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https://www.readbyqxmd.com/read/29344857/adaptation-of-laser-microdissection-technique-to-nanostring-rna-analysis-in-the-study-of-a-spontaneous-metastatic-mammary-carcinoma-mouse-model
#1
Nadia P Castro, Yelena G Golubeva
The mouse model characterized by spontaneous lung metastasis from JygMC (A) cells closely resembles the human triple negative breast cancer (TNBC) subtype. The primary tumors morphologically present both epithelial and spindle-like cells, but metastases in lung parenchyma display only adenocarcinoma properties. In the study of molecular signatures, laser capture microdissection (LCM) on frozen tissue sections was used to separate the following regions of interest: the epithelial-mesenchymal transition (EMT), mesenchymal-epithelial transition (MET), carcinoma, lung metastases, normal mammary gland and normal lung parenchyma...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29339539/the-hippo-pathway-component-taz-promotes-immune-evasion-in-human-cancer-through-pd-l1
#2
Helena J Janse van Rensburg, Taha Azad, Min Ling, Yawei Hao, Brooke Snetsinger, Prem Khanal, Lori M Minassian, Charles H Graham, Michael J Rauh, Xiaolong Yang
The Hippo pathway component WW domain-containing transcription regulator 1 (TAZ) is a transcriptional co-activator and an oncogene in breast and lung cancer. Transcriptional targets of TAZ that modulate immune cell function in the tumour microenvironment are poorly understood. Here, we perform a comprehensive screen for immune-related genes regulated by TAZ and its paralog YAP using NanoString gene expression profiling. We identify the immune checkpoint molecule PD-L1 as a target of Hippo signaling. The upstream kinases of the Hippo pathway, mammalian STE20-like kinase 1 and 2 (MST1/2) and large tumour suppressor 1 and 2 (LATS1/2), suppress PD-L1 expression while TAZ and YAP enhance PD-L1 levels in breast and lung cancer cell lines...
January 16, 2018: Cancer Research
https://www.readbyqxmd.com/read/29329594/modelling-the-structure-of-a-cerna-theoretical-bipartite-microrna-mrna-interaction-network-regulating-intestinal-epithelial-cellular-pathways-using-r-programming
#3
J M Robinson, W A Henderson
OBJECTIVE: We report a method using functional-molecular databases and network modelling to identify hypothetical mRNA-miRNA interaction networks regulating intestinal epithelial barrier function. The model forms a data-analysis component of our cell culture experiments, which produce RNA expression data from Nanostring Technologies nCounter® system. The epithelial tight-junction (TJ) and actin cytoskeleton interact as molecular components of the intestinal epithelial barrier. Upstream regulation of TJ-cytoskeleton interaction is effected by the Rac/Rock/Rho signaling pathway and other associated pathways which may be activated or suppressed by extracellular signaling from growth factors, hormones, and immune receptors...
January 12, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29323465/multiplexed-digital-mrna-expression-analysis-profiles-system-wide-changes-in-mrna-abundance-and-responsiveness-of-upr-specific-gene-expression-changes-during-batch-culture-of-recombinant-chinese-hamster-ovary-cells
#4
Rodrigo Maldonado-Agurto, Alan J Dickson
The unfolded protein response (UPR) signalling pathway is viewed as critical for setting the effectiveness of recombinant protein expression in CHO cells. In this study, we used Nanostring nCounter technology to study expression of a group of genes associated with cellular processes linked to UPR activation under ER stress and the changing environment of a batch culture. Time course induction of ER stress, using tunicamycin (TM), showed a group of genes such as Chop, Trb3, Sqstm1, Grp78 and Herpud1 responded rapidly to TM inhibition of N-glycosylation, whilst others such as Atf5, Odz4 and Birc5 exhibited a delayed response...
