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https://www.readbyqxmd.com/read/28640876/reliability-and-performance-of-commercial-rna-and-dna-extraction-kits-for-ffpe-tissue-cores
#1
Palak G Patel, Shamini Selvarajah, Karl-Philippe Guérard, John M S Bartlett, Jacques Lapointe, David M Berman, John B A Okello, Paul C Park
Cancer biomarker studies often require nucleic acid extraction from limited amounts of formalin-fixed, paraffin-embedded (FFPE) tissues, such as histologic sections or needle cores. A major challenge is low quantity and quality of extracted nucleic acids, which can limit our ability to perform genetic analyses, and have a significant influence on overall study design. This study was aimed at identifying the most reliable and reproducible method of obtaining sufficient high-quality nucleic acids from FFPE tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28634582/cancer-stem-cells-in-moderately-differentiated-lip-squamous-cell-carcinoma-express-components-of-the-renin-angiotensin-system
#2
Rachna S Ram, Helen D Brasch, Jonathan C Dunne, Paul F Davis, Swee T Tan, Tinte Itinteang
AIM: We investigated the expression of the renin-angiotensin system (RAS) by cancer stem cell (CSC) subpopulations we have identified in moderately differentiated lip squamous cell carcinoma (MDLSCC). METHOD: Ten MDLSCC samples underwent 3,3-diaminobenzidine (DAB) and immunofluorescent immunohistochemical (IHC) staining for (pro)renin receptor (PRR), angiotensin-converting enzyme (ACE), angiotensin II receptor 1 (ATIIR1), and receptor 2 (ATIIR2). NanoString analysis and Western blotting (WB) were performed on six MDLSCC samples for gene and protein expression, respectively...
2017: Frontiers in Surgery
https://www.readbyqxmd.com/read/28632792/identification-of-cell-proliferation-immune-response-and-cell-migration-as-critical-pathways-in-a-prognostic-signature-for-her2-er%C3%AE-breast-cancer
#3
Jeffrey C Liu, Miriam Zacksenhouse, Andrea Eisen, Sharon Nofech-Mozes, Eldad Zacksenhaus
BACKGROUND: Multi-gene prognostic signatures derived from primary tumor biopsies can guide clinicians in designing an appropriate course of treatment. Identifying genes and pathways most essential to a signature performance may facilitate clinical application, provide insights into cancer progression, and uncover potentially new therapeutic targets. We previously developed a 17-gene prognostic signature (HTICS) for HER2+:ERα- breast cancer patients, using genes that are differentially expressed in tumor initiating cells (TICs) versus non-TICs from MMTV-Her2/neu mammary tumors...
2017: PloS One
https://www.readbyqxmd.com/read/28624625/a-formalin-fixed-paraffin-embedded-ffpe-based-prognostic-signature-to-predict-metastasis-in-clinically-low-risk-stage-i-ii-microsatellite-stable-colorectal-cancer
#4
Yee Syuen Low, Christopher Blöcker, John R McPherson, See Aik Tang, Ying Ying Cheng, Joyner Y S Wong, Clarinda Chua, Tony K H Lim, Choong Leong Tang, Min Hoe Chew, Patrick Tan, Iain B Tan, Steven G Rozen, Peh Yean Cheah
Approximately 20% early-stage (I/II) colorectal cancer (CRC) patients develop metastases despite curative surgery. We aim to develop a formalin-fixed and paraffin-embedded (FFPE)-based predictor of metastases in early-stage, clinically-defined low risk, microsatellite-stable (MSS) CRC patients. We considered genome-wide mRNA and miRNA expression and mutation status of 20 genes assayed in 150 fresh-frozen tumours with known metastasis status. We selected 193 genes for further analysis using NanoString nCounter arrays on corresponding FFPE tumours...
June 15, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28615018/the-aquaglyceroporin-aqp9-contributes-to-the-sex-specific-effects-of-in-utero-arsenic-exposure-on-placental-gene-expression
#5
Emily F Winterbottom, Devin C Koestler, Dennis Liang Fei, Eric Wika, Anthony J Capobianco, Carmen J Marsit, Margaret R Karagas, David J Robbins
BACKGROUND: Sex-specific factors play a major role in human health and disease, including responses to environmental stresses such as toxicant exposure. Increasing evidence suggests that such sex differences also exist during fetal development. In a previous report using the resources of the New Hampshire Birth Cohort Study (NHBCS), we found that low-to-moderate in utero exposure to arsenic, a highly toxic and widespread pollutant, was associated with altered expression of several key developmental genes in the fetal portion of the placenta...
