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https://www.readbyqxmd.com/read/28919262/pdgfra-is-not-essential-for-the-derivation-and-maintenance-of-mouse-extraembryonic-endoderm-stem-cell-lines
#1
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...
September 8, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28889351/multidimensional-phenotyping-of-breast-cancer-cell-lines-to-guide-preclinical-research
#2
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
https://www.readbyqxmd.com/read/28882697/clinicopathologic-and-gene-expression-analysis-of-initial-biopsies-from-patients-with-eosinophilic-esophagitis-refractory-to-therapy
#3
Ayesha S Siddique, David C Corney, Shamlal Mangray, Kara A Lombardo, Sonja Chen, Alexander S Marwaha, Murray B Resnick, Michael Herzlinger, Andres Matoso
Some patients with eosinophilic esophagitis (EoE) do not respond to therapy. The clinicopathologic characteristics, and gene expression profile at time of presentation could help predict response to therapy. Refractory EoE was defined as persistence of symptoms and biopsies with histologic features of EoE after 6months of therapy with proton pump inhibitors and topical corticosteroids. Initial biopsies from refractory EoE patients (n=21), responder to therapy (n=8), patients who relapsed (n=6), and reflux controls (n=24) were studied...
September 4, 2017: Human Pathology
https://www.readbyqxmd.com/read/28881975/molecular-signatures-that-can-be-transferred-across-different-omics-platforms
#4
M Altenbuchinger, P Schwarzfischer, T Rehberg, J Reinders, Ch W Kohler, W Gronwald, J Richter, M Szczepanowski, N Masqué-Soler, W Klapper, P J Oefner, R Spang
Motivation: Molecular signatures for treatment recommendations are well researched. Still it is challenging to apply them to data generated by different protocols or technical platforms. Results: We analyzed paired data for the same tumors (Burkitt lymphoma, diffuse large B-cell lymphoma) and features that had been generated by different experimental protocols and analytical platforms including the nanoString nCounter and Affymetrix Gene Chip transcriptomics as well as the SWATH and SRM proteomics platforms...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28875995/anti-inflammatory-effects-of-octadecylamine-functionalized-nanodiamond-on-primary-human-macrophages
#5
A E Pentecost, C E Witherel, Y Gogotsi, K L Spiller
Chronic inflammatory disorders such as rheumatoid arthritis are characterized by excessive pro-inflammatory or "M1" activation of macrophages, the primary cells of the innate immune system. Current treatments include delivery of glucocorticoids (e.g. dexamethasone - Dex), which reduce pro-inflammatory M1 behaviour in macrophages. However, these treatments have many off-target effects on cells other than macrophages, resulting in broad immunosuppression. To limit such side effects, drug-incorporated nano- and microparticles may be used to selectively target macrophages via phagocytosis, because of their roles as highly effective phagocytes in the body...
September 6, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28874676/linc-ing-circulating-long-non-coding-rnas-to-the-diagnosis-and-malignant-prediction-of-intraductal-papillary-mucinous-neoplasms-of-the-pancreas
#6
Jennifer B Permuth, Dung-Tsa Chen, Sean J Yoder, Jiannong Li, Andrew T Smith, Jung W Choi, Jongphil Kim, Yoganand Balagurunathan, Kun Jiang, Domenico Coppola, Barbara A Centeno, Jason Klapman, Pam Hodul, Florian A Karreth, Jose G Trevino, Nipun Merchant, Anthony Magliocco, Mokenge P Malafa, Robert Gillies
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that lacks effective biomarkers for early detection. We hypothesized that circulating long non-coding RNAs (lncRNAs) may act as diagnostic markers of incidentally-detected cystic PDAC precursors known as intraductal papillary mucinous neoplasms (IPMNs) and predictors of their pathology/histological classification. Using NanoString nCounter® technology, we measured the abundance of 28 candidate lncRNAs in pre-operative plasma from a cohort of pathologically-confirmed IPMN cases of various grades of severity and non-diseased controls...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28863456/multiplex-detection-of-pediatric-low-grade-glioma-signature-fusion-transcripts-and-duplications-using-the-nanostring-ncounter-system
#7
Scott Ryall, Anthony Arnoldo, Rahul Krishnatry, Matthew Mistry, Kangzi Khor, Javal Sheth, Cino Ling, Stephie Leung, Michal Zapotocky, Ana Guerreiro Stucklin, Alvaro Lassaletta, Mary Shago, Uri Tabori, Cynthia E Hawkins
Previous studies identified recurrent fusion and duplication events in pediatric low-grade glioma (pLGG). In addition to their role in diagnosis, the presence of these events aid in dictating therapy and predicting patient survival. Clinically, BRAF alterations are most commonly identified using fluorescent in situ hybridization (FISH). However, this method is costly, labor-intensive and does not identify nonBRAF events. Here, we evaluated the NanoString nCounter gene expression system for detecting 32 of the most commonly reported fusion/duplication events in pLGG...
