keyword
MENU ▼
Read by QxMD icon Read
search

Nanostring

keyword
https://www.readbyqxmd.com/read/29144959/induction-of-innervation-by-encapsulated-adipocytes-with-engineered-vitamin-a-metabolism
#1
Qiwen Shen, Rumana Yasmeen, Jessica Marbourg, Lu Xu, Lianbo Yu, Paolo Fadda, Alan Flechtner, L James Lee, Phillip G Popovich, Ouliana Ziouzenkova
Innervation is a fundamental basis for function and survival of tissues. In the peripheral tissues, degenerative diseases create a neurotoxic metabolic milieu that either causes neurodegeneration or fails to sustain regenerative growth and reinnervation of injured/diseased tissues. Encapsulation of cells producing neurotrophic factors can augment axon growth and neuron survival; however, sustained innervation in vivo requires a combination of factors promoting axon growth and guidance pathway that are released in a tissue-specific context...
October 28, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/29135973/hdac6-regulates-microrna-27b-that-suppresses-proliferation-promotes-apoptosis-and-target-met-in-diffuse-large-b-cell-lymphoma
#2
Y J Jia, Z B Liu, W G Wang, C B Sun, P Wei, Y L Yang, M J You, B H Yu, X Q Li, X Y Zhou
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. Histone deacetylase 6 (HDAC6) is frequently altered in DLBCL and inhibition of HDAC6 has potent anti-tumor effects in vitro and in vivo. We profiled miRNAs that altered in the HDAC6 knockdown DLBCL cells with NanoString nCounter assay and identified microRNA-27b (miR-27b) as the most significantly increased miRNA. We validated decreased expression of miR-27b in DLBCL tissues, and we found that low expression of miR-27b was associated with poor overall survival of patients with DLBCL...
September 28, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29116224/comparison-of-transcriptomic-platforms-for-analysis-of-whole-blood-from-ebola-infected-cynomolgus-macaques
#3
Emily Speranza, Louis A Altamura, Kirsten Kulcsar, Sandra L Bixler, Cynthia A Rossi, Randal J Schoepp, Elyse Nagle, William Aguilar, Christina E Douglas, Korey L Delp, Timothy D Minogue, Gustavo Palacios, Arthur J Goff, John H Connor
Ebola virus disease (EVD) is a serious illness with mortality rates of 20-90% in various outbreaks. EVD is characterized by robust virus replication and strong host inflammatory response. Analyzing host immune responses has increasingly involved multimodal approaches including transcriptomics to profile gene expression. We studied cynomolgus macaques exposed to Ebola virus Makona via different routes with the intent of comparing RNA-Seq to a NanoString nCounter codeset targeting 769 non-human primate (NHP) genes...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29112706/nanostringnormcnv-pre-processing-of-nanostring-cnv-data
#4
Dorota H Sendorek, Emilie Lalonde, Cindy Q Yao, Veronica Y Sabelnykova, Robert G Bristow, Paul C Boutros
Summary: The NanoString System is a well-established technology for measuring RNA and DNA abundance. Although it can estimate copy number variation, relatively few tools support analysis of these data. To address this gap, we created NanoStringNormCNV, an R package for pre-processing and copy number variant calling from NanoString data. This package implements algorithms for pre-processing, quality-control, normalization and copy number variation detection. A series of reporting and data visualization methods support exploratory analyses...
November 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29112225/global-and-targeted-circulating-microrna-profiling-of-colorectal-adenoma-and-colorectal-cancer
#5
Jinhua Zhang, Gottumakkala S Raju, David W Chang, Shu-Hong Lin, Zhinan Chen, Xifeng Wu
BACKGROUND: Circulating microRNAs (miRNAs) are emerging as promising biomarkers for cancer. The objective of the current study was to investigate the potential of circulating cell-free miRNAs as biomarkers for colorectal cancer (CRC) and its precursor lesion, colorectal adenoma. METHODS: The serum levels of 800 miRNAs were assessed in a discovery set of 21 patients with CRC, 19 patients with adenoma, and 21 healthy controls using the NanoString miRNA analysis platform...
November 7, 2017: Cancer
https://www.readbyqxmd.com/read/29104083/development-and-evaluation-of-a-pan-sarcoma-fusion-gene-detection-assay-using-the-nanostring-ncounter-platform
#6
Kenneth T E Chang, Angela Goytain, Tracy Tucker, Aly Karsan, Cheng-Han Lee, Torsten O Nielsen, Tony L Ng
The NanoString nCounter assay is a high-throughput hybridization technique using target-specific probes that can be customized to test for numerous fusion transcripts in a single assay using RNA from formalin-fixed, paraffin-embedded material. We designed a NanoString assay targeting 174 unique fusion junctions in 25 sarcoma types. The study cohort comprised 212 cases, 96 of which showed fusion gene expression by the NanoString assay, including all 20 Ewing sarcomas, 11 synovial sarcomas, and 5 myxoid liposarcomas tested...