January 11, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29319809/increased-microglial-csf1r-expression-in-the-siv-macaque-model-of-hiv-cns-disease
#5
Audrey C Knight, Samuel A Brill, Suzanne E Queen, Patrick M Tarwater, Joseph L Mankowski
Chronic microglial activation and associated neuroinflammation are key factors in neurodegenerative diseases including HIV-associated neurocognitive disorders. Colony stimulating factor 1 receptor (CSF1R)-mediated signaling is constitutive in cells of the myeloid lineage, including microglia, promoting cell survival, proliferation, and differentiation. In amyotrophic lateral sclerosis and Alzheimers disease, CSF1R is upregulated. Inhibiting CSF1R signaling in animal models of these diseases improved disease outcomes...
January 8, 2018: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/29319621/selective-cd28-inhibition-modulates-alloimmunity-and-cardiac-allograft-vasculopathy-in-anti-cd154-treated-monkeys
#6
Tianshu Zhang, Agnes M Azimzadeh, Wenji Sun, Natalie A O'Neill, Evelyn Sievert, Emily Bergbower, Gheorghe Braileanu, Lars Burdorf, Xiangfei Cheng, Thomas Monahan, Siamak Dahi, Donald Harris, Elana Rybak, Emily Welty, Anthony Kronfli, Chris Avon, Richard N Pierson
BACKGROUND: Selective CD28 inhibition is actively pursued as an alternative to B7 blockade using CTLA4-Ig based on the hypothesis that the checkpoint immune regulators CTLA-4 and PD-L1 will induce tolerogenic immune signals. We previously showed that blocking CD28 using a monovalent nonactivating reagent (single chain anti-CD28 Fv fragment linked to alpha-1 anti-trypsin: sc28AT) synergizes with calcineurin inhibitors in nonhuman primate (NHP) kidney and heart transplantation. Here, we explored the efficacy of combining a 3-week 'induction" sc28AT treatment with prolonged CD154 blockade...
January 10, 2018: Transplantation
https://www.readbyqxmd.com/read/29312568/transcriptional-response-to-hypoxic-stress-in-melanoma-and-prognostic-potential-of-gbe1-and-bnip3
#7
Stéphanie Buart, Stéphane Terry, Muhammad Z Noman, Emilie Lanoy, Céline Boutros, Paul Fogel, Philippe Dessen, Guillaume Meurice, Yann Gaston-Mathé, Philippe Vielh, Séverine Roy, Emilie Routier, Virginie Marty, Sophie Ferlicot, Luc Legrès, Morad El Bouchtaoui, Nyam Kamsu-Kom, Jane Muret, Eric Deutsch, Alexander Eggermont, Jean-Charles Soria, Caroline Robert, Salem Chouaib
Gradients of hypoxia occur in most solid tumors and cells found in hypoxic regions are associated with the most aggressive and therapy-resistant fractions of the tumor. Despite the ubiquity and importance of hypoxia responses, little is known about the variation in the global transcriptional response to hypoxia in melanoma. Using microarray technology, whole genome gene expression profiling was first performed on established melanoma cell lines. From gene set enrichment analyses, we derived a robust 35 probes signature (hypomel for HYPOxia MELanoma) associated with hypoxia-response pathways, including 26 genes up regulated, and 9 genes down regulated...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29309050/hepatitis-b-virus-specific-t-cells-associate-with-viral-control-upon-nucleos-t-ide-analogue-therapy-discontinuation
#8
Laura Rivino, Nina Le Bert, Upkar S Gill, Kamini Kunasegaran, Yang Cheng, Damien Zm Tan, Etienne Becht, Navjyot K Hansi, Graham R Foster, Tung-Hung Su, Tai-Chung Tseng, Seng Gee Lim, Jia-Horng Kao, Evan W Newell, Patrick Tf Kennedy, Antonio Bertoletti
BACKGROUND: The clinical management of chronic hepatitis B virus (HBV) patients is based exclusively on virological parameters that cannot independently determine in which patients nucleos(t)ide-analogue (NUC) therapy can be safely discontinued. NUCs efficiently suppress viral replication, but do not eliminate HBV. Thus, therapy discontinuation can be associated with virological and biochemical relapse and, consequently, therapy in the majority is life-long. METHODS: Since antiviral immunity is pivotal for HBV control, we investigated potential biomarkers for the safe discontinuation of NUCs within immune profiles of chronic HBV patients by utilizing traditional immunological assays (ELISPOT, flow cytometry) in conjunction with analyses of global non-antigen-specific immune populations (NanoString and CyTOF)...