June 14, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/28611989/expression-of-cathepsins-b-d-and-g-in-isocitrate-dehydrogenase-wildtype-glioblastoma
#6
Sabrina P Koh, Agadha C Wickremesekera, Helen D Brasch, Reginald Marsh, Swee T Tan, Tinte Itinteang
AIM: To investigate the expression of cathepsins B, D, and G, in relation to the cancer stem cell (CSC) subpopulations, we have previously characterized within isocitrate dehydogenase (IDH)-wildtype glioblastoma (IDHWGB). METHODS: 3,3-Diaminobezidine (DAB) immunohistochemical (IHC) staining for cathepsins B, D, and G, was performed on 4μm-thick formalin-fixed paraffin-embedded IDHWGB samples obtained from six patients. Two representative DHWGB samples from the original cohort of patients were selected for immunofluorescent (IF) IHC staining, to identify the localization of the cathepsins in relation to the CSC subpopulations...
2017: Frontiers in Surgery
https://www.readbyqxmd.com/read/28600498/deregulation-of-mirnas-in-malignant-pleural-mesothelioma-is-associated-with-prognosis-and-suggests-an-alteration-of-cell-metabolism
#7
Chiara De Santi, Ombretta Melaiu, Alessandra Bonotti, Luciano Cascione, Gianpiero Di Leva, Rudy Foddis, Alfonso Cristaudo, Marco Lucchi, Marco Mora, Anna Truini, Andrea Tironi, Bruno Murer, Renzo Boldorini, Monica Cipollini, Federica Gemignani, Pierluigi Gasparini, Luciano Mutti, Stefano Landi
Malignant pleural mesothelioma (MPM) is an aggressive human cancer and miRNAs can play a key role for this disease. In order to broaden the knowledge in this field, the miRNA expression was investigated in a large series of MPM to discover new pathways helpful in diagnosis, prognosis and therapy. We employed nanoString nCounter system for miRNA profiling on 105 MPM samples and 10 healthy pleura. The analysis was followed by the validation of the most significantly deregulated miRNAs by RT-qPCR in an independent sample set...
June 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28596502/correlation-between-mek-signature-and-ras-gene-alteration-in-advanced-gastric-cancer
#8
Soomin Ahn, Roz Brant, Alan Sharpe, Jonathan R Dry, Darren R Hodgson, Elaine Kilgour, Kyung Kim, Seung Tae Kim, Se Hoon Park, Won Ki Kang, Kyoung-Mee Kim, Jeeyun Lee
MEK inhibitor (selumetinib) is a potent, orally active inhibitor of MAPK/ERK pathway. It is important to develop an accurate and robust method indicative of RAS pathway activity to stratify potential patients who can benefit from selumetinib treatment in gastric cancer (GC). First, we surveyed the sensitivity to selumetinib in a panel of 22 GC cell lines and correlated with MEK signature to selumetinib sensitivity. Next, we analyzed MEK signature via nanostring assay in two Asian cohorts using clinical samples (n = 218) and then performed a correlative analysis with MEK signature status and KRAS genotype in GC...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28575868/increased-breast-tissue-receptor-activator-of-nuclear-factor-%C3%AE%C2%BAb-ligand-rankl-gene-expression-is-associated-with-higher-mammographic-density-in-premenopausal-women
#9
Adetunji T Toriola, Ha X Dang, Ian S Hagemann, Catherine M Appleton, Graham A Colditz, Jingqin Luo, Christopher A Maher
Increased mammographic breast density is associated with a 4-6-fold increased risk of breast cancer, yet lifestyle factors that can reduce dense breasts are yet to be identified, and viable prevention strategies to reduce breast density-associated breast cancer development are yet to be developed. We investigated the associations of breast tissue receptor activator of nuclear factor-κB (RANK) pathway gene expression with mammographic density in 48 premenopausal women, with no previous history of cancer. Gene expression levels were measured in total RNA isolated from formalin-fixed paraffin-embedded breast tissue samples, using the NanoString nCounter platform...