November 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29099775/whole-blood-mrna-expression-based-prognosis-of-metastatic-renal-cell-carcinoma
#7
Karthik V Giridhar, Carlos P Sosa, David W Hillman, Cristobal Sanhueza, Candace L Dalpiaz, Brian A Costello, Fernando J Quevedo, Henry C Pitot, Roxana S Dronca, Donna Ertz, John C Cheville, Krishna Vanaja Donkena, Manish Kohli
The Memorial Sloan Kettering Cancer Center (MSKCC) prognostic score is based on clinical parameters. We analyzed whole blood mRNA expression in metastatic clear cell renal cell carcinoma (mCCRCC) patients and compared it to the MSKCC score for predicting overall survival. In a discovery set of 19 patients with mRCC, we performed whole transcriptome RNA sequencing and selected eighteen candidate genes for further evaluation based on associations with overall survival and statistical significance. In an independent validation of set of 47 patients with mCCRCC, transcript expression of the 18 candidate genes were quantified using a customized NanoString probeset...
November 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29089811/clinical-utility-of-multigene-profiling-assays-in-early-stage-breast-cancer
#8
M C Chang, L H Souter, S Kamel-Reid, M Rutherford, P Bedard, M Trudeau, J Hart, A Eisen
BACKGROUND: This clinical practice guideline was developed to determine the level of evidence supporting the clinical utility of commercially available multigene profiling assays and to provide guidance about whether certain breast cancer patient populations in Ontario would benefit from alternative tests in addition to Oncotype dx (Genomic Health, Redwood City, CA, U.S.A.). METHODS: A systematic electronic Ovid search of the medline and embase databases sought out systematic reviews and primary literature...
October 2017: Current Oncology
https://www.readbyqxmd.com/read/29079455/molecular-and-histopathological-characterization-of-the-tumor-immune-microenvironment-in-advanced-stage-of-malignant-pleural-mesothelioma
#9
Namrata S Patil, Luisella Righi, Hartmut Koeppen, Wei Zou, Stefania Izzo, Federica Grosso, Roberta Libener, Marco Loiacono, Valentina Monica, Consuelo Buttigliero, Silvia Novello, Priti S Hegde, Mauro Papotti, Marcin Kowanetz, Giorgio V Scagliotti
INTRODUCTION: Malignant pleural mesothelioma (MPM) is a rare, highly aggressive, relatively chemo- and radio-resistant malignancy with limited therapeutic options. Our objective was to investigate the prevalence of PD-L1 and the characteristics of immune environment in this disease. METHODS: A total of 99 archival tumors from advanced stage MPM were immunohistochemically tested in parallel for PD-L1 in two different laboratories; and 87 of these were profiled for immune gene expression profiling by NanoString analysis for 800 genes...
October 24, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/29061504/genomic-predictors-of-chemotherapy-efficacy-in-advanced-or-recurrent-gastric-cancer-in-the-gc0301-top002-phase-iii-clinical-trial
#10
Kakoli Das, Masataka Taguri, Hiroshi Imamura, Naotoshi Sugimoto, Kazuhiro Nishikawa, Kazuhiro Yoshida, Patrick Tan, Akira Tsuburaya
Recent gastric cancer clinical trials have aimed to establish the efficacy of combination therapy over monotherapy, however, the role for genomic biomarkers in these trials has remained largely unexplored. Here, using the NanoString expression platform, we analyzed 105 gastric tumors from a randomized phase III Japanese clinical trial (GC0301/TOP002) testing the efficacy of irinotecan plus S-1(IRI-S) versus S-1 therapy. We found that previously established proliferative subtype signatures, were associated with older patients (>65 years) and liver metastasis while mesenchymal subtype signatures were associated with younger patients (≤65 years) and peritoneal metastasis...
October 20, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29050069/-mir-449a-is-a-potential-epigenetic-biomarker-for-wnt-subtype-of-medulloblastoma
#11
Y X Li, L W Shao, T Jiang, Y Liu, Q Chang
Objective: To identify the candidate epigenetic biomarkers of Wnt subtype of medulloblastoma(MB). Methods: MicroRNAs(miRNAs) expression array was used to detect the expression of miRNAs in MB cell lines with or without treatment by demethylation reagent. Nanostring gene expression array was used to detect the expression level of mRNA in 45 samples of primary MB. Molecular subtyping was performed based on the NanoString data. The status of methylation was confirmed by methylation specific PCR. The expression of candidate miRNA was confirmed by real-time PCR...