July 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28846748/plasmacytoid-dendritic-cells-and-rna-containing-immune-complexes-drive-expansion-of-peripheral-b-cell-subsets-with-an-sle-like-phenotype
#8
Olof Berggren, Niklas Hagberg, Andrei Alexsson, Gert Weber, Lars Rönnblom, Maija-Leena Eloranta
BACKGROUND: Hyperactive B cells and a continuous interferon (IFN)-α production by plasmacytoid dendritic cells (pDCs) play a key role in systemic lupus erythematosus (SLE). We asked whether the interaction between B cells and pDCs stimulated with RNA-containing immune complexes affects peripheral B cell subsets. METHODS: B cells and pDCs were isolated from blood of healthy individuals and stimulated with immune complexes consisting of SLE-IgG and U1snRNP (RNA-IC)...
2017: PloS One
https://www.readbyqxmd.com/read/28842510/impact-of-therapy-on-genomics-and-transcriptomics-in-high-risk-prostate-cancer-treated-with-neoadjuvant-docetaxel-and-androgen-deprivation-therapy
#9
Himisha Beltran, Alexander W Wyatt, Edmund Chedgy, Adam Donoghue, Matti Annala, Evan Warner, Kevin Beja, Michael Sigouros, Fan Mo, Ladan Fazli, Colin C Collins, James A Eastham, Michael J Morris, Mary-Ellen Taplin, Andrea Sboner, Susan Halabi, Martin E Gleave
BACKGROUND: The combination of docetaxel chemotherapy and androgen deprivation therapy (ADT) has become a standard treatment for patients with metastatic prostate cancer. The recently accrued Phase III CALGB 90203 trial was designed to investigate the clinical effectiveness of this treatment approach earlier in the disease. Specimens from this trial offer a unique opportunity to interrogate the acute molecular response to docetaxel and ADT and identify predictive biomarkers. METHODS: We evaluated baseline clinical data, needle biopsies and radical prostatectomy (RP) specimens from 52 (of 788) patients enrolled on CALGB 90203 at one high volume center...
August 25, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28831359/embryonic-stem-cell-like-population-in-dupuytren-s-disease-expresses-components-of-the-renin-angiotensin-system
#10
Nicholas On, Sabrina P Koh, Helen D Brasch, Jonathan C Dunne, James R Armstrong, Swee T Tan, Tinte Itinteang
The renin-angiotensin system (RAS) mediates cardiac and renal fibrosis. Dupuytren's disease (DD) is a proliferative fibromatosis affecting the hands. This study investigated the expression of the RAS in DD. METHODS: 3,3-Diaminobenzidine (DAB) and immunofluorescent immunohistochemical (IHC) staining for (pro)renin receptor (PRR), angiotensin-converting enzyme (ACE), angiotensin II receptor 1 (ATIIR1), and angiotensin II receptor 2 (ATIIR2) was performed on 4-μm thick formalin-fixed paraffin-embedded sections of DD cords and nodules from 6 patients...
July 2017: Plastic and Reconstructive Surgery. Global Open
https://www.readbyqxmd.com/read/28830935/differences-in-mirna-expression-profiles-between-wild-type-and-mutated-niftps
#11
Maria Denaro, Clara Ugolini, Anello Marcello Poma, Nicla Borrelli, Gabriele Materazzi, Paolo Piaggi, Massimo Chiarugi, Paolo Miccoli, Paolo Vitti, Fulvio Basolo
Noninvasive encapsulated follicular variants of papillary thyroid carcinomas have been recently reclassified as noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTPs). NIFTPs exhibit a behavior that is very close to that of follicular adenomas but different from the infiltrative and invasive follicular variants of papillary thyroid carcinomas (FVPTCs). The importance of miRNAs to carcinogenesis has been reported in recent years. miRNAs seem to be promising diagnostic and prognostic molecular markers for thyroid cancer, and the combination of miRNA expression and mutational status might improve cytological diagnosis...