May 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28572860/pulmonary-microrna-profiling-implications-in-upper-lobe-predominant-lung-disease
#10
David A Armstrong, Amanda B Nymon, Carol S Ringelberg, Corina Lesseur, Haley F Hazlett, Louisa Howard, Carmen J Marsit, Alix Ashare
BACKGROUND: Numerous pulmonary diseases manifest with upper lobe predominance including cystic fibrosis, smoking-related chronic obstructive pulmonary disease, and tuberculosis. Zonal hypoxia, characteristic of these pulmonary maladies, and oxygen stress in general is known to exert profound effects on various important aspects of cell biology. Lung macrophages are major participants in the pulmonary innate immune response and regional differences in macrophage responsiveness to hypoxia may contribute in the development of lung disease...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28555079/muc1-inhibition-leads-to-decrease-in-pd-l1-levels-via-up-regulation-of-mirnas
#11
A R Pyzer, D Stroopinsky, J Rosenblatt, E Anastasiadou, H Rajabi, A Washington, A Tagde, J-H Chu, M Coll, A L Jiao, L T Tsai, D E Tenen, L Cole, K Palmer, A Ephraim, R K Leaf, M Nahas, A Apel, Mb-N Zommer, S Jain, M McMasters, L Mendez, J Arnason, B A Raby, F Slack, D Kufe, D Avigan
The PD-L1/PD-1 pathway is a critical component of the immunosuppressive tumor microenvironment in AML, but little is known about its regulation. We investigated the role of the MUC1 oncoprotein in modulating PD-L1 expression in AML. Silencing of MUC1 in AML cell lines suppressed PD-L1 expression without a decrease in PD-L1 mRNA levels, suggesting a post-transcriptional mechanism of regulation. We identified the microRNAs miR-200c and miR-34a as key regulators of PD-L1 expression in AML. Silencing of MUC1 in AML cells led to a marked increase in miR-200c and miR-34a levels, without changes in precursor microRNA, suggesting that MUC1 might regulate microRNA processing...
May 30, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28549458/detection-of-alk-fusion-transcripts-in-ffpe-lung-cancer-samples-by-nanostring-technology
#12
Adriane F Evangelista, Maicon F Zanon, Adriana Cruvinel Carloni, Flávia E de Paula, Mariana Andozia Morini, Maressa Ferreira-Neto, Iberê Cauduro Soares, Jose Elias Miziara, Pedro de Marchi, Cristovam Scapulatempo-Neto, Rui M Reis
BACKGROUND: ALK-rearranged lung cancers exhibit specific pathologic and clinical features and are responsive to anti-ALK therapies. Therefore, the detection of ALK-rearrangement is fundamental for personalized lung cancer therapy. Recently, new molecular techniques, such as NanoString nCounter, have been developed to detect ALK fusions with more accuracy and sensitivity. METHODS: In the present study, we intended to validate a NanoString nCounter ALK-fusion panel in routine biopsies of FFPE lung cancer patients...
May 26, 2017: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/28516114/measurement-of-mrna-decay-in-mouse-embryonic-fibroblasts
#13
Lian-Qun Qiu, Wi S Lai, Deborah J Stumpo, Perry J Blackshear
mRNA stability control is a critical step in the post-transcriptional regulation of gene expression. Actinomycin D, an antibiotic initially used as an anti-cancer drug, has turned out to be a convenient tool for studying the turnover rates of transcripts in cells, due to its inhibition of mRNA synthesis. Here, we describe a protocol for the measurement of mRNA decay after adding actinomycin D into the medium of stable fibroblast cell lines derived from wild-type and tristetraprolin (TTP)-deficient mouse embryonic fibroblast (MEF) cultures, as well as a protocol for determining the relative transcript abundance using semi-quantitative real time RT-PCR...
July 5, 2016: Bio-protocol
https://www.readbyqxmd.com/read/28507813/deep-exploration-of-the-immune-infiltrate-and-outcome-prediction-in-testicular-cancer-by-quantitative-multiplexed-immunohistochemistry-and-gene-expression-profiling
#14
Peter J Siska, Romany A N Johnpulle, Alice Zhou, Jennifer Bordeaux, Ju Young Kim, Bashar Dabbas, Naveen Dakappagari, Jeffrey C Rathmell, W Kimryn Rathmell, Alicia K Morgans, Justin M Balko, Douglas B Johnson
Platinum-based chemotherapy is usually curative for patients with testicular germ cell tumors (TGCT), but a subset of patients experience disease progression and poor clinical outcomes. Here, we tested whether immune profiling of TGCT could identify novel prognostic markers and therapeutic targets for this patient cohort. We obtained primary and metastatic TGCT samples from one center. We performed immune profiling using multiplexed fluorescence immunohistochemistry (FIHC) for T-cell subsets and immune checkpoints, and targeted gene expression profiling (Nanostring nCounter Immune panel)...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28488345/patterns-of-pd-1-pd-l1-and-pd-l2-expression-in-pediatric-solid-tumors
#15
Navin Pinto, Julie R Park, Erin Murphy, Jennifer Yearley, Terri McClanahan, Lakshmanan Annamalai, Douglas S Hawkins, Erin R Rudzinski
BACKGROUND: Significant antitumor effects have been observed in a variety of malignancies via blockade of immune checkpoints. Interaction of programmed death 1 (PD-1) with its ligands PD-L1 and PD-L2 suppresses T-cell function and restricts immune-mediated tumor killing. We examined expression of these proteins in children with solid tumors, as expression may serve as biomarkers of response to this class of drugs. METHODS: Sections cut from formalin-fixed paraffin-embedded (FFPE) tissue blocks were processed and evaluated for PD-1, PD-L1, and PD-L2 by immunohistochemistry (IHC) as well as by mRNA expression...