October 8, 2017: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/29046873/embryonic-stem-cell-like-subpopulations-in-venous-malformation
#12
Elysia M S Tan, Sam Duro Siljee, Helen D Brasch, Susana Enriquez, Swee T Tan, Tinte Itinteang
BACKGROUND: Venous malformation (VM) consists of a network of ectatic anomalous thin-walled venous channels. A role for an activating TIE2 mutation in the development of the dilated luminal vessels in VM, and its proposed involvement of embryonic stem cells (ESCs), led us to investigate the expression of ESC markers in subcutaneous VM (SCVM) and intramuscular VM (IMVM). METHODS: Formalin-fixed paraffin-embedded sections of SCVM from seven patients and IMVM samples from seven patients were analyzed for the expression of Nanog, pSTAT3, OCT4, SOX2, SALL4, and CD44, using 3,3'-diaminobenzidine (DAB) immunohistochemical (IHC) staining...
2017: Frontiers in Medicine
https://www.readbyqxmd.com/read/29029636/gene-expression-modules-in-primary-breast-cancers-as-risk-factors-for-organotropic-patterns-of-first-metastatic-spread-a-case-control-study
#13
Katherine Lawler, Efterpi Papouli, Cristina Naceur-Lombardelli, Anca Mera, Kayleigh Ougham, Andrew Tutt, Siker Kimbung, Ingrid Hedenfalk, Jun Zhan, Hongquan Zhang, Richard Buus, Mitch Dowsett, Tony Ng, Sarah E Pinder, Peter Parker, Lars Holmberg, Cheryl E Gillett, Anita Grigoriadis, Arnie Purushotham
BACKGROUND: Metastases from primary breast cancers can involve single or multiple organs at metastatic disease diagnosis. Molecular risk factors for particular patterns of metastastic spread in a clinical population are limited. METHODS: A case-control design including 1357 primary breast cancers was used to study three distinct clinical patterns of metastasis, which occur within the first six months of metastatic disease: bone and visceral metasynchronous spread, bone-only, and visceral-only metastasis...
October 13, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29029513/development-of-mesenchymal-subtype-gene-signature-for-clinical-application-in-gastric-cancer
#14
Jeeyun Lee, Razvan Cristescu, Kyoung-Mee Kim, Kyung Kim, Seung Tae Kim, Se Hoon Park, Won Ki Kang
Previously, in the Asian Cancer Research Group (ACRG) project, we defined four distinct molecular subtypes in gastric cancer (GC). Mesenchymal (microsatellite stable with epithelial-to-mesenchymal transition phenotype, MSS/EMT) tumors showed the worst prognosis among all the subtypes. To develop a gene signature for predicting mesenchymal subtype GC, we conducted gene expression profiling using a NanoString assay in 70 ACRG specimens. The gene signature was validated in an independent set obtained from the prospective Adjuvant chemoRadioTherapy In Stomach Tumor (ARTIST) trial...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29023267/enhanced-th17-responses-in-patients-with-il10-receptor-deficiency-and-infantile-onset-ibd
#15
Dror S Shouval, Liza Konnikova, Alexandra E Griffith, Sarah M Wall, Amlan Biswas, Lael Werner, Moran Nunberg, Jochen Kammermeier, Jeremy A Goettel, Rajsavi Anand, Hannah Chen, Batia Weiss, Jian Li, Anthony Loizides, Baruch Yerushalmi, Tadahiro Yanagi, Rita Beier, Laurie S Conklin, Christen L Ebens, Fernanda G M S Santos, Mary Sherlock, Jeffery D Goldsmith, Daniel Kotlarz, Sarah C Glover, Neil Shah, Athos Bousvaros, Holm H Uhlig, Aleixo M Muise, Christoph Klein, Scott B Snapper
BACKGROUND: IL10 receptor (IL10R) deficiency causes severe infantile-onset inflammatory bowel disease. Intact IL10R-dependent signals have been shown to be important for innate and adaptive immune cell functions in mice. We have previously reported a key role of IL10 in the generation and function of human anti-inflammatory macrophages. Independent of innate immune cell defects, the aim of the current study was to determine the role of IL10R signaling in regulating human CD4 T-cell function...
