrix proteins, resulting in loss of the proper periodontal attachment apparatus and primary failure of tooth eruption, closely resembling human genetic conditions caused by PPR mutations. These findings reveal a unique mechanism whereby proper cell fates of mesenchymal progenitor cells are tightly maintained by an autocrine system mediated by PTHrP-PPR signaling to achieve functional formation of skeletal tissues.
Mutations in RELT Cause Autosomal Recessive Amelogenesis Imperfecta.

Clin Genet. 2018 Dec 3.

2018 Dec 03

Kim JW, Zhang H, Seymen F, Koruyucu M, Hu Y, Kang J, Kim YJ, Ikeda A, Kasimoglu Y, Bayram M, Zhang C, Kawasaki K, Bartlett JD, Saunders TL, Simmer JP, Hu JCC.
PMID: 30506946 | DOI: 10.1111/cge.13487

Amelogenesis imperfecta (AI) is a collection of isolated (non‐syndromic) inherited diseases affecting dental enamel formation or a clinical phenotype in syndromic conditions. We characterized three consanguineous AI families with generalized irregular hypoplastic enamel with rapid attrition that perfectly segregated with homozygous defects in a novel gene: RELT that is a member of the tumor necrosis factor receptor superfamily (TNFRSF). RNAscope in situ hybridization of wild‐type mouse molars and incisors demonstrated specific Relt mRNA expression by secretory stage ameloblasts and by odontoblasts. Relt‐/‐ mice generated by CRISPR/Cas9 exhibited incisor and molar enamel malformations. Relt‐/‐ enamel had a rough surface and underwent rapid attrition. Normally unmineralized spaces in the deep enamel near the dentino‐enamel junction (DEJ) were as highly mineralized as the adjacent enamel, which likely altered the mechanical properties of the DEJ. Phylogenetic analyses demonstrated the existence of selective pressure on RELT gene outside of tooth development, indicating that the human condition may be syndromic, which possibly explains the history of small stature and severe childhood infections in two of the probands. Knowing a TNFRSF member is critical during the secretory stage of enamel formation advances our understanding of amelogenesis and improves our ability to diagnose human conditions featuring enamel malformations.
Nanoscale tweezers for single-cell biopsies.

Nat Nanotechnol. 2018 Dec 3.

2018 Dec 03

Nadappuram BP, Cadinu P, Barik A, Ainscough AJ, Devine MJ, Kang M, Gonzalez-Garcia J, Kittler JT, Willison KR, Vilar R, Actis P, Wojciak-Stothard B, Oh SH, Ivanov AP, Edel JB.
PMID: 30510280 | DOI: 10.1038/s41565-018-0315-8

Much of the functionality of multicellular systems arises from the spatial organization and dynamic behaviours within and between cells. Current single-cell genomic methods only provide a transcriptional ‘snapshot’ of individual cells. The real-time analysis and perturbation of living cells would generate a step change in single-cell analysis. Here we describe minimally invasive nanotweezers that can be spatially controlled to extract samples from living cells with single-molecule precision. They consist of two closely spaced electrodes with gaps as small as 10–20 nm, which can be used for the dielectrophoretic trapping of DNA and proteins. Aside from trapping single molecules, we also extract nucleic acids for gene expression analysis from living cells without affecting their viability. Finally, we report on the trapping and extraction of a single mitochondrion. This work bridges the gap between single-molecule/organelle manipulation and cell biology and can ultimately enable a better understanding of living cells.
Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.

Nat Commun. 2018 Dec 4;9(1):5150.

