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https://www.readbyqxmd.com/read/29673738/tbk1-a-key-regulator-and-potential-treatment-target-for-interferon-positive-sj%C3%A3-gren-s-syndrome-systemic-lupus-erythematosus-and-systemic-sclerosis
#1
Iris L A Bodewes, Erika Huijser, Cornelia G van Helden-Meeuwsen, Liselotte Tas, Ruth Huizinga, Virgil A S H Dalm, P Martin van Hagen, Noortje Groot, Sylvia Kamphuis, Paul L A van Daele, Marjan A Versnel
OBJECTIVE: Upregulation of type I interferons (IFN-I) is a hallmark of systemic autoimmune diseases like primary Sjögren's syndrome (pSS), systemic lupus erythematosus (SLE) and systemic sclerosis (SSc). Expression of IFN-I is induced by three different receptor families: Toll-like receptors (TLRs), RIG-like receptors (RLRs) and DNA-sensing receptors (DSRs). TANK-binding kinase (TBK1) is an important signaling hub downstream of RLRs and DSRs. TBK1 activates IRF3 and IRF7, leading to IFN-I production and subsequent induction of interferon stimulated genes (ISGs)...
April 16, 2018: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29659661/rna-and-microrna-stability-in-paxgene-fixed-paraffin-embedded-tissue-blocks-after-seven-years-storage
#2
Ignacio Sanchez, Fay Betsou, Bénédicte Culot, Sonia Frasquilho, Siobhan C McKay, Stephanos Pericleous, Colleen Smith, Gerry Thomas, William Mathieson
Objectives: To evaluate the stability of RNA and microRNA (miRNA) in PAXgene-fixed paraffin-embedded tissue blocks after 7 years' storage. Methods: RNA and miRNA were extracted from PAXgene-fixed paraffin-embedded (PFPE) blocks in 2009 then stored at -80°C. Seven years later, RNA and miRNA were again extracted from the same blocks. RNA and miRNA integrity in the 2009 and 2016 extractions were compared using RNA integrity number (RIN), paraffin-embedded RNA metric (PERM), reverse transcription polymerase chain reaction (RT-PCR) for different amplicon lengths, and quantitative RT-PCR (qRT-PCR) for three mRNA and three miRNA targets...
April 5, 2018: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29613823/analysis-of-gene-expression-changes-in-pha-m-stimulated-lymphocytes-unraveling-pha-activity-as-prerequisite-for-dicentric-chromosome-analysis
#3
C Beinke, M Port, R Ullmann, K Gilbertz, M Majewski, M Abend
Dicentric chromosome analysis (DCA) is the gold standard for individual radiation dose assessment. However, DCA is limited by the time-consuming phytohemagglutinin (PHA)-mediated lymphocyte activation. In this study using human peripheral blood lymphocytes, we investigated PHA-associated whole genome gene expression changes to elucidate this process and sought to identify suitable gene targets as a means of meeting our long-term objective of accelerating cell cycle kinetics to reduce DCA culture time. Human peripheral whole blood from three healthy donors was separately cultured in RPMI/FCS/antibiotics with BrdU and PHA-M...
April 3, 2018: Radiation Research
https://www.readbyqxmd.com/read/29603574/event-free-survival-of-infants-and-toddlers-enrolled-in-the-hr-nbl-1-siopen-trial-is-associated-with-the-level-of-neuroblastoma-mrnas-at-diagnosis
#4
Maria V Corrias, Stefano Parodi, Andrei Tchirkov, Tim Lammens, Ales Vicha, Claudia Pasqualini, Catarina Träger, Yania Yáñez, Sandro Dallorso, Luigi Varesio, Roberto Luksch, Genevieve Laureys, Dominique Valteau-Couanet, Adela Canete, Ulrike Pöetschger, Ruth Ladenstein, Susan A Burchill
BACKGROUND: The purpose of this study was to evaluate whether levels of neuroblastoma mRNAs in bone marrow and peripheral blood from stage M infants (≤12 months of age at diagnosis, MYCN amplified) and toddlers (between 12 and 18 months, any MYCN status) predict event-free survival (EFS). METHODS: Bone marrow aspirates and peripheral blood samples from 97 infants/toddlers enrolled in the European High-Risk Neuroblastoma trial were collected at diagnosis in PAXgene™ blood RNA tubes...