January 8, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29305787/molecular-profiling-of-short-term-and-long-term-surviving-patients-identifies-cd34-mrna-level-as-prognostic-for-glioblastoma-survival
#9
Signe Regner Michaelsen, Thomas Urup, Lars Rønn Olsen, Helle Broholm, Ulrik Lassen, Hans Skovgaard Poulsen
Despite extensive treatment, overall survival (OS) for glioblastoma (GBM) remains poor. A small proportion of patients present long survival over 3 years, but the underlying molecular background separating these long-term survivors (LTS) from short-term survivors (STS) are insufficiently understood. Accordingly, study aim was to identify independent prognostic biomarkers for survival. Study cohort consisted of 93 primary GBM patients treated with radiation-, chemo- and bevacizumab therapy, among which 14 STS (OS ≤ 12 months) and 6 LTS (OS ≥ 36 months) were identified, all confirmed being IDH wild-type...
January 5, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29302618/time-restricted-feeding-improves-circadian-dysfunction-as-well-as-motor-symptoms-in-the-q175-mouse-model-of-huntington-s-disease
#10
Huei-Bin Wang, Dawn H Loh, Daniel S Whittaker, Tamara Cutler, David Howland, Christopher S Colwell
Huntington's disease (HD) patients suffer from a progressive neurodegeneration that results in cognitive, psychiatric, cardiovascular, and motor dysfunction. Disturbances in sleep/wake cycles are common among HD patients with reports of delayed sleep onset, frequent bedtime awakenings, and fatigue during the day. The heterozygous Q175 mouse model of HD has been shown to phenocopy many HD core symptoms including circadian dysfunctions. Because circadian dysfunction manifests early in the disease in both patients and mouse models, we sought to determine if early intervention that improve circadian rhythmicity can benefit HD and delay disease progression...
January 2018: ENeuro
https://www.readbyqxmd.com/read/29298797/development-and-validation-of-a-gene-signature-for-patients-with-head-and-neck-squamous-cell-carcinomas-treated-by-postoperative-radio-chemo-therapy
#11
Stefan Schmidt, Annett Linge, Alex Zwanenburg, Stefan Leger, Fabian Lohaus, Constanze Krenn, Steffen Appold, Volker Gudziol, Alexander Nowak, Clare von Neubeck, Ingeborg Tinhofer, Volker Budach, Ali Sak, Martin Stuschke, Panagiotis Balermpas, Claus Rödel, Hatice Bunea, Anca Ligia Grosu, Amir Abdollahi, Juergen Debus, Ute Ganswindt, Claus Belka, Steffi U Pigorsch, Stephanie Elisabeth Combs, David Mönnich, Daniel Zips, Gustavo B Baretton, Frank Buchholz, Michael Baumann, Mechthild Krause, Steffen Löck
PURPOSE: The aim of this study was to identify and independently validate a novel gene signature predicting loco-regional tumor control (LRC) for treatment individualization of patients with locally advanced HPV-negative head and neck squamous cell carcinomas (HNSCC) who are treated with postoperative radio(chemo)therapy (PORT-C). EXPERIMENTAL DESIGN: Gene expression analyses were performed using nanoString technology on a multicenter training cohort of 130 patients and an independent validation cohort of 121 patients...
