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https://www.readbyqxmd.com/read/28212540/expression-of-met-in-circulating-tumor-cells-correlates-with-expression-in-tumor-tissue-from-advanced-stage-lung-cancer-patients
#1
Marius Ilie, Edith Szafer-Glusman, Véronique Hofman, Elodie Long-Mira, Rebecca Suttmann, Walter Darbonne, Catherine Butori, Salomé Lalvée, Julien Fayada, Eric Selva, Wei Yu, Charles-Hugo Marquette, David S Shames, Elizabeth Punnoose, Paul Hofman
Given the difficulty in obtaining adequate tissue in NSCLC, we investigated the utility of circulating tumor cells (CTCs) for MET status assessment in NSCLC patients. We used two platforms for CTC capture, and assessed MET expression in CTCs and matched-bronchial biopsies in patients with advanced-stage III/IV lung adenocarcinoma. Baseline peripheral blood was collected from 256 advanced-stage III/IV NSCLC patients from Genentech clinical trials, and from 106 patients with advanced-stage III/IV lung adenocarcinoma treated at the Department of Pneumology, Pasteur Hospital, Nice...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28210822/plasma-dna-methylation-of-p16-and-shp1-in-patients-with-b-cell-non-hodgkin-lymphoma
#2
Kai Ding, Xiaoshuang Chen, Yihao Wang, Hui Liu, Wenjing Song, Lijuan Li, Guojin Wang, Jia Song, Zonghong Shao, Rong Fu
BACKGROUND: Early diagnosis and treatment of non-Hodgkin lymphoma (NHL) are progressively important. It has been shown that aberrant promoter methylation contributes to the development and progression of lymphoma. We tried to explore the effect of methylation of p16 and shp1 genes in plasma in the diagnosis of B-NHL patients. METHODS: The methylation of p16 and shp1 genes in plasma were detected by methylation specific polymerase chain reaction in 103 patients with B-NHL, and compared with peripheral blood leukocytes (PBLs) and formaldehyde-fixed paraffin-embedded (FFPE) tumor tissues...
February 16, 2017: International Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28206954/rassf1a-promoter-methylation-in-high-grade-serous-ovarian-cancer-a-direct-comparison-study-in-primary-tumors-adjacent-morphologically-tumor-cell-free-tissues-and-paired-circulating-tumor-dna
#3
Lydia Giannopoulou, Issam Chebouti, Kitty Pavlakis, Sabine Kasimir-Bauer, Evi S Lianidou
The RASSF1A promoter is frequently methylated in high-grade serous ovarian cancer (HGSC). We examined RASSF1A promoter methylation in primary tumors, adjacent morphologically tumor cell-free tissues and corresponding circulating tumor DNA (ctDNA) samples of patients with HGSC, using a real-time methylation specific PCR (real-time MSP) and a methylation-sensitive high-resolution melting analysis (MS-HRMA) assay for the detection and semi-quantitative estimation of methylation, respectively. Two groups of primary HGSC tumor FFPE samples were recruited (Group A n=67 and Group B n=61), along with matched adjacent morphologically tumor cell-free tissues (n=58) and corresponding plasma samples (n=59) for group B...
February 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28201998/clinical-performance-evaluation-of-a-sensitive-rapid-low-throughput-test-for-kras-mutation-analysis-using-formalin-fixed-paraffin-embedded-tissue-samples
#4
Christine Weyn, Sofie Van Raemdonck, Robina Dendooven, Vincent Maes, Karen Zwaenepoel, Suzan Lambin, Patrick Pauwels
BACKGROUND: Testing for KRAS mutations in metastatic colorectal cancer (mCRC) on formalin-fixed, paraffin embedded (FFPE) tumor tissue has become standard of care. Different molecular methods exist to determine hotspot KRAS mutations in exon 2, 3 and 4, but testing is often limited by the sensitivity and the speed of analysis. The aim of this retrospective study was to establish the clinical performance of the Idylla™ KRAS Mutation Test on FFPE tumor samples of patients with mCRC. METHODS: KRAS mutation analysis was performed using the therascreen KRAS on the RotorGene Q platform (CE-IVD; Qiagen) and results were subsequently compared to the Idylla™ KRAS Mutation Test...
February 16, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28199399/mirna-148a-serves-as-a-prognostic-factor-and-suppresses-migration-and-invasion-through-wnt1-in-non-small-cell-lung-cancer
#5
Yong Chen, Lingfeng Min, Chuanli Ren, Xingxiang Xu, Jianqi Yang, Xinchen Sun, Tao Wang, Fang Wang, Changjiang Sun, Xizhi Zhang
Lung cancer is the leading cause of cancer death in the world, and aberrant expression of miRNA is a common feature during the cancer initiation and development. Our previous study showed that levels of miRNA-148a assessed by quantitative real-time polymerase chain reaction (qRT-PCR) were a good prognosis factor for non-small cell lung cancer (NSCLC) patients. In this study, we used high-throughput formalin-fixed and paraffin-embedded (FFPE) lung cancer tissue arrays and in situ hybridization (ISH) to determine the clinical significances of miRNA-148a and aimed to find novel target of miRNA-148a in lung cancer...
