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Bernard Omolo, Mingli Yang, Fang Yin Lo, Michael J Schell, Sharon Austin, Kellie Howard, Anup Madan, Timothy J Yeatman
BACKGROUND: The KRAS gene is mutated in about 40 % of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistance to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60 % of patients with a wild type KRAS fail to respond to EGFRi combination therapies, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues...
October 19, 2016: BMC Medical Genomics
Rebecca Baum, Shruti Sharma, Jason M Organ, Christopher Jakobs, Veit Hornung, David B Burr, Ann Marshak-Rothstein, Katherine A Fitzgerald, Ellen M Gravallese
OBJECTIVE: Cytosolic DNA sensors detect microbial DNA and promote type I interferon and pro-inflammatory cytokine production through the adaptor stimulator of interferon genes (STING) to resolve infection. Endogenous DNA also engages the STING pathway, contributing to autoimmune disease. We identified a novel role for STING in bone in arthritic DNase II/IFNaR double deficient (DKO) mice, and sought to define the bone phenotype in these mice and to address mechanism. METHODS: Bone parameters were evaluated in DKO, STING/DNaseII/IFNaR triple deficient and control mice by microcomputed tomography and histomorphometry...
October 14, 2016: Arthritis & Rheumatology
Stefanie G Wohl, Thomas A Reh
The profile of miRNAs in mature glia is not well characterized, and most studies have been done in cultured glia. In order to identify the miRNAs in adult and young (postnatal day 11/12) Müller glia of the neural retina, we isolated the Müller glia from Rlbp-CreER: Stop(f/f)-tdTomato mice by means of fluorescent activated cell sorting and analyzed their miRNAs using NanoStrings Technologies(®). In freshly isolated adult Müller glia, we identified 7 miRNAs with high expression levels in the glia, but very low levels in the retinal neurons...
October 14, 2016: Scientific Reports
Heather Marion Ames, Ming Yuan, Maria Adelita Vizcaíno, Wayne Yu, Fausto J Rodriguez
Low-grade (WHO I-II) gliomas and glioneuronal tumors represent the most frequent primary tumors of the central nervous system in children. They often have a good prognosis following total resection, however they can create many neurological complications due to mass effect, and may be difficult to resect depending on anatomic location. MicroRNAs have been identified as molecular regulators of protein expression/translation that can repress multiple mRNAs concurrently through base pairing, and have an important role in cancer, including brain tumors...
October 14, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Roz G Brant, Alan Sharpe, Tom Liptrot, Jonathan Dry, Elizabeth A Harrington, J Carl Barrett, Nicky Whalley, Chris Womack, Paul D Smith, Darren Hodgson
PURPOSE: To develop a clinically viable gene expression assay to measure RAS/RAF/MEK/ERK (RAS-ERK) pathway output suitable for hypothesis testing in non-small cell lung cancer (NSCLC) clinical studies. EXPERIMENTAL DESIGN: A published MEK-functional-activation signature (MEK signature) that measures RAS-ERK functional output was optimized for NSCLC in silico. NanoString assays were developed for the NSCLC optimized MEK signature and the 147-gene RAS signature. First, platform transfer from Affymetrix to NanoString, and signature modulation following treatment with KRAS siRNA and MEK inhibitor, were investigated in cell lines...
October 12, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Therese Featherston, Helen H Yu, Jonathan C Dunne, Alice M Chibnall, Helen D Brasch, Paul F Davis, Swee T Tan, Tinte Itinteang
AIM: We have recently identified and characterized cancer stem cell (CSC) subpopulations within moderately differentiated buccal mucosal squamous cell carcinoma (MDBMSCC). We hypothesized that these CSCs express components of the renin-angiotensin system (RAS). METHODS: 3,3'-Diaminobenzidine (DAB) immunohistochemical (IHC) staining was performed on formalin-fixed paraffin-embedded MDBMSCC samples to investigate the expression of the components of the RAS: (pro)renin receptor (PRR), angiotensin converting enzyme (ACE), angiotensin II receptor 1 (ATIIR1), and angiotensin II receptor 2 (ATIIR2)...