March 30, 2018: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/29559120/existing-blood-transcriptional-classifiers-accurately-discriminate-active-tuberculosis-from-latent-infection-in-individuals-from-south-india
#5
Samantha Leong, Yue Zhao, Noyal M Joseph, Natasha S Hochberg, Sonali Sarkar, Jane Pleskunas, David Hom, Subitha Lakshminarayanan, C Robert Horsburgh, Gautam Roy, Jerrold J Ellner, W Evan Johnson, Padmini Salgame
Several studies have identified blood transcriptomic signatures that can distinguish active from latent Tuberculosis (TB). The purpose of this study was to assess how well these existing gene profiles classify TB disease in a South Indian population. RNA sequencing was performed on whole blood PAXgene samples collected from 28 TB patients and 16 latently TB infected (LTBI) subjects enrolled as part of an ongoing household contact study. Differential gene expression and clustering analyses were performed and compared with explicit predictive testing of TB and LTBI individuals based on established gene signatures...
March 2018: Tuberculosis
https://www.readbyqxmd.com/read/29511559/genetic-biopsy-for-prediction-of-surveillance-intervals-after-endoscopic-resection-of-colonic-polyps-results-of-the-genesis-study
#6
Andreas W Berger, Katja Raedler, Cord Langner, Leopold Ludwig, Nektarios Dikopoulos, Karl F Becker, Julia Slotta-Huspenina, Michael Quante, Daniel Schwerdel, Lukas Perkhofer, Alexander Kleger, Eugen Zizer, Franz Oswald, Thomas Seufferlein, Alexander Meining
Background and objective: Current surveillance strategies for colorectal cancer following polypectomy are determined by endoscopic and histopathological factors. Such a distinction has been challenged. The present study was designed to identify molecular parameters in colonic polyps potentially defining new sub-groups at risk. Methods: One hundred patients were enrolled in this multicentre study. Polyps biopsies underwent formalin-free processing (PAXgene, PreAnalytiX) and targeted next generation sequencing (38 genes (QIAGEN), NextSeq 500 platform (Illumina))...
March 2018: United European Gastroenterology Journal
https://www.readbyqxmd.com/read/29346412/a-comparative-analysis-of-preservation-techniques-for-the-optimal-molecular-detection-of-hookworm-dna-in-a-human-fecal-specimen
#7
Marina Papaiakovou, Nils Pilotte, Ben Baumer, Jessica Grant, Kristjana Asbjornsdottir, Fabian Schaer, Yan Hu, Raffi Aroian, Judd Walson, Steven A Williams
BACKGROUND: Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time...
January 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29313979/whole-blood-fpr1-mrna-expression-predicts-both-non-small-cell-and-small-cell-lung-cancer
#8
Scott Morris, Anil Vachani, Harvey I Pass, William N Rom, Kirk Ryden, Glen J Weiss, D K Hogarth, George Runger, Donald Richards, Troy Shelton, David W Mallery
While long-term survival rates for early-stage lung cancer are high, most cases are diagnosed in later stages that can negatively impact survival rates. We aim to design a simple, single biomarker blood test for early-stage lung cancer that is robust to preclinical variables and can be readily implemented in the clinic. Whole blood was collected in PAXgene tubes from a training set of 29 patients, and a validation set of 260 patients, of which samples from 58 patients were prospectively collected in a clinical trial specifically for our study...
June 1, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29148410/th17-gene-expression-in-psoriatic-arthritis-synovial-fluid-and-peripheral-blood-compared-to-osteoarthritis-and-cutaneous-psoriasis
#9
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
#10
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...
December 14, 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
#11
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...
March 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29024724/paxgene-fixation-enables-comprehensive-metabolomic-and-proteomic-analyses-of-tissue-specimens-by-maldi-msi
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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...
October 2017: Molecular Diagnosis & Therapy
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