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https://www.readbyqxmd.com/read/29148410/th17-gene-expression-in-psoriatic-arthritis-synovial-fluid-and-peripheral-blood-compared-to-osteoarthritis-and-cutaneous-psoriasis
#1
Fatima Abji, Remy A Pollock, Kun Liang, Vinod Chandran, Dafna D Gladman
OBJECTIVES: The IL-23/IL-17 axis is central to the pathogenesis of psoriatic arthritis (PsA). We aimed to identify Th17 signalling genes that are dysregulated in synovial fluid of PsA compared to osteoarthritis (OA) patients and to determine if differences in peripheral blood can distinguish PsA from psoriasis patients and controls. METHODS: Synovial fluid cells (SFCs) from 14 PsA and 9 OA patients were obtained and stored in TRIzol reagent. RNA was isolated by phenol-chloroform extraction and purified with RNeasy miniprep kits...
November 9, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/29132989/differential-gene-expression-elicited-by-children-in-response-to-the-2015-16-live-attenuated-versus-inactivated-influenza-vaccine
#2
Kelly Stefano Cole, Judith M Martin, William T Horne, Chyongchiou J Lin, Mary Patricia Nowalk, John F Alcorn, Richard K Zimmerman
BACKGROUND: In recent influenza seasons, the live attenuated influenza vaccine (LAIV) has not demonstrated the same level of vaccine effectiveness as that observed among children who received the inactivated influenza vaccine (IIV). To better understand this difference, this study compared the mRNA sequencing transcription profile (RNA seq) in children who received either IIV or LAIV. METHODS: Children 3-17years of age receiving quadrivalent influenza vaccine were enrolled...
November 10, 2017: Vaccine
https://www.readbyqxmd.com/read/29076129/the-mosaicc-study-assessing-feasibility-for-biological-sample-collection-in-epidemiology-studies-and-comparison-of-dna-yields-from-saliva-and-whole-blood-samples
#3
Glen James, Mary Frances McMullin, Andrew S Duncombe, Mike Clarke, Lesley A Anderson
Biological sample collection is becoming more common in epidemiology research to obtain DNA for genetic analysis. There are many different DNA collection methods but little evidence on their relative effectiveness. Therefore, we took the opportunity of a prospective case-control study in myeloproliferative neoplasms (MPNs) to compare DNA yield from 8.5 mL PAXgene tubes for whole blood collection versus 2 mL Oragene OG-500 saliva collection kits. MPNs include polycythaemia vera, essential thrombocythaemia, and primary myelofibrosis...
October 27, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/29024724/paxgene-fixation-enables-comprehensive-metabolomic-and-proteomic-analyses-of-tissue-specimens-by-maldi-msi
#4
Christian Urban, Achim Buck, Jens T Siveke, Florian Lordick, Birgit Luber, Axel Walch, Michaela Aichler
An alcohol-based non-crosslinking tissue fixative, PAXgene Tissue System, has been proposed as alternative fixation method to formalin, providing superior and morphological preservation. To date, metabolites have not been assessed in PAXgene-fixed tissues. The study focuses on a comparison between PAXgene and standard formalin fixation for metabolomic analysis by MALDI mass spectrometry imaging. Therefore, fifty-six samples from seven mice organs were fixed with PAXgene (PFPE) or formalin (FFPE), embedded in paraffin, and processed to a tissue microarray...
January 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28984675/feasibility-of-prostate-paxgene-fixation-for-molecular-research-and-diagnostic-surgical-pathology-comparison-of-matched-fresh-frozen-ffpe-and-pfpe-tissues
#5
Gunilla Högnäs, Kati Kivinummi, Heini M L Kallio, Reija Hieta, Pekka Ruusuvuori, Antti Koskenalho, Juha Kesseli, Teuvo L J Tammela, Jarno Riikonen, Joanna Ilvesaro, Saara Kares, Pasi P Hirvikoski, Marita Laurila, Tuomas Mirtti, Matti Nykter, Paula M Kujala, Tapio Visakorpi, Teemu Tolonen, G Steven Bova
Advances in prostate cancer biology and diagnostics are dependent upon high-fidelity integration of clinical, histomorphologic, and molecular phenotypic findings. In this study, we compared fresh frozen, formalin-fixed paraffin-embedded (FFPE), and PAXgene-fixed paraffin-embedded (PFPE) tissue preparation methods in radical prostatectomy prostate tissue from 36 patients and performed a preliminary test of feasibility of using PFPE tissue in routine prostate surgical pathology diagnostic assessment. In addition to comparing histology, immunohistochemistry, and general measures of DNA and RNA integrity in each fixation method, we performed functional tests of DNA and RNA quality, including targeted Miseq RNA and DNA sequencing, and implemented methods to relate DNA and RNA yield and quality to quantified DNA and RNA picogram nuclear content in each tissue volume studied...
October 3, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28975156/moderate-blast-exposure-alters-gene-expression-and-levels-of-amyloid-precursor-protein
#6
Jessica Gill, Ann Cashion, Nicole Osier, Lindsay Arcurio, Vida Motamedi, Kristine C Dell, Walter Carr, Hyung-Suk Kim, Sijung Yun, Peter Walker, Stephen Ahlers, Matthew LoPresti, Angela Yarnell
OBJECTIVE: To explore gene expression after moderate blast exposure (vs baseline) and proteomic changes after moderate- (vs low-) blast exposure. METHODS: Military personnel (N = 69) donated blood for quantification of protein level, and peak pressure exposures were detected by helmet sensors before and during a blast training program (10 days total). On day 7, some participants (n = 29) sustained a moderate blast (mean peak pressure = 7.9 psi) and were matched to participants with no/low-blast exposure during the training (n = 40)...
October 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28821222/impact-of-blood-collection-and-processing-on-peripheral-blood-gene-expression-profiling-in-type-1-diabetes
#7
Linda Yip, Rebecca Fuhlbrigge, Mark A Atkinson, C Garrison Fathman
BACKGROUND: The natural history of type 1 diabetes (T1D) is challenging to investigate, especially as pre-diabetic individuals are difficult to identify. Numerous T1D consortia have been established to collect whole blood for gene expression analysis from individuals with or at risk to develop T1D. However, with no universally accepted protocol for their collection, differences in sample processing may lead to variances in the results. Here, we examined whether the choice of blood collection tube and RNA extraction kit leads to differences in the expression of genes that are changed during the progression of T1D, and if these differences could be minimized by measuring gene expression directly from the lysate of whole blood...
August 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28815047/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
#8
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)...
2017: Journal for Immunotherapy of Cancer
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
#9
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
#10
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
#11
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) 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...
September 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
#12
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
#13
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 ongoing race. Techniques to fight 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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