October 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28830445/responses-of-rat-and-mouse-primary-microglia-to-pro-and-anti-inflammatory-stimuli-molecular-profiles-k-channels-and-migration
#12
Doris Lam, Starlee Lively, Lyanne C Schlichter
BACKGROUND: Acute CNS damage is commonly studied using rat and mouse models, but increasingly, molecular analysis is finding species differences that might affect the ability to translate findings to humans. Microglia can undergo complex molecular and functional changes, often studied by in vitro responses to discrete activating stimuli. There is considerable evidence that pro-inflammatory (M1) activation can exacerbate tissue damage, while anti-inflammatory (M2) states help resolve inflammation and promote tissue repair...
August 22, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28815002/a-comprehensive-method-for-identification-of-suitable-reference-genes-in-extracellular-vesicles
#13
Kenneth Gouin, Kiel Peck, Travis Antes, Jennifer Leigh Johnson, Chang Li, Sharon Denise Vaturi, Ryan Middleton, Geoff de Couto, Ann-Sophie Walravens, Luis Rodriguez-Borlado, Rachel Ruckdeschel Smith, Linda Marbán, Eduardo Marbán, Ahmed Gamal-Eldin Ibrahim
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is one of the most sensitive, economical and widely used methods for evaluating gene expression. However, the utility of this method continues to be undermined by a number of challenges including normalization using appropriate reference genes. The need to develop tailored and effective strategies is further underscored by the burgeoning field of extracellular vesicle (EV) biology. EVs contain unique signatures of small RNAs including microRNAs (miRs)...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28811492/interferon-alpha-treatment-rapidly-clears-hepatitis-e-virus-infection-in-humanized-mice
#14
Martijn D B van de Garde, Suzan D Pas, Gertine W van Oord, Lucio Gama, Youkyung Choi, Robert A de Man, Andre Boonstra, Thomas Vanwolleghem
Antiviral treatment options for chronic Hepatitis E Virus (HEV) infections are limited and immunological determinants of viral persistence remain largely unexplored. We studied the antiviral potency of pegylated interferon-α (pegIFNα) against HEV infections in humanized mice and modelled intrahepatic interferon stimulated gene (ISG) responses. Human gene expression levels in humanized mouse livers were analyzed by qPCR and Nanostring. Human CXCL10 was measured in mouse serum. HEV genotype 3 (gt3) infections were cleared from liver and feces within 8 pegIFNα doses in all mice and relapsed after a single pegIFNα injection in only half of treated animals...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798985/nanostring-based-breast-cancer-risk-prediction-for-women-with-sclerosing-adenosis
#15
Stacey J Winham, Christine Mehner, Ethan P Heinzen, Brendan T Broderick, Melody Stallings-Mann, Aziza Nassar, Robert A Vierkant, Tanya L Hoskin, Ryan D Frank, Chen Wang, Lori A Denison, Celine M Vachon, Marlene H Frost, Lynn C Hartmann, E Aubrey Thompson, Mark E Sherman, Daniel W Visscher, Amy C Degnim, Derek C Radisky
PURPOSE: Sclerosing adenosis (SA), found in ¼ of benign breast disease (BBD) biopsies, is a histological feature characterized by lobulocentric proliferation of acini and stromal fibrosis and confers a two-fold increase in breast cancer risk compared to women in the general population. We evaluated a NanoString-based gene expression assay to model breast cancer risk using RNA derived from formalin-fixed, paraffin-embedded (FFPE) biopsies with SA. METHODS: The study group consisted of 151 women diagnosed with SA between 1967 and 2001 within the Mayo BBD cohort, of which 37 subsequently developed cancer within 10 years (cases) and 114 did not (controls)...
August 10, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28765929/characterization-and-predicted-role-of-microrna-expression-profiles-associated-with-early-childhood-obesity
#16
Shengrong Ouyang, Renqiao Tang, Zhuo Liu, Feifei Ma, Yuanyuan Li, Jianxin Wu
MicroRNAs (miRNAs) are implicated in the pathogenesis of obesity. The aim of the present study was to characterize the miRNA profile associated with early childhood obesity in peripheral blood mononuclear cells (PBMCs). A total of 12 children (6 obese and 6 lean controls) aged 36 months old to 48 months old were recruited. The miRNA expression profile from PBMCs was detected using the multiplexed NanoString nCounter system. Bioinformatics was employed to detect target genes and miRNA‑regulated biological function...
