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https://www.readbyqxmd.com/read/28807052/whole-blood-rna-transcript-based-models-can-predict-clinical-response-in-two-large-independent-clinical-studies-of-patients-with-advanced-melanoma-treated-with-the-checkpoint-inhibitor-tremelimumab
#1
Philip Friedlander, Karl Wassmann, Alan M Christenfeld, David Fisher, Chrisann Kyi, John M Kirkwood, Nina Bhardwaj, William K Oh
BACKGROUND: Tremelimumab is an antibody that blocks CTLA-4 and demonstrates clinical efficacy in a subset of advanced melanoma patients. An unmet clinical need exists for blood-based response-predictive gene signatures to facilitate clinically effective and cost-efficient use of such immunotherapeutic interventions. METHODS: Peripheral blood samples were collected in PAXgene® tubes from 210 treatment-naïve melanoma patients receiving tremelimumab in a worldwide, multicenter phase III study (discovery dataset)...
August 15, 2017: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/28742859/whole-blood-microrna-expression-may-not-be-useful-for-screening-non-small-cell-lung-cancer
#2
Santosh K Patnaik, Eric D Kannisto, Reema Mallick, Anil Vachani, Sai Yendamuri
At least seven studies have suggested that microRNA levels in whole blood can be diagnostic for lung cancer. We conducted a large bi-institutional study to validate this. Qiagen® PAXgene™ Blood miRNA System was used to collect blood and extract RNA from it for 85 pathologic stage I-IV non-small cell lung cancer (NSCLC) cases and 76 clinically-relevant controls who had a benign pulmonary mass, or a high risk of developing lung cancer because of a history of cigarette smoking or age >60 years. Cases and controls were similar for age, gender, race, and blood hemoglobin and leukocyte but not platelet levels (0...
2017: PloS One
https://www.readbyqxmd.com/read/28679647/technical-stability-and-biological-variability-in-micrornas-from-dried-blood-spots-a-lung-cancer-therapy-monitoring-showcase
#3
Mustafa Kahraman, Thomas Laufer, Christina Backes, Hannah Schrörs, Tobias Fehlmann, Nicole Ludwig, Jochen Kohlhaas, Eckart Meese, Thomas Wehler, Robert Bals, Andreas Keller
BACKGROUND: Different work flows have been proposed to use miRNAs as blood-borne biomarkers. In particular, the method used for collecting blood from patients can considerably influence the diagnostic results. METHODS: We explored whether dried blood spots (DBSs)(5) facilitate stable miRNA measurements and compared its technical stability with biological variability. First, we tested the stability of DBS samples by generating from 1 person 18 whole-genome-wide miRNA profiles of DBS samples that were exposed to different temperature and humidity conditions...
July 5, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28631163/evaluation-of-streck-bct-and-paxgene-stabilised-blood-collection-tubes-for-cell-free-circulating-dna-studies-in-plasma
#4
Kristina Warton, Nicole L Yuwono, Mark J Cowley, Mark J McCabe, Alwin So, Caroline E Ford
INTRODUCTION: Blood samples for studies of circulating DNA in disease are often collected in clinical settings where prompt processing of samples is not possible. In order to avoid problems associated with leukocyte lysis after prolonged blood storage, stabilised blood tubes have been developed containing preservatives that prevent cell lysis. We evaluated Streck BCT tubes and PAXgene ccfDNA tubes, as well as standard EDTA blood collection tubes, in terms of DNA yield and fragment size...
June 19, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28382793/rna-sample-preparation-applied-to-gene-expression-profiling-for-the-horse-biological-passport
#5
Ludovic Bailly-Chouriberry, Florent Baudoin, Florence Cormant, Yohan Glavieux, Benoit Loup, Patrice Garcia, Marie-Agnès Popot, Yves Bonnaire
The improvement of doping control is an on-going race. Techniques to fight against doping are usually based on the direct detection of drugs or their metabolites by analytical methods such as chromatography hyphenated to mass spectrometry after ad hoc sample preparation. Nowadays, omic methods constitute an attractive development and advances have been achieved particularly by application of molecular biology tools for detection of anabolic androgenic steroids (AAS), erythropoiesis-stimulating agent (ESA) or to control human growth hormone misuses...
