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Rebecca L King, Grzegorz S Nowakowski, Thomas E Witzig, David W Scott, Richard F Little, Fangxin Hong, Randy D Gascoyne, Brad S Kahl, William R Macon
ECOG/ACRIN 1412 (E1412) is a randomized, phase II open-label study of lenalidomide/RCHOP vs. RCHOP alone in adults with newly diagnosed de novo diffuse large B-cell lymphoma (DLBCL) and requires NanoString gene expression profiling (GEP) for cell-of-origin testing. Because of high ineligibility rate on retrospective expert central pathology review (ECPR), real-time (RT) ECPR was instituted to confirm diagnosis and ensure adequate tissue for GEP prior to study enrollment. Goal was notification of eligibility within 2 working days (WD)...
February 28, 2018: Blood Cancer Journal
Rebecca C Arend, Angelina I Londono, Allison M Montgomery, Haller J Smith, Zachary C Dobbin, Ashwini A Katre, Alba Martinez, Eddy S Yang, Ronald D Alvarez, Warner K Huh, Kerri S Bevis, J Michael Straughn, Jacob M Estes, Lea Novak, David K Crossman, Sara J Cooper, Charles N Landen, Charles A Leath
While high-grade serous ovarian carcinoma (HGSOC) is the most common histological subtype of ovarian cancer, significant tumor heterogeneity exists. In addition, chemotherapy induces changes in gene expression and alters the mutational profile. To evaluate the notion that patients with HGSOC could be better classified for optimal treatment based on gene expression, we compared genetic variants (by DNA next-generation sequencing [NGS] using a 50 gene Ion Torrent panel) and gene expression (using the NanoString® PanCancer 770 gene Panel) in the tumor from 20 patients with HGSOC before and after neoadjuvant chemotherapy (NACT)...
March 9, 2018: Molecular Cancer Research: MCR
Ali Hashemi Gheinani, Mike Vögeli, Ulrich Baumgartner, Erik Vassella, Annette Draeger, Fiona C Burkhard, Katia Monastyrskaya
Circulating miRNAs are detected in extracellular space and body fluids such as urine. Circulating RNAs can be packaged in secreted urinary extracellular vesicles (uEVs) and thus protected from degradation. Urinary exosome preparations might contain specific miRNAs, relevant as biomarkers in renal and bladder diseases. Major difficulties in application of uEVs into the clinical environment are the high variability and low reproducibility of uEV isolation methods. Here we used five different methods to isolate uEVs and compared the size distribution, morphology, yield, presence of exosomal protein markers and RNA content of uEVs...
March 2, 2018: Scientific Reports
K Y P Liu, X J D Lu, Y Zhu, S Yip, C F Poh
Lymph nodal disease (LN+) is the most significant prognostic factor of oral squamous cell carcinoma (OSCC). Current risk indicator(s) for guiding elective neck dissection (END) is insufficient for clinically node-negative (cN0) patients, resulting in under- or overtreatment. While the role of immunological events in tumorigenesis and metastasis is evident, the prognostic implication in OSCC remains unclear. The study objective was to investigate large-scale immune-related gene expression and determine its prognostic value on node-free survival (NFS)...
February 1, 2018: Journal of Dental Research
Yingrou Tan, Jackson Liang Li, Bernett Teck Kwong Lee, Josephine Lum, Zacharias Aloysius Dwi Pramono, Maximilien Evrard, Michael Poidinger, Hong Liang Tey, Lai Guan Ng
No abstract text is available yet for this article.
February 28, 2018: Acta Dermato-venereologica
Maria J Merino, Sara Gil, Carmen Garcia Macias, Karlena Lara
Mature microRNAs (miRNAs) are small non-protein coding RNAs that modulate gene expression after transcription. Few studies have shown that male breast cancer (MBC) shows distinctive miRNAs pattern, suggesting its relevance in this pathology. To study this, we performed a profile of 800 miRNAs in 9 MBC samples and in normal epithelial cells of 3 MBC cases. EXPERIMENTAL DESIGN: Of FFPE tissues, miRNA was extracted for profiles using the NanoString method. miRNAs were obtained by comparing tumor samples versus normal epithelium...
2018: Journal of Cancer
Sarah Huet, Bruno Tesson, Jean-Philippe Jais, Andrew L Feldman, Laura Magnano, Emilie Thomas, Alexandra Traverse-Glehen, Benoit Albaud, Marjorie Carrère, Luc Xerri, Stephen M Ansell, Lucile Baseggio, Cécile Reyes, Karin Tarte, Sandrine Boyault, Corinne Haioun, Brian K Link, Pierre Feugier, Armando Lopez-Guillermo, Hervé Tilly, Pauline Brice, Sandrine Hayette, Fabrice Jardin, Fritz Offner, Pierre Sujobert, David Gentien, Alain Viari, Elias Campo, James R Cerhan, Gilles Salles
BACKGROUND: Patients with follicular lymphoma have heterogeneous outcomes. Predictor models to distinguish, at diagnosis, between patients at high and low risk of progression are needed. The objective of this study was to use gene-expression profiling data to build and validate a predictive model of outcome for patients treated in the rituximab era. METHODS: A training set of fresh-frozen tumour biopsies was prospectively obtained from 160 untreated patients with high-tumour-burden follicular lymphoma enrolled in the phase 3 randomised PRIMA trial, in which rituximab maintenance was evaluated after rituximab plus chemotherapy induction (median follow-up 6·6 years [IQR 6·0-7·0])...