2016: Frontiers in Surgery
Amy Ruth Bradshaw, Agadha Crisantha Wickremesekera, Helen D Brasch, Alice M Chibnall, Paul F Davis, Swee T Tan, Tinte Itinteang
AIM: To investigate the expression of the renin-angiotensin system (RAS) in cancer stem cells (CSCs), we have previously characterized in glioblastoma multiforme (GBM). METHODS: 3,3-Diaminobenzidine (DAB) immunohistochemical (IHC) staining for the stem cell marker, SOX2, and components of the RAS: angiotensin converting enzyme (ACE), (pro)renin receptor (PRR), angiotensin II receptor 1 (ATIIR1), and angiotensin II receptor 2 (ATIIR2) on 4 μm-thick formalin-fixed paraffin-embedded sections of previously characterized GBM samples in six patients was undertaken...
2016: Frontiers in Surgery
Joseph Markowitz, Zachary Abrams, Naduparambil K Jacob, Xiaoli Zhang, John N Hassani, Nicholas Latchana, Lai Wei, Kelly E Regan, Taylor R Brooks, Sarvani R Uppati, Kala M Levine, Tanios Bekaii-Saab, Kari L Kendra, Gregory B Lesinski, J Harrison Howard, Thomas Olencki, Philip R Payne, William E Carson
BACKGROUND: MicroRNAs (miRNAs) are short noncoding RNAs that function to repress translation of mRNA transcripts and contribute to the development of cancer. We hypothesized that miRNA array-based technologies work best for miRNA profiling of patient-derived plasma samples when the techniques and patient populations are precisely defined. METHODS: Plasma samples were obtained from five sources: melanoma clinical trial of interferon and bortezomib (12), purchased normal donor plasma samples (four), gastrointestinal tumor bank (nine), melanoma tumor bank (ten), or aged-matched normal donors (eight) for the tumor bank samples...
2016: OncoTargets and Therapy
Joelle M Fenger, Ryan D Roberts, O Hans Iwenofu, Misty D Bear, Xiaoli Zhang, Jason I Couto, Jaime F Modiano, William C Kisseberth, Cheryl A London
BACKGROUND: MicroRNAs (miRNAs) regulate the expression of networks of genes and their dysregulation is well documented in human malignancies; however, limited information exists regarding the impact of miRNAs on the development and progression of osteosarcoma (OS). Canine OS exhibits clinical and molecular features that closely resemble the corresponding human disease and it is considered a well-established spontaneous animal model to study OS biology. The purpose of this study was to investigate miRNA dysregulation in canine OS...
October 10, 2016: BMC Cancer
Robert W Hoffman, Joan T Merrill, Marta M E Alarcón-Riquelme, Michelle Petri, Ernst R Dow, Eric Nantz, Laura K Nisenbaum, Krista M Schroeder, Wendy J Komocsar, Narayanan B Perumal, Matthew D Linnik, David C Airey, Yushi Liu, Guilherme V Rocha, Richard E Higgs
OBJECTIVE: Systemic lupus erythematosus (SLE) has substantial unmet medical need and its pathogenesis is incompletely understood. This study characterized baseline gene expression and pharmacodynamic (PD)-induced changes in whole blood gene expression from two phase III, 52-week (W), randomized, placebo-controlled, double-blind studies of 1,760 SLE patients treated with the B cell activating factor (BAFF)-blocking IgG4 monoclonal antibody, tabalumab. METHODS: Patient samples were obtained from ILLUMINATE-1 and -2 while control samples were from healthy donors...