January 3, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29296181/correlation-between-mek-signature-and-ras-gene-alteration-in-advanced-gastric-cancer
#12
Soomin Ahn, Roz Brant, Alan Sharpe, Jonathan R Dry, Darren R Hodgson, Elaine Kilgour, Kyung Kim, Seung Tae Kim, Se Hoon Park, Won Ki Kang, Kyoung-Mee Kim, Jeeyun Lee
MEK inhibitor (selumetinib) is a potent, orally active inhibitor of MAPK/ERK pathway. It is important to develop an accurate and robust method indicative of RAS pathway activity to stratify potential patients who can benefit from selumetinib treatment in gastric cancer (GC). First, we surveyed the sensitivity to selumetinib in a panel of 22 GC cell lines and correlated with MEK signature to selumetinib sensitivity. Next, we analyzed MEK signature via nanostring assay in two Asian cohorts using clinical samples (n = 218) and then performed a correlative analysis with MEK signature status and KRAS genotype in GC...
December 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/29286578/rna-expression-profiling-of-renal-allografts-in-a-non-human-primate-identifies-variation-in-nk-and-endothelial-gene-expression
#13
R N Smith, B A Adam, I A Rosales, M Matsunami, T Oura, A B Cosimi, T Kawai, M Mengel, R B Colvin
RNA transcript expression estimates are a promising method to study the mechanisms and classification of renal allograft rejections. Here we use the Nanostring platform to profile RNA expression in renal allografts in a non-human primate (NHP), the Cynomolgus monkey. We analyzed protocol and indication 278 archival renal allograft samples, both protocol and indication from 76 animals with diagnoses of chronic antibody (CAMR), acute cellular rejection (TCMR) and MIXED (both CAMR and TCMR), plus normals and samples with no pathological rejection using a Cynomolgus specific probe set of 67 genes...
December 29, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/29237087/type-frequency-and-spatial-distribution-of-immune-cell-infiltrates-in-cns-germinomas-evidence-for-inflammatory-and-immunosuppressive-mechanisms
#14
Pia Zapka, Evelyn Dörner, Verena Dreschmann, Noriaki Sakamato, Glen Kristiansen, Gabriele Calaminus, Christian Vokuhl, Ivo Leuschner, Torsten Pietsch
Central nervous system germinomas are characterized by a massive immune cell infiltrate. We systematically characterized these immune cells in 28 germinomas by immunophenotyping and image analysis. mRNA expression was analyzed by Nanostring technology and in situ RNA hybridization. Tumor infiltrating lymphocytes (TILs) were composed of 61.8% ± 3.1% (mean ± SE) CD3-positive T cells, including 45.2% ± 3.5% of CD4-positive T-helper cells, 23.4% ± 1.5% of CD8-positive cytotoxic T cells, 5.5% ± 0...
December 11, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/29225709/immunomodulatory-effects-of-human-cryopreserved-viable-amniotic-membrane-in-a-pro-inflammatory-environment-in-vitro
#15
Claire E Witherel, Tony Yu, Mark Concannon, Will Dampier, Kara L Spiller
Introduction: Chronic wounds remain a major clinical challenge. Human cryopreserved viable amniotic membrane (hCVAM) is among the most successful therapies, but the mechanisms of action remain loosely defined. Because proper regulation of macrophage behavior is critical for wound healing with biomaterial therapies, we hypothesized that hCVAM would positively regulate macrophage behavior in vitro, and that soluble factors released from the hCVAM would be important for this effect. Materials and Methods: Primary human pro-inflammatory (M1) macrophages were seeded directly onto intact hCVAM or cultured in separation via transwell inserts (Soluble Factors) in the presence of pro-inflammatory stimuli (interferon-γ and lipopolysaccharide) to simulate the chronic wound environment...
