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https://www.readbyqxmd.com/read/28516114/measurement-of-mrna-decay-in-mouse-embryonic-fibroblasts
#1
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
#2
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
#3
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
#4
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
#5
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)...
May 2, 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
#6
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...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28442586/therapeutic-targeting-of-ptk7-is-cytotoxic-in-atypical-teratoid-rhabdoid-tumors
#7
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 radiation therapy, 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
#8
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
https://www.readbyqxmd.com/read/28423512/kinase-analysis-of-penile-squamous-cell-carcinoma-on-multiple-platforms-to-identify-potential-therapeutic-targets
#9
Eddy S Yang, Christopher D Willey, Amitkumar Mehta, Michael R Crowley, David K Crossman, Dongquan Chen, Joshua C Anderson, Gurudatta Naik, Deborah L Della Manna, Tiffiny S Cooper, Guru Sonpavde
Penile squamous cell carcinoma (PSCC) is an orphan malignancy with poorly understood biology and suboptimal systemic therapy. Given that kinases may be drivers and readily actionable, we performed comprehensive multiplatform analysis of kinases in PSCC tumor and normal tissue. Fresh frozen tumors were collected from 11 patients with PSCC. After macrodissection to demarcate tumor from normal tissue, the samples underwent multiplatform analysis of kinases. Next Generation Sequencing (NGS) of 517 kinase genes was performed using Agilent Kinome capture and run on the Illumina MiSeq at PE150bp...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419168/dynamic-patterns-of-expression-for-genes-regulating-cytokinin-metabolism-and-signaling-during-rice-inflorescence-development
#10
Maria V Yamburenko, Joseph J Kieber, G Eric Schaller
Inflorescence development in cereals, including such important crops as rice, maize, and wheat, directly affects grain number and size and is a key determinant of yield. Cytokinin regulates meristem size and activity and, as a result, has profound effects on inflorescence development and architecture. To clarify the role of cytokinin action in inflorescence development, we used the NanoString nCounter system to analyze gene expression in the early stages of rice panicle development, focusing on 67 genes involved in cytokinin biosynthesis, degradation, and signaling...
2017: PloS One
https://www.readbyqxmd.com/read/28417935/diagnostic-limitation-of-fine-needle-aspiration-fna-on-indeterminate-thyroid-nodules-can-be-partially-overcome-by-preoperative-molecular-analysis-assessment-of-ret-ptc1-rearrangement-in-braf-and-ras-wild-type-routine-air-dried-fna-specimens
#11
Young Sin Ko, Tae Sook Hwang, Ja Yeon Kim, Yoon-La Choi, Seung Eun Lee, Hye Seung Han, Wan Seop Kim, Suk Kyeong Kim, Kyoung Sik Park
Molecular markers are helpful diagnostic tools, particularly for cytologically indeterminate thyroid nodules. Preoperative RET/PTC1 rearrangement analysis in BRAF and RAS wild-type indeterminate thyroid nodules would permit the formulation of an unambiguous surgical plan. Cycle threshold values according to the cell count for detection of the RET/PTC1 rearrangement by real-time reverse transcription-polymerase chain reaction (RT-PCR) using fresh and routine air-dried TPC1 cells were evaluated. The correlation of RET/PTC1 rearrangement between fine-needle aspiration (FNA) and paired formalin-fixed paraffin-embedded (FFPE) specimens was analyzed...