February 20, 2018: Lancet Oncology
Tania B Porras, Pushpinder Kaur, Alexander Ring, Naomi Schechter, Julie E Lang
Circulating tumor cells (CTCs) have potential utility as a surrogate biomarker of tumor biology via a liquid biopsy. The aim of this study was to evaluate if the nCounter NanoString assay could be used for accurate gene expression profiling of CTCs using the PAM50 research-use-only CodeSet. Analysis was performed on CTCs isolated by the ANGLE Parsortix system from healthy blood spiked with the breast cancer cell lines Hs578T, SkBr3, MDA-MB-231 or MCF7. Using cell lines as gold standard positive controls and Parsortix processed blood without spiking (unspiked) as negative controls, we found an average of 12 significantly differentially expressed genes among spiked samples versus unspiked controls...
January 23, 2018: Oncotarget
Sachiko Akiyoshi, Tomohiro Ishii, Zhaodai Bai, Peter Mombaerts
The mouse vomeronasal organ is specialized in the detection of pheromones. Vomeronasal sensory neurons (VSNs) express chemosensory receptors of two large gene repertoires, V1R and V2R, which encode G-protein coupled receptors. Phylogenetically four families of V2R genes can be discerned: A, B, C, and D. VSNs located in the basal layer of the vomeronasal epithelium coordinately coexpress V2R genes from two families: approximately half of basal VSNs coexpress Vmn2r1 of family C with a single V2R gene of family A8-10, B, or D ("C1 type of V2Rs"), and the other half coexpress Vmn2r2 through Vmn2r7 of family C with a single V2R gene of family A1-6 ("C2 type V2Rs")...
February 21, 2018: European Journal of Neuroscience
Divya Bhagirath, Thao Ly Yang, Nathan Bucay, Kirandeep Sekhon, Shahana Majid, Varahram Shahryari, Rajvir Dahiya, Yuichiro Tanaka, Sharanjot Saini
Due to high heterogeneity, molecular characterization of prostate cancer (PCa) based on biopsy sampling is often challenging. Hence, a minimally invasive method to determine the molecular imprints of a patient's tumor for risk stratification would be advantageous. In this study, we employ a novel, digital amplification-free quantification method using the nCounter technology (Nanostring Technologies) to profile exosomal serum miRNAs (ex-miRNA) from aggressive PCa cases, benign prostatic hyperplasia (BPH), and disease-free controls...
February 1, 2018: Cancer Research
Maria Łastowska, Joanna Trubicka, Magdalena Niemira, Magdalena Paczkowska-Abdulsalam, Agnieszka Karkucińska-Więckowska, Magdalena Kaleta, Monika Drogosiewicz, Marta Perek-Polnik, Adam Krętowski, Bożena Cukrowska, Wiesława Grajkowska, Bożenna Dembowska-Bagińska, Ewa Matyja
Medulloblastoma, the most common malignant pediatric brain tumor, is a heterogeneous disease, with the existence of at least four molecular types: Wingless (WNT), Sonic Hedgehog (SHH), Group 3 and Group 4 tumors. The latter two groups, which can be identified by an application of multi-gene expression or methylation profiling, show sometimes ambiguous categorization and are still classified for diagnostic reason as non-SHH/non-WNT medulloblastomas in updated WHO 2016 classification. In order to better characterize non-SHH/non-WNT tumors, we applied the method based on the Nanostring nCounter Technology, using the 26 genes codeset in 68 uniformly treated medulloblastoma patients...
February 9, 2018: Journal of Neuro-oncology
Yenenesh K Tekletsion, Hannah Christensen, Adam Finn
Detection of bacterial gene transcripts in low density mucosal samples is challenging. We evaluated the NanoString nCounter system for transcript detection in Neisseria meningitidis (Nm) cultures. The method was sensitive, reproducible (R2 = 0.99) and demonstrated changes in gene expression. Studying Nm transcripts from pharyngeal samples may be feasible using this approach.
February 6, 2018: Journal of Microbiological Methods
Aylia Mohammadi, Orlaith B Kelly, Melissa Filice, Boyko Kabakchiev, Michelle I Smith, Mark S Silverberg
Background and Aims: MicroRNAs (miRNAs) have emerged as important regulators in inflammatory bowel disease (IBD). This study investigated differential expression of miRNAs across clinical phenotypes in a well-characterized cohort of IBD patients and healthy controls (HCs). Methods: A cohort with Crohn's disease (CD), ulcerative colitis (UC), and HC was prospectively accrued. Total RNA was extracted from peripheral blood mononuclear cells for all subjects. MiRNA expression was measured using NanoString Technologies...