October 2017: Cellular and Molecular Bioengineering
https://www.readbyqxmd.com/read/29219788/differential-patterns-of-metastatic-dissemination-across-medulloblastoma-subgroups
#16
Michal Zapotocky, Daddy Mata-Mbemba, David Sumerauer, Petr Liby, Alvaro Lassaletta, Josef Zamecnik, Lenka Krskova, Martin Kyncl, Jan Stary, Suzanne Laughlin, Anthony Arnoldo, Cynthia Hawkins, Uri Tabori, Michael D Taylor, Eric Bouffet, Charles Raybaud, Vijay Ramaswamy
OBJECTIVE Metastatic dissemination is a major treatment challenge and cause of death in patients with medulloblastoma. However, the influence of molecular biology on the pattern of metastatic dissemination at diagnosis is not known. In this study, the authors sought to define the location, pattern, and imaging characteristics of medulloblastoma metastases across subgroups at diagnosis. METHODS A consecutive cohort of patients with metastatic medulloblastoma at The Hospital for Sick Children and the University Hospital Motol, who underwent up-front MRI of the craniospinal axis, was assembled and allocated to subgroups using NanoString limited gene-expression profiling...
December 8, 2017: Journal of Neurosurgery. Pediatrics
https://www.readbyqxmd.com/read/29216931/vista-deficiency-attenuates-antibody-induced-arthritis-and-alters-macrophage-gene-expression-in-response-to-simulated-immune-complexes
#17
Sabrina Ceeraz, Susan K Eszterhas, Petra A Sergent, David A Armstrong, Alix Ashare, Thomas Broughton, Li Wang, Dov Pechenick, Christopher M Burns, Randolph J Noelle, Matthew P Vincenti, Roy A Fava
BACKGROUND: In addition to activated T cells, the immune checkpoint inhibitor "V domain-containing Ig suppressor of T-cell activation" (VISTA) is expressed by myeloid cell types, including macrophages and neutrophils. The importance of VISTA expression by myeloid cells to antibody-induced arthritis and its potential for relevance in human disease was evaluated. METHODS: VISTA was immunolocalized in normal and arthritic human synovial tissue sections and synovial tissue lysates were subjected to western blot analysis...
December 8, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/29211799/comparison-of-mirna-quantitation-by-nanostring-in-serum-and-plasma-samples
#18
Catherine Foye, Irene K Yan, Waseem David, Neha Shukla, Yacob Habboush, Lori Chase, Kristen Ryland, Vivek Kesari, Tushar Patel
Circulating microRNAs that are associated with specific diseases have garnered much attention for use in diagnostic assays. However, detection of disease-associated miRNA can be affected by several factors such as release of contaminating cellular miRNA during sample collection, variations due to amplification of transcript for detection, or controls used for normalization for accurate quantitation. We analyzed circulating miRNA in serum and plasma samples obtained concurrently from 28 patients, using a Nanostring quantitative assay platform...
2017: PloS One
https://www.readbyqxmd.com/read/29193461/site-specific-gene-expression-analysis-from-archived-human-intestine-samples-combining-laser-capture-microdissection-and-multiplexed-color-coded-probes
#19
A Braun, C Martinez, S Schmitteckert, R Röth, F Lasitschka, B Niesler
BACKGROUND: Alterations of site-specific gene expression profiles in disease-relevant networks within the different layers of the intestinal wall may contribute to the onset and clinical course of gastrointestinal disorders. To date, no systematic analysis has assessed and compared sub-regional gene expression patterns in all distinct layers of the gut using fresh frozen human samples. Our aim was to establish an optimized protocol for site-specific RNA isolation in order to achieve maximum RNA quality and amount for subsequent gene expression analysis combining laser-capture microdissection (LCM) with a probe-based technology, the NanoString nCounter Analysis system...
November 28, 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/29186505/robust-detection-of-chromosomal-interactions-from-small-numbers-of-cells-using-low-input-capture-c
#20
A Marieke Oudelaar, James O J Davies, Damien J Downes, Douglas R Higgs, Jim R Hughes
Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000-20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String...
November 23, 2017: Nucleic Acids Research
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