April 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28415793/clinical-framework-for-next-generation-sequencing-based-analysis-of-treatment-predictive-mutations-and-multiplexed-gene-fusion-detection-in-non-small-cell-lung-cancer
#12
Kajsa Ericson Lindquist, Anna Karlsson, Per Levéen, Hans Brunnström, Christel Reuterswärd, Karolina Holm, Mats Jönsson, Karin Annersten, Frida Rosengren, Karin Jirström, Jaroslaw Kosieradzki, Lars Ek, Åke Borg, Maria Planck, Göran Jönsson, Johan Staaf
Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (~90% advanced stage patients)...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28392786/expression-of-serum-micrornas-is-altered-during-acute-graft-versus-host-disease
#13
Rachel E Crossland, Jean Norden, Mateja Kralj Juric, Kile Green, Kim F Pearce, Clare Lendrem, Hildegard T Greinix, Anne M Dickinson
Acute graft-versus-host disease (aGvHD) is the most frequent and serious complication following hematopoietic stem cell transplantation (HSCT), with a high mortality rate. A clearer understanding of the molecular pathogenesis may allow for improved therapeutic options or guide personalized prophylactic protocols. Circulating microRNAs are expressed in body fluids and have recently been associated with the etiology of aGvHD, but global expression profiling in a HSCT setting is lacking. This study profiled expression of n = 799 mature microRNAs in patient serum, using the NanoString platform, to identify microRNAs that showed altered expression at aGvHD diagnosis...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28385922/multiplex-digital-colour-coded-barcode-technology-on-rna-extracted-from-routine-cytological-samples-of-patients-with-non-small-cell-lung-cancer-pilot-study
#14
Roberta Sgariglia, Pasquale Pisapia, Mariantonia Nacchio, Caterina De Luca, Francesco Pepe, Maria Russo, Claudio Bellevicine, Giancarlo Troncone, Umberto Malapelle
In the advanced stages of non-small cell lung cancer (NSCLC), molecular testing is often performed on archival cytological smears. The nCounter system (NanoString Technologies) is a new promising multiplex digital colour-coded barcode technology. However, its feasibility to evaluate the RNA expression of clinical relevant biomarkers on routine cytological smears is still uncertain. To this end, RNA was extracted from 12 NSCLC routine stained cytological smears, and nCounter analysis performed by using a 48-gene panel...
April 6, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28382134/an-investigation-of-the-role-of-gene-copy-number-variations-in-sorafenib-sensitivity-in-metastatic-hepatocellular-carcinoma-patients
#15
Ji Yun Lee, Mineui Hong, Jeeyun Lee, Sujin Lee, Kyoung-Mee Kim, Cheolkeun Park, Ho Yeong Lim
Background: Metastatic hepatocellular carcinoma (HCC) is a highly aggressive tumor with limited treatment options. While sorafenib has recently been shown to provide a survival advantage in patients with advanced HCC, the overall outcomes such as time to progression (TTP) and overall survival (OS) ought to be further improved. To that end, several targeted agents aimed at amplified oncogenes such as HER2 and FGFR2 have recently been developed. In this study, we aimed to identify genetic markers in the form of copy number variations (CNVs) that influence clinical outcomes post-sorafenib treatment in advanced HCC patients...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28376219/intrinsic-subtype-and-therapeutic-response-among-her2-positive-breast-tumors-from-the-ncctg-alliance-n9831-trial
#16
Edith A Perez, Karla V Ballman, Afshin Mashadi-Hossein, Kathleen S Tenner, Jennifer M Kachergus, Nadine Norton, Brian M Necela, Jennifer M Carr, Sean Ferree, Charles M Perou, Frederick Baehner, Maggie Chon U Cheang, E Aubrey Thompson
Background: Genomic data from human epidermal growth factor receptor 2-positive (HER2+) tumors were analyzed to assess the association between intrinsic subtype and clinical outcome in a large, well-annotated patient cohort. Methods: Samples from the NCCTG (Alliance) N9831 trial were analyzed using the Prosigna algorithm on the NanoString platform to define intrinsic subtype, risk of recurrence scores, and risk categories for 1392 HER2+ tumors. Subtypes were evaluated for recurrence-free survival (RFS) using Kaplan-Meier and Cox model analysis following adjuvant chemotherapy (n = 484) or chemotherapy plus trastuzumab (n = 908)...