April 5, 2017: Drug Testing and Analysis
https://www.readbyqxmd.com/read/28373054/liquid-biopsy-performance-of-the-paxgene%C3%A2-blood-ccfdna-tubes-for-the-isolation-and-characterization-of-cell-free-plasma-dna-from-tumor-patients
#6
Bernd Schmidt, Dana Reinicke, Iris Reindl, Ines Bork, Bettina Wollschläger, Nina Lambrecht, Michael Fleischhacker
BACKGROUND: In most research laboratories the use of EDTA tubes for the isolation of plasma DNA from tumor patients is standard. Unfortunately these tubes do not allow for an extended storage of samples before processing and prevent EDTA tubes from being shipped at ambient temperature. The aim of our study was to compare the quantity and quality of plasma DNA isolated from EDTA and PAXgene® Blood ccfDNA Tubes in different downstream applications. METHODS: We enrolled 29 patients in our study...
March 31, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28335817/gene-expression-differences-between-paxgene-and-tempus-blood-rna-tubes-are-highly-reproducible-between-independent-samples-and-biobanks
#7
Anne Heidi Skogholt, Einar Ryeng, Sten Even Erlandsen, Frank Skorpen, Svanhild A Schønberg, Pål Sætrom
BACKGROUND: Gene expression profiling from blood is sensitive to technology choices. For example, the main blood RNA collection systems-the PAXgene and Tempus tubes-differently influence RNA expression signatures. The aim of this study was to establish a common RNA isolation protocol for these two systems and investigate if it could reduce the differences in gene expression between them. RESULTS: We collected identical blood samples on the PAXgene and Tempus systems and retrieved blood samples from two independent biobanks-NOWAC and HUNT3-which are based on PAXgene and Tempus, respectively...
March 23, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28209402/chemokine-receptor-patterns-and-right-heart-failure-in-mechanical-circulatory-support
#8
Aditi Nayak, Colin Neill, Robert L Kormos, Luigi Lagazzi, Indrani Halder, Charles McTiernan, Jennifer Larsen, Ana Inashvili, Jeffrey Teuteberg, Timothy N Bachman, Karen Hanley-Yanez, Dennis M McNamara, Marc A Simon
BACKGROUND: Right ventricular failure (RVF) complicates 9% to 44% of left ventricular assist device (LVAD) implants post-operatively. Current prediction scores perform only modestly in validation studies, and do not include immune markers. Chemokines are inflammatory signaling molecules with a fundamental role in cardiac physiology and stress adaptation. In this study we investigated chemokine receptor regulation in LVAD recipients who develop RVF. METHODS: Expression of chemokine receptor (CCR) genes 3 to 8 were examined in the peripheral blood of 111 LVAD patients, collected 24 hours before implant...
June 2017: Journal of Heart and Lung Transplantation
https://www.readbyqxmd.com/read/27943079/assessment-of-type-i-interferon-signaling-in-pediatric-inflammatory-disease
#9
Gillian I Rice, Isabelle Melki, Marie-Louise Frémond, Tracy A Briggs, Mathieu P Rodero, Naoki Kitabayashi, Anthony Oojageer, Brigitte Bader-Meunier, Alexandre Belot, Christine Bodemer, Pierre Quartier, Yanick J Crow
PURPOSE: Increased type I interferon is considered relevant to the pathology of a number of monogenic and complex disorders spanning pediatric rheumatology, neurology, and dermatology. However, no test exists in routine clinical practice to identify enhanced interferon signaling, thus limiting the ability to diagnose and monitor treatment of these diseases. Here, we set out to investigate the use of an assay measuring the expression of a panel of interferon-stimulated genes (ISGs) in children affected by a range of inflammatory diseases...
February 2017: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/27916491/gene-expression-profiling-to-identify-the-toxicities-and-potentially-relevant-human-disease-outcomes-associated-with-environmental-heavy-metal-exposure
#10
Hesham M Korashy, Ibraheem M Attafi, Konrad S Famulski, Saleh A Bakheet, Mohammed M Hafez, Abdulaziz M S Alsaad, Abdul Rahman M Al-Ghadeer
Heavy metals are the most commonly encountered toxic substances that increase susceptibility to various diseases after prolonged exposure. We have previously shown that healthy volunteers living near a mining area had significant contamination with heavy metals associated with significant changes in the expression of some detoxifying genes, xenobiotic metabolizing enzymes, and DNA repair genes. However, alterations of most of the molecular target genes associated with diseases are still unknown. Thus, the aims of this study were to (a) evaluate the gene expression profile and (b) identify the toxicities and potentially relevant human disease outcomes associated with long-term human exposure to environmental heavy metals in mining area using microarray analysis...