February 6, 2018: Journal of Crohn's & Colitis
Roy Kessous, David Octeau, Kathleen Klein, Patricia N Tonin, Celia M T Greenwood, Manuela Pelmus, Ido Laskov, Liron Kogan, Shannon Salvador, Susie Lau, Amber Yasmeen, Walter H Gotlieb
OBJECTIVE: The expression of homologous recombination (HR) genes in high grade ovarian cancer (HGOC) samples from debulking surgeries were correlated to outcomes in patients selected for chemotherapy treatment regimens. STUDY DESIGN: RNA was extracted from 96 fresh frozen tumor samples from debulking surgeries from chemotherapy naïve patients with HGOC (primary derived surgeries (PDS), n = 55) or following neoadjuvant chemotherapy treatment (NACT), n = 41)...
January 29, 2018: Gynecologic Oncology
Neha Shukla, Irene K Yan, Tushar Patel
Several different types of RNA molecules such as microRNAs (miRNAs) have been detected within extracellular vesicles in the circulation. The detection and potential utility of these as disease biomarkers requires the ability to detect their presence with adequate sensitivity and to quantitate their expression. The potential for circulating miRNA to serve as biomarkers can be evaluated through their detection in association with specific disease states. Multiplexed detection of several miRNA simultaneously can be useful for discovery studies...
2018: Methods in Molecular Biology
Atsuko Katsumoto, Aline S Miranda, Oleg Butovsky, Antônio L Teixeira, Richard M Ransohoff, Bruce T Lamb
BACKGROUND: Traumatic brain injury (TBI) is a critical public health and socio-economic problem worldwide. A growing body of evidence supports the involvement of inflammatory events in TBI. It has been reported that resident microglia and infiltrating monocytes promote an inflammatory reaction that leads to neuronal death and eventually behavioral and cognitive impairment. Currently, there is no effective treatment for TBI and the development of new therapeutic strategies is a scientific goal of highest priority...
January 30, 2018: Journal of Neuroinflammation
Robin Sachdeva, Andrea Schlotterer, Dagmar Schumacher, Christin Matka, Ilka Mathar, Nadine Dietrich, Rebekka Medert, Ulrich Kriebs, Jihong Lin, Peter Nawroth, Lutz Birnbaumer, Thomas Fleming, Hans-Peter Hammes, Marc Freichel
OBJECTIVE: Diabetic retinopathy (DR) is induced by an accumulation of reactive metabolites such as ROS, RNS, and RCS species, which were reported to modulate the activity of cation channels of the TRPC family. In this study, we use Trpc1/4/5/6-/- compound knockout mice to analyze the contribution of these TRPC proteins to diabetic retinopathy. METHODS: We used Nanostring- and qPCR-based analysis to determine mRNA levels of TRPC channels in control and diabetic retinae and retinal cell types...
January 5, 2018: Molecular Metabolism
Greta Alì, Rossella Bruno, Mauro Savino, Riccardo Giannini, Serena Pelliccioni, Maura Menghi, Laura Boldrini, Agnese Proietti, Antonio Chella, Alessandro Ribechini, Gabriella Fontanini
CONTEXT: - Patients with non-small cell lung cancer harboring ALK receptor tyrosine kinase ( ALK), ROS proto-oncogene 1 ( ROS1), and ret proto-oncogene ( RET) gene rearrangements can benefit from specific kinase inhibitors. Detection of fusion genes is critical for determining the best treatment. Assessing rearrangements in non-small cell lung cancer remains challenging, particularly for lung cytology. OBJECTIVE: - To examine the possible application of the multiplex, transcript-based NanoString system (NanoString Technologies, Seattle, Washington) in the evaluation of fusion genes in lung adenocarcinoma samples...
January 26, 2018: Archives of Pathology & Laboratory Medicine
Yong-Xiao Li, Zhen-Wei Yu, Tao Jiang, Li-Wei Shao, Yan Liu, Na Li, Yu-Feng Wu, Chen Zheng, Xiao-Yu Wu, Ming Zhang, Dan-Feng Zheng, Xue-Ling Qi, Min Ding, Jing Zhang, Qing Chang
Medulloblastoma (MB) is the most common malignant brain tumor in childhood. It contains at least four distinct molecular subgroups. The aim of this study is to explore novel diagnostic and potential therapeutic markers within each subgroup of MB, in particular within Group 4, the largest subgroup, to facilitate diagnosis together with gene therapy. Total 106 MB samples were recruited. Tumor subtype was evaluated with the NanoString assay. Several novel tumor related genes were shown to have high subgroup sensitivity and specificity, including PDGFRA, FGFR1 and ALK in the WNT group; CCND1 in the SHH group; as well as α-synuclein (SNCA)in Group 4...
January 25, 2018: Cancer Science
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
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