May 10, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28469417/plasma-microrna-levels-following-resection-of-metastatic-melanoma
#16
Nicholas Latchana, Zachary B Abrams, J Harrison Howard, Kelly Regan, Naduparambil Jacob, Paolo Fadda, Alicia Terando, Joseph Markowitz, Doreen Agnese, Philip Payne, William E Carson
Melanoma remains the leading cause of skin cancer-related deaths. Surgical resection and adjuvant therapies can result in disease-free intervals for stage III and stage IV disease; however, recurrence is common. Understanding microRNA (miR) dynamics following surgical resection of melanomas is critical to accurately interpret miR changes suggestive of melanoma recurrence. Plasma of 6 patients with stage III (n = 2) and stage IV (n = 4) melanoma was evaluated using the NanoString platform to determine pre- and postsurgical miR expression profiles, enabling analysis of more than 800 miRs simultaneously in 12 samples...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28466156/mirna-regulation-is-important-for-dna-damage-repair-and-recognition-in-malignant-pleural-mesothelioma
#17
Fabian Dominik Mairinger, Robert Werner, Elena Flom, Jan Schmeller, Sabrina Borchert, Michael Wessolly, Jeremias Wohlschlaeger, Thomas Hager, Thomas Mairinger, Jens Kollmeier, Daniel Christian Christoph, Kurt Werner Schmid, Robert Fred Henry Walter
Platin-containing regimes are currently considered as state-of-the-art therapies in malignant pleural mesotheliomas (MPM) but show dissatisfying response rates ranging from 6 to 16% only. Still, the reasons for the rather poor efficacy remain largely unknown. A clear stratification of patients based on new biomarkers seems to be a promising approach to enhance clinical management, which would be a long-needed improvement for MPM patients but does not seem likely soon unless new biomarkers can be validated. Twenty-four formalin-fixed, paraffin-embedded (FFPE) tumour specimens were subjected to a miRNA expression screening of 800 important miRNAs using digital quantification via the nCounter technique (NanoString)...
June 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28445152/multiplexed-gene-expression-profiling-identifies-the-fgfr4-pathway-as-a-novel-biomarker-in-intrahepatic-cholangiocarcinoma
#18
Changhoon Yoo, Jihoon Kang, Deokhoon Kim, Kyu-Pyo Kim, Baek-Yeol Ryoo, Seung-Mo Hong, Jung Jin Hwang, Seong-Yun Jeong, Shin Hwang, Ki-Hun Kim, Young-Joo Lee, Klaus P Hoeflich, Oleg Schmidt-Kittler, Stephen Miller, Eun Kyung Choi
BACKGROUND: The fibroblast growth factor receptor 4 (FGFR4) pathway is an essential regulatory component of bile acid synthesis, and its relationship with hepatocellular carcinoma (HCC) has been reported. We investigated the gene expression and clinical significance of FGFR4 and related pathways in intrahepatic cholangiocarcinoma (iCCA). RESULTS: The median age was 56 years (range 30-78) and 34 patients (74%) were male. Six patients (13%) had hepatitis B virus infection, with or without liver cirrhosis...
June 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28442586/therapeutic-targeting-of-ptk7-is-cytotoxic-in-atypical-teratoid-rhabdoid-tumors
#19
Shanta M Messerli, Mariah M Hoffman, Etienne Z Gnimpieba, Ratan D Bhardwaj
Novel discoveries involving the evaluation of potential therapeutics are based on newly identified molecular targets for atypical teratoid rhabdoid tumors (ATRT), which are the most common form of infantile brain tumors. Central nervous system ATRTs are rare, aggressive, and fast growing tumors of the brain and spinal cord and carry a very poor prognosis. Currently, the standard of care for ATRT patients is based on surgical resection followed by systemic chemotherapy and radiotherapy, which result in severe side effects...
April 25, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28423544/cell-of-origin-of-diffuse-large-b-cell-lymphomas-determined-by-the-lymph2cx-assay-better-prognostic-indicator-than-hans-algorithm
#20
Nara Yoon, Soomin Ahn, Hae Yong Yoo, Suk Jin Kim, Won Seog Kim, Young Hyeh Ko
Diffuse large B-cell lymphomas (DLBCLs) are clinically heterogeneous and need a biomarker that can predict the outcome of treatments accurately. To assess the prognostic significance of the cell-of-origin type for DLBCLs, we applied the Lymph2Cx assay using a NanoString gene expression platform on formalin-fixed paraffin wax-embedded pretreatment tissues obtained from 82 patients with de novo DLBCL, not otherwise specified. All patients were treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) as the first line of chemotherapy...
March 28, 2017: Oncotarget
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