October 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28760805/h1n1-vaccination-in-sj%C3%A3-gren-s-syndrome-triggers-polyclonal-b-cell-activation-and-promotes-autoantibody-production
#17
Susanna Brauner, Lasse Folkersen, Marika Kvarnström, Sabrina Meisgen, Sven Petersen, Michaela Franzén-Malmros, Johannes Mofors, Karl A Brokstad, Lars Klareskog, Roland Jonsson, Lisa S Westerberg, Christina Trollmo, Vivianne Malmström, Aurelie Ambrosi, Vijay K Kuchroo, Gunnel Nordmark, Marie Wahren-Herlenius
OBJECTIVES: Vaccination of patients with rheumatic disease has been reported to result in lower antibody titres than in healthy individuals. However, studies primarily include patients on immunosuppressive therapy. Here, we investigated the immune response of treatment-naïve patients diagnosed with primary Sjögren's syndrome (pSS) to an H1N1 influenza vaccine. METHODS: Patients with Sjögren's syndrome without immunomodulatory treatment and age-matched and gender-matched healthy controls were immunised with an H1N1 influenza vaccine and monitored for serological and cellular immune responses...
July 31, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28753783/gene-expression-profiling-of-advanced-penile-squamous-cell-carcinoma-receiving-cisplatin-based-chemotherapy-improves-prognostication-and-identifies-potential-therapeutic-targets
#18
Andrea Necchi, Bernhard J Eigl, Eddy Shih-Hsin Yang, Sejong Bae, Darshan Chandrashekar, Dongquan Chen, Gurudatta Naik, Amitkumar Mehta, Patrizia Giannatempo, Maurizio Colecchia, Jennifer Gordetsky, Shi Wei, Tiffiny Cooper, Sooryanarayana Varambally, Guru Sonpavde
In men with advanced penile squamous cell carcinoma receiving first-line chemotherapy, visceral metastases (VM) and Eastern Cooperative Oncology Group performance status ≥1 are poor prognostic factors for overall survival (OS). We hypothesized that tumor gene expression profiling may enhance prognostic stratification and identify potential therapeutic targets. In this retrospective study, RNA extracted from macrodissected tumors underwent profiling for the expression of 738 genes using NanoString. Univariate and multivariate analyses assessed the association of genes, VM, and performance status with OS...
August 27, 2016: European Urology Focus
https://www.readbyqxmd.com/read/28750583/association-of-a-history-of-child-abuse-with-impaired-myelination-in-the-anterior-cingulate-cortex-convergent-epigenetic-transcriptional-and-morphological-evidence
#19
Pierre-Eric Lutz, Arnaud Tanti, Alicja Gasecka, Sarah Barnett-Burns, John J Kim, Yi Zhou, Gang G Chen, Marina Wakid, Meghan Shaw, Daniel Almeida, Marc-Aurele Chay, Jennie Yang, Vanessa Larivière, Marie-Noël M'Boutchou, Léon C van Kempen, Volodymyr Yerko, Josée Prud'homme, Maria Antonietta Davoli, Kathryn Vaillancourt, Jean-François Théroux, Alexandre Bramoullé, Tie-Yuan Zhang, Michael J Meaney, Carl Ernst, Daniel Côté, Naguib Mechawar, Gustavo Turecki
OBJECTIVE: Child abuse has devastating and long-lasting consequences, considerably increasing the lifetime risk of negative mental health outcomes such as depression and suicide. Yet the neurobiological processes underlying this heightened vulnerability remain poorly understood. The authors investigated the hypothesis that epigenetic, transcriptomic, and cellular adaptations may occur in the anterior cingulate cortex as a function of child abuse. METHOD: Postmortem brain samples from human subjects (N=78) and from a rodent model of the impact of early-life environment (N=24) were analyzed...
July 28, 2017: American Journal of Psychiatry
https://www.readbyqxmd.com/read/28744745/circulating-mrna-in-maternal-plasma-at-the-second-trimester-of-pregnancy-a-possible-screening-tool-for-cardiac-conotruncal-and-left-ventricular-outflow-tract-abnormalities
#20
Elena Contro, Lara Stefani, Silvia Berto, Cristina Lapucci, Diego Arcelli, Daniela Prandstraller, Antonella Perolo, Nicola Rizzo, Antonio Farina
OBJECTIVE: Maternal plasma is a source of circulating placental nucleic acids. This study was designed to detect aberrantly expressed placental mRNA genes circulating in the maternal plasma of pregnancies affected with fetal conotruncal anomalies (CNTRA) and left-ventricular outflow tract (LVOT) obstruction in the second trimester of pregnancy. METHODS: This was a retrospective monocentric study conducted from 1 Jan 2016 to 31 Dec 2016. NanoString technology was used to identify aberrantly expressed genes, comparing 36 women carrying a fetus with CNTRA or LVOT obstruction to 42 controls at 19-24 weeks of gestation...
July 25, 2017: Molecular Diagnosis & Therapy
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