2018 Dec 04

Bartoschek M, Oskolkov N, Bocci M, Lövrot J, Larsson C, Sommarin M, Madsen CD, Lindgren D, Pekar G, Karlsson G, Ringnér M, Bergh J, Björklund A, Pietras K.
PMID: 30514914 | DOI: 10.1038/s41467-018-07582-3

Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression and treatment response remain unclear due to significant heterogeneity. Here, following a negative selection strategy combined with single-cell RNA sequencing of 768 transcriptomes of mesenchymal cells from a genetically engineered mouse model of breast cancer, we define three distinct subpopulations of CAFs. Validation at the transcriptional and protein level in several experimental models of cancer and human tumors reveal spatial separation of the CAF subclasses attributable to different origins, including the peri-vascular niche, the mammary fat pad and the transformed epithelium. Gene profiles for each CAF subtype correlate to distinctive functional programs and hold independent prognostic capability in clinical cohorts by association to metastatic disease. In conclusion, the improved resolution of the widely defined CAF population opens the possibility for biomarker-driven development of drugs for precision targeting of CAFs.
SOX10 Immunoexpression in Basaloid Squamous Cell Carcinomas: A Diagnostic Pitfall for Ruling out Salivary Differentiation.

Head Neck Pathol. 2018 Nov 29.

2018 Nov 29

Rooper LM, McCuiston AM, Westra WH, Bishop JA.
PMID: 30498968 | DOI: 10.1007/s12105-018-0990-7

SOX10 immunoexpression is increasingly recognized in salivary gland tumors, including but not limited to those with myoepithelial, serous acinar, and intercalated duct differentiation. However, SOX10 expression has not been extensively evaluated in other epithelial tumors that can mimic salivary origin. Basaloid squamous cell carcinoma (SCC) is a unique variant of SCC that shows morphologic overlap with several salivary tumors, including adenoid cystic carcinoma, basal cell adenocarcinoma, and myoepithelial carcinoma. We performed SOX10 immunohistochemistry on 22 basaloid SCCs and 280 non-basaloid SCCs. If tissue was available, we also performed immunohistochemistry for S100 and p16, and in-situ hybridization for high-risk HPV RNA. SOX10 was positive in 13/22 basaloid SCCs (59%), including 5/6 (83%) that were HPV-positive and 6/12 (50%) that were HPV-negative. Only 2/12 basaloid SCC (17%) demonstrated focal S100 expression. All non-basaloid SCCs were SOX10 negative. Frequent positivity for SOX10 in basaloid SCC presents a significant diagnostic pitfall for distinguishing these tumors from various basaloid salivary carcinomas. The preponderance of SOX10 expression in the basaloid variant of HPV-positive SCC also presents a diagnostic challenge in separating it from HPV-related multiphenotypic sinonasal carcinoma. SOX10 may be more broadly considered a marker of basal differentiation and should not be assumed to be specific for salivary origin in epithelial head and neck tumors.
B7-H3 and B7-H4 expression in phyllodes tumors of the breast detected by RNA in situ hybridization and immunohistochemistry: Association with clinicopathological features and T-cell infiltration.

Tumour Biol. 2018 Nov;40(11):1010428318815032.

2018 Nov 01

Kim GE, Kim NI, Park MH, Lee JS.
PMID: 30486739 | DOI: 10.1177/1010428318815032

Phyllodes tumors are rare biphasic breast tumors with the potential for both local recurrence and distant metastasis. The aberrant expression of B7-H3 and B7-H4 B7 molecules could be potential targets for future development of immunotherapeutic approaches. This work was undertaken to evaluate the expression of B7-H3 and B7-H4 in phyllodes tumors and assess the association with the grade and clinical behavior of phyllodes tumors. In addition, the roles of B7-H3 and B7-H4 in the regulation of tumor immune surveillance were evaluated by assessing the relationship between B7-H3/B7-H4 expression and T-cell infiltration. The messenger RNA and protein expression of B7-H3/B7-H4 were determined by RNAscope in situ hybridization and immunohistochemistry, respectively, in 101 phyllodes tumors (60 benign, 26 borderline, and 15 malignant) using a tissue microarray. Immunohistochemistry for CD3 and CD8 was also performed. B7-H3 messenger RNA and protein appeared to be concentrated mainly in the stromal compartment of phyllodes tumors. However, B7-H4 messenger RNA and protein were undetectable in the stromal compartment of phyllodes tumors. Stromal B7-H3 messenger RNA and protein expression were noted in 10 (16.7%) and 31 (51.7%) of 60 benign phyllodes tumors, 12 (46.1%) and 20 (76.9%) of 26 borderline phyllodes tumors, and 10 (66.7%) and 13 (86.7%) of 15 malignant phyllodes tumors, respectively. Stromal B7-H3 messenger RNA and protein expression increased as phyllodes tumors progressed from benign to borderline and finally to the malignant grade (Pearson's R = 0.411, p < 0.001 and Pearson's R = 0.293, p = 0.003, respectively). The recurrence rate was higher in the stromal B7-H3 messenger RNA or protein-positive group than in the negative group, but this difference was not significant. Stromal B7-H3 protein expression inversely correlated with the densities of CD3+ and CD8+ T-cell infiltrates ( p = 0.001 and p = 0.027, respectively). These results suggest that B7-H3 is involved in the progression of phyllodes tumors and may contribute to their immune surveillance.
ROBO2 is a stroma suppressor gene in the pancreas and acts via TGF-β signalling.