October 9, 2016: Arthritis & Rheumatology
R Roat, M M Hossain, J Christopherson, C Free, S Jain, C Guay, R Regazzi, Z Guo
Currently there is no effective approach for monitoring early β cell loss during islet graft rejection following human islet transplantation (HIT). Due to ethical and technical constraints, it is difficult to directly study biomarkers of islet destruction in humans. Here, we established a humanized mouse model with induced human β cell death using adoptive lymphocyte transfer (ALT). Human islet grafts of ALT-treated mice had peri-graft lymphocyte infiltration, fewer insulin(+) β cells, and increased β cell apoptosis...
October 3, 2016: American Journal of Transplantation
Robert Fred Henry Walter, Claudia Vollbrecht, Robert Werner, Thomas Mairinger, Jan Schmeller, Elena Flom, Jeremias Wohlschlaeger, Nikolaos Barbetakis, Dimitrios Paliouras, Fotios Chatzinikolaou, Vasilis Adamidis, Kosmas Tsakiridis, Paul Zarogoulidis, Georgia Trakada, Daniel Christian Christoph, Kurt Werner Schmid, Fabian Dominik Mairinger
BACKGROUND: Malignant pleural mesothelioma (MPM) is a rare, predominantly asbestos-related and biologically highly aggressive tumour leading to a dismal prognosis. Multimodality therapy consisting of platinum-based chemotherapy is the treatment of choice. The reasons for the rather poor efficacy of platinum compounds remain largely unknown. MATERIAL AND METHODS: For this exploratory mRNA study, 24 FFPE tumour specimens were screened by digital gene expression analysis...
2016: Journal of Cancer
Dasaradha Jalapothu, Margherita Boieri, Rachel E Crossland, Pranali Shah, Isha A Butt, Jean Norden, Ralf Dressel, Anne M Dickinson, Marit Inngjerdingen
MicroRNAs (miRNA) have emerged as central regulators of diverse biological processes and contribute to driving pathology in several diseases. Acute graft-versus-host disease (aGvHD) represents a major complication after allogeneic hematopoietic stem cell transplantation, caused by alloreactive donor T cells attacking host tissues leading to inflammation and tissue destruction. Changes in miRNA expression patterns occur during aGvHD, and we hypothesized that we could identify miRNA signatures in target tissues of aGvHD that may potentially help understand the underlying molecular pathology of the disease...
2016: Frontiers in Immunology
Neeta L Vora, Lisa Smeester, Kim Boggess, Rebecca C Fry
Second-trimester amniotic fluid supernatant (AFS) contains cell-free fetal RNA (cffRNA) transcripts that can provide information about fetal gene expression. In a retrospective case-control study, we measured second-trimester fetal gene expression using cffRNA extracted from AFS in women who had spontaneous preterm birth (sPTB) <34 weeks and in women who delivered >37 weeks. We extracted cffRNA from AFS of women with singletons who had second-trimester genetic amniocenteses. Twenty-one gravidas who had sPTB and 21 term controls were matched 1:1 for maternal age, fetal sex, race, gestational age (GA) at the time of amniocentesis, and medication exposure...
September 27, 2016: Reproductive Sciences
Joanna M Peloquin, Gautam Goel, Lingjia Kong, Hailiang Huang, Talin Haritunians, R Balfour Sartor, Mark J Daly, Rodney D Newberry, Dermot P McGovern, Vijay Yajnik, Sergio A Lira, Ramnik J Xavier
GWAS have linked SNPs to risk of inflammatory bowel disease (IBD), but a systematic characterization of disease-associated genes has been lacking. Prior studies utilized microarrays that did not capture many genes encoded within risk loci or defined expression quantitative trait loci (eQTLs) using peripheral blood, which is not the target tissue in IBD. To address these gaps, we sought to characterize the expression of IBD-associated risk genes in disease-relevant tissues and in the setting of active IBD. Terminal ileal (TI) and colonic mucosal tissues were obtained from patients with Crohn's disease or ulcerative colitis and from healthy controls...