2017: PloS One
https://www.readbyqxmd.com/read/28197533/deciphering-tumor-heterogeneity-from-ffpe-tissues-its-promise-and-challenges
#6
Alan J Simmons, Ken S Lau
An impediment to the understanding of cancer is the heterogeneous nature of cell populations within a tumor microenvironment. We reported a method to query protein signaling in single epithelial cells from formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissues. Here, we discuss the feasibility and limitations of this approach for investigating signaling state heterogeneity.
2017: Molecular & Cellular Oncology
https://www.readbyqxmd.com/read/28197385/prognostic-and-predictive-aspects-of-the-tumor-immune-microenvironment-and-immune-checkpoints-in-malignant-pleural-mesothelioma
#7
Elly Marcq, Vasiliki Siozopoulou, Jorrit De Waele, Jonas van Audenaerde, Karen Zwaenepoel, Eva Santermans, Niel Hens, Patrick Pauwels, Jan P van Meerbeeck, Evelien L J Smits
Malignant pleural mesothelioma (MPM) is an aggressive cancer with a poor prognosis and an increasing incidence, for which novel therapeutic strategies are urgently required. Since the immune system has been described to play a presumed role in the protection against MPM, characterization of its tumor immune microenvironment (TME) and immune checkpoints can identify new immunotherapeutic targets and their predictive and/or prognostic value. To characterize the TME and the immune checkpoint expression profile, we performed immunohistochemistry (IHC) on formalin-fixed paraffin embedded (FFPE) tissue sections from 54 MPM patients (40 at time of diagnosis; 14 treated with chemotherapy)...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28196074/clinical-applicability-and-cost-of-a-46-gene-panel-for-genomic-analysis-of-solid-tumours-retrospective-validation-and-prospective-audit-in-the-uk-national-health-service
#8
Angela Hamblin, Sarah Wordsworth, Jilles M Fermont, Suzanne Page, Kulvinder Kaur, Carme Camps, Pamela Kaisaki, Avinash Gupta, Denis Talbot, Mark Middleton, Shirley Henderson, Anthony Cutts, Dimitrios V Vavoulis, Nick Housby, Ian Tomlinson, Jenny C Taylor, Anna Schuh
BACKGROUND: Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing...
February 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28193082/expression-analysis-of-previously-verified-fecal-and-plasma-dow-regulated-micrornas-mir-4478-1295-3p-142-3p-and-26a-5p-in-ffpe-tissue-samples-of-crc-patients
#9
Reza Ghanbari, Sama Rezasoltani, Javad Hashemi, Ashraf Mohamadkhani, Arash Tahmasebifar, Ehsan Arefian, Naser Mobarra, Jahanbakhsh Asadi, Ehsan Nazemalhosseini Mojarad, Yaghoub Yazdani, Sakari Knuutila, Reza Malekzadeh
BACKGROUND: Colorectal cancer (CRC) is one of the most common causes of cancer-related mortality worldwide. Early diagnosis of this neoplasm is critical and may reduce patients' mortality. MicroRNAs are small non-coding RNA molecules whose expression pattern can be altered in various diseases such as CRC. METHODS: In this study, we evaluated the expression levels of miR-142-3p, miR-26a-5p (their reduced expression in plasma samples of CRC patients was previously confirmed), miR-4478 and miR-1295-3p (their reduced expression in stool samples of CRC patients was previously confirmed) in tissue samples of CRC patients in comparison to healthy subjects...
February 2017: Archives of Iranian Medicine
https://www.readbyqxmd.com/read/28192086/variant-call-concordance-between-two-laboratory-developed-solid-tumor-targeted-genomic-profiling-assays-using-distinct-workflows-and-sequencing-instruments
#10
Ken J Hampel, Francine B de Abreu, Nikoletta Sidiropoulos, Jason D Peterson, Gregory J Tsongalis
Targeted genomic profiling (TGP) using massively parallel DNA sequencing is becoming the standard methodology in clinical laboratories for detecting somatic variants in solid tumors. The variety of methodologies and sequencing platforms in the marketplace for TGP has resulted in a variety of clinical TGP laboratory developed tests (LDT). The variability of LDTs is a challenge for test-to-test and laboratory-to-laboratory reliability. At the University of Vermont Medical Center (UVMMC), we validated a TGP assay for solid tumors which utilizes DNA hybridization capture and complete exon and selected intron sequencing of 29 clinically actionable genes...