February 2017: Environmental Pollution
https://www.readbyqxmd.com/read/27906977/development-of-a-pcr-assay-to-detect-low-level-trypanosoma-cruzi-in-blood-specimens-collected-with-paxgene-blood-dna-tubes-for-clinical-trials-treating-chagas-disease
#11
Bo Wei, Lei Chen, Miho Kibukawa, John Kang, Hetty Waskin, Matthew Marton
Chagas disease is caused by the parasitic infection of Trypanosoma cruzi (T. cruzi). The STOP CHAGAS clinical trial was initiated in 2011 to evaluate posaconazole in treating Chagas disease, with treatment success defined as negative qualitative PCR results of detecting the parasites in blood specimens collected post-treatment. PAXgene Blood DNA tubes were utilized as a simple procedure to collect and process blood specimens. However, the PAXgene blood specimens challenged published T. cruzi PCR methods, resulting in poor sensitivity and reproducibility...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27784773/leukocyte-response-is-regulated-by-microrna-let7i-in-patients-with-acute-ischemic-stroke
#12
Glen C Jickling, Bradley P Ander, Natasha Shroff, Miles Orantia, Boryana Stamova, Cheryl Dykstra-Aiello, Heather Hull, Xinhua Zhan, DaZhi Liu, Frank R Sharp
OBJECTIVE: To evaluate microRNA let7i in ischemic stroke and its regulation of leukocytes. METHODS: A total of 212 patients were studied: 106 with acute ischemic stroke and 106 controls matched for risk factors. RNA from circulating leukocytes was isolated from blood collected in PAXgene tubes. Let7i microRNA expression was assessed using TaqMan quantitative reverse transcription PCR. To assess let7i regulation of gene expression in stroke, messenger RNA (mRNA) from leukocytes was measured by whole-genome Human Transcriptome Array Affymetrix microarray...
November 22, 2016: Neurology
https://www.readbyqxmd.com/read/27629910/annals-express-stabilization-of-circulating-thyroglobulin-mrna-transcripts-in-patients-treated-for-differentiated-thyroid-carcinoma
#13
Søren Feddersen, Lars Bastholt, Susanne Møller Pedersen
BACKGROUND: The clinical utility of serum thyroglobulin (TG) in the follow-up of patients with differentiated thyroid carcinoma (DTC) may be compromised by the presence of endogenous anti-thyroglobulin antibodies (TGAb). To prevent interference by TGAb several groups have developed real-time PCR (RT-PCR) based assays for quantification of blood TG mRNA levels. For accurate quantification of TG mRNA in blood preanalytical factors must be recognized and controlled. In this study we evaluate the effect of different blood RNA stabilizing systems - the Tempus(T)(M) Blood RNA system and the PAXgene(T)(M) Blood RNA system - and storage time on RNA yield and quality, and TG mRNA stability...
September 13, 2016: Annals of Clinical Biochemistry
https://www.readbyqxmd.com/read/27601501/methodology-of-aa-crash-a-prospective-observational-study-evaluating-the-incidence-and-pathogenesis-of-adverse-post-traumatic-sequelae-in-african-americans-experiencing-motor-vehicle-collision
#14
Sarah D Linnstaedt, JunMei Hu, Andrea Y Liu, April C Soward, Kenneth A Bollen, Henry E Wang, Phyllis L Hendry, Erin Zimny, Christopher Lewandowski, Marc-Anthony Velilla, Kathia Damiron, Claire Pearson, Robert Domeier, Sangeeta Kaushik, James Feldman, Mark Rosenberg, Jeffrey Jones, Robert Swor, Niels Rathlev, Samuel A McLean
INTRODUCTION: A motor vehicle collision (MVC) is one of the most common life-threatening events experienced by individuals living in the USA. While most individuals recover following MVC, a significant proportion of individuals develop adverse post-traumatic sequelae such as post-traumatic stress disorder or persistent musculoskeletal pain. Adverse post-traumatic sequelae are common, morbid and costly public health problems in the USA and other industrialised countries. The pathogenesis of these disorders following MVC remains poorly understood...
September 6, 2016: BMJ Open
https://www.readbyqxmd.com/read/27567668/micro-rna-21-biomarker-and-global-longitudinal-strain-functional-marker-in-detection-of-myocardial-fibrotic-burden-in-severe-aortic-valve-stenosis-a-pilot-study
#15
Iacopo Fabiani, Cristian Scatena, Chiara Maria Mazzanti, Lorenzo Conte, Nicola Riccardo Pugliese, Sara Franceschi, Francesca Lessi, Michele Menicagli, Andrea De Martino, Stefano Pratali, Uberto Bortolotti, Antonio Giuseppe Naccarato, Salvatore La Carrubba, Vitantonio Di Bello
AIMS: Myocardial fibrosis (MF) is a deleterious consequence of aortic valve stenosis (AVS). Global longitudinal strain (GLS) is a novel left ventricular (LV) functional parameter potentially useful to non-invasively estimate MF. MicroRNAs (miRNAs) are non-coding small ribonucleic acids (RNA) modulating genes function, mainly through RNA degradation. miRNA-21 is a biomarker associated with MF in pressure overload. The aim of the present study was to find an integrated algorithm for detection of MF using a combined approach with both bio- and functional markers...