2016: JCI Insight
Sergei E Titov, Pavel S Demenkov, Mikhail K Ivanov, Ekaterina S Malakhina, Tatiana L Poloz, Elena V Tsivlikova, Maria S Ganzha, Sergei P Shevchenko, Lyudmila F Gulyaeva, Nikolay N Kolesnikov
Fine needle aspiration cytology (FNAC) is currently the method of choice for malignancy prediction in thyroid nodules. Nevertheless, in some cases the interpretation of FNAC results may be problematic due to limitations of the method. The expression level of some microRNAs changes with the development of thyroid tumors, and its quantitation can be used to refine the FNAC results. For this quantitation to be reliable, the obtained data must be adequately normalized. Currently, no reference genes are universally recognized for quantitative assessments of microRNAs in thyroid nodules...
September 20, 2016: Oncology Reports
Nicholas Latchana, Kelly Regan, John Harrison Howard, Jennifer H Aldrink, Mark A Ranalli, Sara B Peters, Xiaoli Zhang, Alejandro Gru, Philip R O Payne, Lorena P Suarez-Kelly, William E Carson
BACKGROUND: Melanoma skin cancer remains the leading cause of skin cancer-related deaths. Spitz lesions represent a subset of melanocytic skin lesions characterized by epithelioid or spindled melanocytes organized in nests. These lesions occupy a spectrum ranging from benign Spitz and atypical Spitz lesions all the way to malignant Spitz tumors. Appropriate management is reliant on accurate diagnostic classification, yet this effort remains challenging using current light microscopic techniques...
October 2016: Journal of Surgical Research
Kevin A Murach, R Grace Walton, Christopher S Fry, Sami L Michaelis, Jason S Groshong, Brian S Finlin, Philip A Kern, Charlotte A Peterson
This investigation evaluated whether moderate-intensity cycle ergometer training affects satellite cell and molecular responses to acute maximal concentric/eccentric resistance exercise in middle-aged women. Baseline and 72 h postresistance exercise vastus lateralis biopsies were obtained from seven healthy middle-aged women (56 ± 5 years, BMI 26 ± 1, VO2max 27 ± 4) before and after 12 weeks of cycle training. Myosin heavy chain (MyHC) I- and II-associated satellite cell density and cross-sectional area was determined via immunohistochemistry...
September 2016: Physiological Reports
Colm Keane, Clare Gould, Kimberley Jones, David Hamm, Dipti Talaulikar, Jonathan Ellis, Frank Vari, Simone Birch, Erica Han, Peter Wood, Kim-Anh Le Cao, Michael R Green, Pauline Crooks, Sanjiv Jain, Joshua Tobin, Raymond J Steptoe, Maher K Gandhi
PURPOSE: To investigate the relationship between the intra-tumoral T-cell receptor (TCR) repertoire and the tumor microenvironment (TME) in de novo Diffuse Large B-cell Lymphoma (DLBCL), and the TCR's impact on survival. EXPERIMENTAL DESIGN: We performed high-throughput unbiased TCRBeta sequencing on a population based cohort of 92 DLBCL patients treated with conventional (i.e. non-checkpoint blockade) frontline 'R-CHOP' therapy. Key immune checkpoint genes within the TME were digitally quantified by nanoString{trade mark, serif}...
September 20, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Maria J Gutierrez, Jose L Gomez, Geovanny F Perez, Krishna Pancham, Stephanie Val, Dinesh K Pillai, Mamta Giri, Sarah Ferrante, Robert Freishtat, Mary C Rose, Diego Preciado, Gustavo Nino
BACKGROUND: Innate immune responses are fine-tuned by small noncoding RNA molecules termed microRNAs (miRs) that modify gene expression in response to the environment. During acute infections, miRs can be secreted in extracellular vesicles (EV) to facilitate cell-to-cell genetic communication. The purpose of this study was to characterize the baseline population of miRs secreted in EVs in the airways of young children (airway secretory microRNAome) and examine the changes during rhinovirus (RV) infection, the most common cause of asthma exacerbations and the most important early risk factor for the development of asthma beyond childhood...
2016: PloS One
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