November 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28988016/characterisation-of-the-immune-related-transcriptome-in-resected-biliary-tract-cancers
#16
Michele Ghidini, Luciano Cascione, Pietro Carotenuto, Andrea Lampis, Francesco Trevisani, Maria Chiara Previdi, Jens C Hahne, Ian Said-Huntingford, Maya Raj, Alessandro Zerbi, Claudia Mescoli, Umberto Cillo, Massimo Rugge, Massimo Roncalli, Guido Torzilli, Lorenza Rimassa, Armando Santoro, Nicola Valeri, Matteo Fassan, Chiara Braconi
Although biliary tract cancers (BTCs) are known to have an inflammatory component, a detailed characterisation of immune-related transcripts has never been performed. In these studies, nCounter PanCancer Immune Profiling Panel was used to assess the expression of 770 immune-related transcripts in the tumour tissues (TTs) and matched adjacent tissues (ATs) of resected BTCs. Cox regression analysis and Kaplan-Meier methods were used to correlate findings with relapse-free survival (RFS). The first analysis in the TT and AT of an exploratory set (n = 22) showed deregulation of 39 transcripts associated with T-cell activation...
October 5, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28970855/nanostring-ncounter%C3%A2-approach-in-breast-cancer-a-comparative-analysis-with-quantitative-real-time-polymerase-chain-reaction-in-situ-hybridization-and-immunohistochemistry
#17
Jiyeon Hyeon, Soo Youn Cho, Min Eui Hong, So Young Kang, Ingu Do, Young Hyuck Im, Eun Yoon Cho
PURPOSE: Accurate testing for estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) is essential for breast cancer treatment. At present, immunohistochemistry (IHC)/florescence in situ hybridization (FISH) are widely accepted as the standard testing methods. To investigate the value of NanoString nCounter®, we performed its comparative analysis with IHC/FISH and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) for the assessment of ER, PR, and HER2...
September 2017: Journal of Breast Cancer
https://www.readbyqxmd.com/read/28968537/pf4-hit-antibody-kko-complexes-activate-broad-innate-immune-and-inflammatory-responses
#18
Lydia A Haile, Roshni Rao, Swamy K Polumuri, Gowthami M Arepally, David A Keire, Daniela Verthelyi, Cynthia D Sommers
INTRODUCTION: Heparin-induced thrombocytopenia (HIT) is an immune-mediated complication of heparin anticoagulation therapy resulting in thrombocytopenia frequently accompanied by thrombosis. Current evidence suggests that HIT is associated with antibodies developed in response to multi-molecular complexes formed by platelet factor 4 (PF4) bound to heparin or cell surface glycosaminoglycans. These antibody complexes activate platelets and monocytes typically through FcγRIIA receptors increasing the production of PF4, inflammatory mediators, tissue factor and thrombin...
September 21, 2017: Thrombosis Research
https://www.readbyqxmd.com/read/28919262/pdgfra-is-not-essential-for-the-derivation-and-maintenance-of-mouse-extraembryonic-endoderm-stem-cell-lines
#19
Jiangwei Lin, Mona Khan, Bolek Zapiec, Peter Mombaerts
Extraembryonic endoderm stem (XEN) cell lines can be derived and maintained in vitro and reflect the primitive endoderm lineage. Platelet-derived growth factor receptor alpha (PDGFRA) is thought to be essential for the derivation and maintenance of mouse XEN cell lines. Here, we have re-evaluated this requirement for PDGFRA. We derived multiple PDGFRA-deficient XEN cell lines from postimplantation and preimplantation embryos of a PDGFRA-GFP knockout strain. We also converted PDGFRA-deficient embryonic stem cell lines into XEN cell lines chemically by transient culturing with retinoic acid and Activin A...
October 10, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28889351/multidimensional-phenotyping-of-breast-cancer-cell-lines-to-guide-preclinical-research
#20
Jodi M Saunus, Chanel E Smart, Jamie R Kutasovic, Rebecca L Johnston, Priyakshi Kalita-de Croft, Mariska Miranda, Esdy N Rozali, Ana Cristina Vargas, Lynne E Reid, Eva Lorsy, Sibylle Cocciardi, Tatjana Seidens, Amy E McCart Reed, Andrew J Dalley, Leesa F Wockner, Julie Johnson, Debina Sarkar, Marjan E Askarian-Amiri, Peter T Simpson, Kum Kum Khanna, Georgia Chenevix-Trench, Fares Al-Ejeh, Sunil R Lakhani
PURPOSE: Cell lines are extremely useful tools in breast cancer research. Their key benefits include a high degree of control over experimental variables and reproducibility. However, the advantages must be balanced against the limitations of modelling such a complex disease in vitro. Informed selection of cell line(s) for a given experiment now requires essential knowledge about molecular and phenotypic context in the culture dish. METHODS: We performed multidimensional profiling of 36 widely used breast cancer cell lines that were cultured under standardised conditions...
September 9, 2017: Breast Cancer Research and Treatment
keyword
keyword
10071
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"