Nat Commun. 2018 Nov 30;9(1):5083.

2018 Nov 30

Pinho AV, Van Bulck M, Chantrill L, Arshi M, Sklyarova T, Herrmann D, Vennin C, Gallego-Ortega D, Mawson A, Giry-Laterriere M, Magenau A, Leuckx G, Baeyens L, Gill AJ, Phillips P, Timpson P, Biankin AV, Wu J, Rooman I.
PMID: 30504844 | DOI: 10.1038/s41467-018-07497-z

Whereas genomic aberrations in the SLIT-ROBO pathway are frequent in pancreatic ductal adenocarcinoma (PDAC), their function in the pancreas is unclear. Here we report that in pancreatitis and PDAC mouse models, epithelial Robo2 expression is lost while Robo1 expression becomes most prominent in the stroma. Cell cultures of mice with loss of epithelial Robo2 (Pdx1Cre;Robo2F/F) show increased activation of Robo1+ myofibroblasts and induction of TGF-β and Wnt pathways. During pancreatitis, Pdx1Cre;Robo2F/F mice present enhanced myofibroblast activation, collagen crosslinking, T-cell infiltration and tumorigenic immune markers. The TGF-β inhibitor galunisertib suppresses these effects. In PDAC patients, ROBO2 expression is overall low while ROBO1 is variably expressed in epithelium and high in stroma. ROBO2low;ROBO1high patients present the poorest survival. In conclusion, Robo2 acts non-autonomously as a stroma suppressor gene by restraining myofibroblast activation and T-cell infiltration. ROBO1/2 expression in PDAC patients may guide therapy with TGF-β inhibitors or other stroma /immune modulating agents.
Tumour-vasculature development via endothelial-to-mesenchymal transition after radiotherapy controls CD44v6+ cancer cell and macrophage polarization.

Nat Commun. 2018 Nov 30;9(1):5108.

2018 Nov 30

Choi SH, Kim AR, Nam JK, Kim JM, Kim JY, Seo HR, Lee HJ, Cho J, Lee YJ.
PMID: 30504836 | DOI: 10.1038/s41467-018-07470-w

It remains controversial whether targeting tumour vasculature can improve radiotherapeutic efficacy. We report that radiation-induced endothelial-to-mesenchymal transition (EndMT) leads to tumour vasculature with abnormal SMA+NG2+ pericyte recruitment during tumour regrowth after radiotherapy. Trp53 (but not Tgfbr2) deletion in endothelial cells (ECs) inhibited radiation-induced EndMT, reducing tumour regrowth and metastases with a high CD44v6+ cancer-stem-cell (CSC) content after radiotherapy. Osteopontin, an EndMT-related angiocrine factor suppressed by EC-Trp53 deletion, stimulated proliferation in dormant CD44v6+ cells in severely hypoxic regions after radiation. Radiation-induced EndMT significantly regulated tumour-associated macrophage (TAM) polarization. CXCR4 upregulation in radioresistant tumour ECs was highly associated with SDF-1+ TAM recruitment and M2 polarization of TAMs, which was suppressed by Trp53 deletion. These EndMT-related phenomena were also observed in irradiated human lung cancer tissues. Our findings suggest that targeting tumour EndMT might enhance radiotherapy efficacy by inhibiting the re-activation of dormant hypoxic CSCs and promoting anti-tumour immune responses.

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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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