2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27548617/method-validation-for-extraction-of-nucleic-acids-from-peripheral-whole-blood
#16
Conny Mathay, Gaël Hamot, Estelle Henry, Kathleen Mommaerts, Audur Thorlaksdottir, Johanna Trouet, Fay Betsou
BACKGROUND: This article is the fifth in a series of publications providing formal method validation for biospecimen processing. We report the optimization and validation of methodology to obtain nucleic acids of sufficient quantity and quality from blood. METHODS: DNA was extracted using the Chemagic DNA Blood Kit on an MSM I. Extraction was optimized in terms of blood volume, elution buffer volume, and lysis conditions. The optimal protocol was validated for reproducibility, robustness (delay to buffy coat extraction, blood vs...
December 2016: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/27449259/a-whole-blood-assay-for-ar-v7-and-ar-v567es-in-patients-with-prostate-cancer
#17
Xichun Liu, Elisa Ledet, Dongying Li, Ary Dotiwala, Allie Steinberger, Allison Feibus, Jianzhuo Li, Yanfeng Qi, Jonathan Silberstein, Benjamin Lee, Yan Dong, Oliver Sartor, Haitao Zhang
PURPOSE: Most prostate cancer mortality can be attributed to metastatic castration resistant prostate cancer, an advanced stage that remains incurable despite recent advances. The AR (androgen receptor) signaling axis remains active in castration resistant prostate cancer. Recent studies suggest that expression of the AR-V (AR splice variant) AR-V7 may underlie resistance to abiraterone and enzalutamide. However, controversy exists over the optimal assay. Our objective was to develop a fast and sensitive assay for AR-Vs in patients...
December 2016: Journal of Urology
https://www.readbyqxmd.com/read/27409982/assessment-of-paxgene-fixation-on-preservation-of-morphology-and-nucleic-acids-in-microdissected-retina-tissue
#18
Ying Liu, Deepak P Edward
AIM: To compare the effect of the two fixatives on tissue morphology and utility to obtain good quality nucleic acids for molecular analysis from micro-dissected retinal samples. METHODS: Enucleated specimens from New Zealand white rabbits were fixed in formalin or PAXgene fixative according to standard protocols, and then processed and embedded in paraffin for sectioning. Sections were stained with hematoxylin and eosin to assess the structural integrity of retina...
January 2017: Current Eye Research
https://www.readbyqxmd.com/read/27402607/a-critical-evaluation-of-the-paxgene-tissue-fixation-system-%C3%A2-morphology-immunohistochemistry-molecular-biology-and-proteomics
#19
William Mathieson, Nathalie Marcon, Laurent Antunes, David A Ashford, Fay Betsou, Sonia G Frasquilho, Olga A Kofanova, Siobhan C McKay, Stephan Pericleous, Colleen Smith, Kristian M Unger, Constanze Zeller, Geraldine A Thomas
OBJECTIVES: To evaluate the PAXgene tissue fixation system. METHODS: Clinical biospecimens (n = 46) were divided into PAXgene-fixed paraffin-embedded (PFPE), formalin-fixed paraffin-embedded (FFPE), and fresh-frozen (FF) blocks. PFPE and FFPE sections were compared for histology (H&E staining) and immunohistochemistry (14 antibodies) using tissue microarrays. PFPE, FFPE, and FF samples were compared in terms of RNA quality (RNA integrity number, polymerase chain reaction [PCR] amplicon length, and quantitative reverse transcription PCR), DNA quality (gel electrophoresis and methylation profiling) and protein quality (liquid chromatography-mass spectrometry [LC-MS/MS])...
July 2016: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/27389555/comparison-of-antibodies-for-immunohistochemistry-based-detection-of-her3-in-breast-cancer
#20
Satu Luhtala, Synnöve Staff, Mark Barok, Minna Tanner, Jorma Isola
BACKGROUND: Growth factor receptor HER3 (ErbB3) lacks standardized immunohistochemistry (IHC)-based methods for formalin-fixed paraffin-embedded (FFPE) tissue samples. We compared 4 different anti-HER3 antibodies to explain the differences found in the staining results reported in the literature. MATERIALS AND METHODS: Four commercial HER3 antibodies were tested on FFPE samples including mouse monoclonal antibody clones, DAK-H3-IC and RTJ1, rabbit monoclonal antibody clone SP71, and rabbit polyclonal antibody (SAB4500793)...
July 6, 2016: Applied Immunohistochemistry & Molecular Morphology: AIMM
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