February 10, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28185613/development-of-quantitative-real-time-pcr-assays-for-postmortem-detection-of-mycobacterium-spp-common-in-zebrafish-danio-rerio-research-colonies
#11
Danielle M Meritet Donna M Mulrooney Michael L Kent And Christiane V Löhr
Mycobacterium spp. infections are common in zebrafish kept in research facilities. These comorbidities can substantiallymodulate the responses of these fish to external and internal stimuli. Therefore, diagnostic tests to detect Mycobacterium spp.infections in zebrafish colonies prove essential. Here, we outline the development of quantitative simplex real-time PCRassays to detect the 3 Mycobacterium species most commonly identified in laboratory zebrafish. The assays targeted the heatshock protein 65 gene of M...
February 9, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28182792/somatostatin-receptor-staining-in-ffpe-sections-using-a-ligand-derivative-dye-as-an-alternative-to-immunostaining
#12
Koki Hasegawa, Shinji Kudoh, Takaaki Ito
The confirmation of target expression in tissues is a prerequisite for molecular-targeted therapy. However, difficulties are sometimes associated with the production of appropriate antibodies against receptors. We herein developed a ligand derivative dye for the staining of receptors. The somatostatin receptor (sstr) was selected as the target and FITC-octreotate as the detective agent. We performed a blot analysis to detect sstr in the transfer membrane. The sstr2 recombinant protein or cell lysate from a small cell lung carcinoma cell line (H69) was boiled and loaded onto SDS-PAGE, and the proteins were transferred to a membrane...
2017: PloS One
https://www.readbyqxmd.com/read/28166931/evaluation-of-a-panel-of-antibodies-for-the-immunohistochemical-identification-of-immune-cells-in-paraffin-embedded-lymphoid-tissues-of-new-and-old-world-camelids
#13
Ann-Kathrin Uhde, Annika Lehmbecker, Wolfgang Baumgärtner, Ingo Spitzbarth
Different species of camelids play an important role in the epidemiology of various emerging infectious diseases such as Middle East respiratory syndrome. For precise investigations of the immunopathogenesis in these host species, appropriate immunohistochemical markers are highly needed in order to phenotype distinct immune cells populations in camelids. So far, specific immunohistochemical markers for camelid immune cells are rarely commercially available, and cross-reactivity studies are restricted to the use of frozen dromedary tissues...
February 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/28164568/methylation-analysis-of-brca1-and-apc-in-breast-cancer-and-it-s-relationship-to-clinicopathological-features
#14
Halaleh Shakeri, Ashraf Fakhrjou, Alireza Nikanfar, Seyyed M Mohaddes-Ardebili
BACKGROUND: Promoter methylation of tumor suppressor genes is an important epigenetic alteration that occurs in the primary stages of human tumors, including breast cancer. Identification of methylated genes and their relationship to clinical features can contribute to the prognosis and early detection of tumors. In this study, we explored the methylation status of APC and BRCA1 genes and their relationship to clinical factors in breast cancer patients. METHODS: BRCA1 and APC promoter methylation was examined by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay in formalin-fixed paraffin embedded (FFPE) breast tissue from 75 patients...
December 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28161958/comprehensive-metaboproteomics-of-burkitt-s-and-diffuse-large-b-cell-lymphoma-cell-lines-and-primary-tumor-tissues-reveals-distinct-differences-in-pyruvate-content-and-metabolism
#15
Philipp Schwarzfischer, Joerg Reinders, Katja Dettmer, Karsten Kleo, Lora Dimitrova, Michael Hummel, Maren Feist, Dieter Kube, Monika Szczepanowski, Wolfram Klapper, Franziska Taruttis, Julia C Engelmann, Rainer Spang, Wolfram Gronwald, Peter J Oefner
Burkitt's lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL) are pathologically and clinically distinct subtypes of aggressive non-Hodgkin B-cell lymphoma. To learn more about their biology, we employed metabolomic and proteomic methods to study both established cell lines as well as cryopreserved and formalin-fixed paraffin-embedded (FFPE) tissue sections of BL and DLBCL. Strikingly, NMR analyses revealed DLBCL cell lines to produce and secrete significantly (padj=1.72 x 10-22) more pyruvic acid than BL cell lines...