February 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28347920/mir-200b-and-mir-155-as-predictive-biomarkers-for-the-efficacy-of-chemoradiation-in-locally-advanced-head-and-neck-squamous-cell-carcinoma
#17
Anne-Katrin Hess, Annika Müer, Fabian Dominik Mairinger, Wilko Weichert, Albrecht Stenzinger, Michael Hummel, Volker Budach, Ingeborg Tinhofer
BACKGROUND: The predictive value of microRNAs (miRNAs) in tumour cells and infiltrating immune cells for the efficacy of chemoradiation (CRTX) in locally advanced head and neck squamous cell carcinoma (HNSCC) was evaluated. METHODS: Formalin-fixed, paraffin-embedded tumour material was collected from patients with locally advanced HNSCC treated within the ARO-0401 phase III trial with radiotherapy in combination with either 5-fluorouracil/cisplatin (CDDP-CRTX) or 5-fluorouracil/mitomycin C (MMC-CRTX)...
March 24, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28338501/alk-expression-is-a-novel-marker-for-the-wnt-activated-type-of-pediatric-medulloblastoma-and-an-indicator-of-good-prognosis-for-patients
#18
Maria Łastowska, Joanna Trubicka, Magdalena Niemira, Magdalena Paczkowska-Abdulsalam, Agnieszka Karkucińska-Więckowska, Magdalena Kaleta, Monika Drogosiewicz, Magdalena Tarasińska, Marta Perek-Polnik, Adam Krętowski, Bożenna Dembowska-Bagińska, Wiesława Grajkowska, Maciej Pronicki, Ewa Matyja
ALK gene rearrangements were identified in a variety of cancers, including neuroblastoma, where the presence of ALK expression is associated with adverse prognosis. ALK mutations have recently been found in the pediatric brain tumor medulloblastoma, and microarray data indicate that ALK is highly expressed in a subset of these tumors. Therefore, we investigated whether ALK expression correlates with transcriptional profiles and clinical features of medulloblastoma. Tumors from 116 medulloblastoma patients were studied at diagnosis for the detection of ALK expression at the RNA level by an application of NanoString technology and at the protein level by immunohistochemistry using antibody ALK clone D5F3...
June 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28321397/the-identification-of-three-cancer-stem-cell-subpopulations-within-moderately-differentiated-lip-squamous-cell-carcinoma
#19
Rachna Ram, Helen D Brasch, Jonathan C Dunne, Paul F Davis, Swee T Tan, Tinte Itinteang
AIM: To identify and characterize cancer stem cells (CSCs) in moderately differentiated lip squamous cell carcinoma (MDLSCC). METHOD: MDLSCC samples underwent 3,3-diaminobenzidine (DAB) immunohistochemical (IHC) staining for squamous cell carcinoma marker EMA, CSC marker CD44 and embryonic stem cell markers NANOG, octamer-binding transcription factor 4 (OCT4), spalt-like transcription factor 4 (SALL4), sex-determining region Y-box 2 (SOX2), and phosphorylated signal transducer and activator of transcription 3 (pSTAT3)...
2017: Frontiers in Surgery
https://www.readbyqxmd.com/read/28318799/transcriptome-analysis-of-il-10-stimulated-m2c-macrophages-by-next-generation-sequencing
#20
Emily B Lurier, Donald Dalton, Will Dampier, Pichai Raman, Sina Nassiri, Nicole M Ferraro, Ramakrishan Rajagopalan, Mahdi Sarmady, Kara L Spiller
Alternatively activated "M2" macrophages are believed to function during late stages of wound healing, behaving in an anti-inflammatory manner to mediate the resolution of the pro-inflammatory response caused by "M1" macrophages. However, the differences between two main subtypes of M2 macrophages, namely interleukin-4 (IL-4)-stimulated "M2a" macrophages and IL-10-stimulated "M2c" macrophages, are not well understood. M2a macrophages are characterized by their ability to inhibit inflammation and contribute to the stabilization of angiogenesis...
February 20, 2017: Immunobiology
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