February 6, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28160367/cerebral-amyloidoma-is-characterized-by-b-cell-clonality-and-a-stable-clinical-course
#16
Katharina Heß, Jan Purrucker, Ute Hegenbart, Benjamin Brokinkel, Rouven Berndt, Kathy Keyvani, Camelia M Monoranu, Mario Löhr, Guido Reifenberger, Christopher Munoz-Bendix, Jörg Kalla, Justus Groß, Uta Schick, Jennifer Kollmer, Wolfram Klapper, Christoph Röcken, Martin Hasselblatt, Werner Paulus
Amyloidomas are rare amyloid-containing lesions, which may also occur in the central nervous system. Etiology, pathogenesis and clinical course are poorly understood. To gain more insight into the biology of cerebral amyloidoma, we aimed to characterize its histopathological, molecular and clinical features in a retrospective series of seven patients. FFPE tissue specimens were examined using immunohistochemistry, chromogenic in situ hybridization (CISH) for light chains kappa and lambda as well as an IgH gene clonality analysis...
February 4, 2017: Brain Pathology
https://www.readbyqxmd.com/read/28159814/bevacizumab-may-differentially-improve-ovarian-cancer-outcome-in-patients-with-proliferative-and-mesenchymal-molecular-subtypes
#17
Stefan Kommoss, Boris Winterhoff, Ann Oberg, Gottfried E Konecny, Chen Wang, Shaun M Riska, Jian-Bing Fan, Matthew J Maurer, Craig April, Viji Shridhar, Friedrich Kommoss, Andreas du Bois, Felix Hilpert, Sven Mahner, Klaus Baumann, Willibald Schroeder, Alexander Burges, Ulrich Canzler, Jeremy Chien, Andrew C Embleton, Mahesh Parmar, Richard Kaplan, Timothy Perren, Lynn C Hartmann, Ellen L Goode, Sean C Dowdy, Jacobus Pfisterer
PURPOSE: Recent progress in understanding the molecular biology of epithelial ovarian cancer has not yet translated into individualized treatment for these women or improvements in their disease outcome. Gene expression has been utilized to identify distinct molecular subtypes, but there have been no reports investigating whether or not molecular subtyping is predictive of response to bevacizumab in ovarian cancer. EXPERIMENTAL DESIGN: DASL gene expression arrays were performed on FFPE tissue from patients enrolled on the ICON7 trial...
February 3, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28152060/expression-quantitative-trait-loci-qtl-in-tumor-adjacent-normal-breast-tissue-and-breast-tumor-tissue
#18
Alejandro Quiroz-Zárate, Benjamin J Harshfield, Rong Hu, Nick Knoblauch, Andrew H Beck, Susan E Hankinson, Vincent Carey, Rulla M Tamimi, David J Hunter, John Quackenbush, Aditi Hazra
We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic or intronic regions. To explore regulatory impacts of these variants we conducted expression quantitative loci (eQTL) analyses on tissue samples from 376 invasive postmenopausal breast cancer cases in the Nurses' Health Study (NHS) diagnosed from 1990-2004. Expression analysis was conducted on all formalin-fixed paraffin-embedded (FFPE) tissue samples (and on 264 adjacent normal samples) using the Affymetrix Human Transcriptome Array...
2017: PloS One
https://www.readbyqxmd.com/read/28149329/improved-results-of-line-1-methylation-analysis-in-formalin-fixed-paraffin-embedded-tissues-with-the-application-of-a-heating-step-during-the-dna-extraction-process
#19
Xianyu Wen, Seorin Jeong, Younghoon Kim, Jeong Mo Bae, Nam Yun Cho, Jung Ho Kim, Gyeong Hoon Kang
BACKGROUND: Formalin-fixed, paraffin-embedded (FFPE) tissues are important resources for profiling DNA methylation changes and for studying a variety of diseases. However, formalin fixation introduces inter-strand crosslinking, which might cause incomplete bisulfite conversion of unmethylated cytosines, which might lead to falsely elevated measurements of methylation levels in pyrosequencing assays. Long interspersed nucleotide element-1 (LINE-1) is a major constituent of repetitive transposable DNA elements, and its methylation is referred to correlates with global DNA methylation...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28147344/detection-and-localization-of-viral-infection-in-the-pancreas-of-patients-with-type-1-diabetes-using-short-fluorescently-labelled-oligonucleotide-probes
#20
Niels Busse, Federico Paroni, Sarah J Richardson, Jutta E Laiho, Maarit Oikarinen, Gun Frisk, Heikki Hyöty, Eelco de Koning, Noel G Morgan, Kathrin Maedler
Enteroviruses, specifically of the Coxsackie B virus family, have been implicated in triggering islet autoimmunity and type 1 diabetes, but their presence in pancreata of patients with diabetes has not been fully confirmed.To detect the presence of very low copies of the virus genome in tissue samples from T1D patients, we designed a panel of fluorescently labeled oligonucleotide probes, each of 17-22 nucleotides in length with a unique sequence to specifically bind to the enteroviral genome of the picornaviridae family...
29, 2017: Oncotarget
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