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https://www.readbyqxmd.com/read/28432840/detection-of-egfr-mutations-in-patients-with-non-small-cell-lung-cancer-by-high-resolution-melting-comparison-with-other-methods
#1
Carlos Martínez-Carretero, Fernando Iguaz Pascual, Antonio Rus, Ivan Bernardo
BACKGROUND: The discovery of mutations in the epidermal growth factor receptor gene (EGFR) related to the clinical response to tyrosine kinase inhibitors, has transformed the management of non-small cell lung cancer (NSCLC). Several methods have been developed for determination of mutations in EGFR, with different sensitivity and potential ability to detect a different number of mutations. METHODS: We developed a screening method by high resolution melting (HRM) to detect EGFR mutations, and compared the results of 123 fixed in formalin and paraffin embedded (FFPE) tumor tissue samples with the detection of mutations by allele-specific PCR...
April 22, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28432562/increased-expression-of-the-microrna-106b-25-cluster-and-its-host-gene-mcm7-in-corticotroph-pituitary-adenomas-is-associated-with-tumor-invasion-and-crooke-s-cell-morphology
#2
Filip Garbicz, Dawid Mehlich, Beata Rak, Emir Sajjad, Maria Maksymowicz, Wiktor Paskal, Grzegorz Zieliński, Paweł K Włodarski
PURPOSE: MCM7 (minichromosome maintenance complex component 7), a DNA replication licensing factor, is a host gene for the oncogenic miR-106b~25 cluster. It has been recently revealed as a relevant prognostic biomarker in a variety of cancers, including pituitary adenomas. The purpose of this study was to assess whether miR-106b~25 and MCM7 levels correlate with tumor invasiveness in a cohort of ACTH-immunopositive adenomas. METHODS: Tissue samples were obtained intraoperatively from 25 patients with pituitary adenoma...
April 21, 2017: Pituitary
https://www.readbyqxmd.com/read/28430953/gastric-proteins-muc5ac-and-tff1-as-potential-diagnostic-markers-of-colonic-sessile-serrated-adenomas-polyps
#3
Magomed Khaidakov, Keith K Lai, D Roudachevski, Julietta Sargsyan, Hannah E Goyne, Rish K Pai, Laura W Lamps, Curt H Hagedorn
Objectives: A subset of colon cancers originates from sessile serrated adenomas/polyps (SSA/Ps). Our goal was to identify markers for SSA/Ps that could aid in distinguishing them from hyperplastic polyps (HPs). Methods: We performed immunostaining for gastric proteins MUC5AC and TFF1 in formalin-fixed, paraffin-embedded (FFPE) samples of HPs (n = 47), SSA/Ps (n = 37), and normal colon (n = 30). Results: Control mucosa expressed only trace amounts of MUC5AC and TFF1...
November 1, 2016: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28428887/differential-intratumoral-distributions-of-cd8-and-cd163-immune-cells-as-prognostic-biomarkers-in-breast-cancer
#4
Sotirios P Fortis, Michael Sofopoulos, Nectaria N Sotiriadou, Christoforos Haritos, Christoforos K Vaxevanis, Eleftheria A Anastasopoulou, Nicole Janssen, Niki Arnogiannaki, Alexandros Ardavanis, Graham Pawelec, Sonia A Perez, Constantin N Baxevanis
BACKGROUND: Tumor immune cell infiltrates are essential in hindering cancer progression and may complement the TNM classification. CD8+ and CD163+ cells have prognostic impact in breast cancer but their spatial heterogeneity has not been extensively explored in this type of cancer. Here, their potential as prognostic biomarkers was evaluated, depending on their combined densities in the tumor center (TC) and the tumor invasive margin (IM). METHODS: CD8+ and CD163+ cells were quantified by immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE) tumor tissue samples from a cohort totaling 162 patients with histologically-confirmed primary invasive non-metastatic ductal breast cancer diagnosed between 2000 and 2015...
2017: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/28427242/epidermal-growth-factor-receptor-variant-iii-in-head-and-neck-squamous-cell-carcinoma-is-not-relevant-for-targeted-therapy-and-irradiation
#5
Dominik Thomas Koch, Anja Pickhard, Lena Gebel, Anna Maria S Buchberger, Murat Bas, Carolin Mogler, Rudolf Reiter, Guido Piontek, Markus Wirth
BACKGROUND: The epidermal growth factor receptor (EGFR) is an important regulator of cell growth and survival, and is highly variable in tumor cells. The most prevalent variation of the EGFR extracellular domain is the EGFR variant III (EGFRvIII). Some studies imply that EGFRvIII may be responsible for the poor response to the monoclonal EGFR-antibody Cetuximab, used therapeutically in head and neck squamous cell carcinoma (HNSCC). Due to inconsistent data in the literature regarding EGFRvIII prevalence and clinical relevance in HNSCC, especially its predictive value, we examined EGFRvIII-transfected cell lines and patient tissue samples...
March 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424278/detection-of-hpv-subtypes-by-mass-spectrometry-in-ffpe-tissue-specimens-a-reliable-tool-for-routine-diagnostics
#6
Mark Kriegsmann, Petra Wandernoth, Katharina Lisenko, Rita Casadonte, Rémi Longuespée, Norbert Arens, Jörg Kriegsmann
AIMS: Human papilloma virus (HPV) infection is a causative agent for approximately 5% of all new cancer cases in humans. The virus is detected in cervical, anal, vaginal, penile, vulvar and head and neck cancers and has prognostic implications. Thus, test systems are required to detect high-risk but also low-risk HPV subtypes with high specificity and sensitivity in a time-effective and cost-effective manner. In the present study we developed a new mass spectrometry (MS)-based test system for the detection of HPV infections in formalin-fixed paraffin-embedded (FFPE) tissue samples...
May 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28423635/quantification-of-her2-and-estrogen-receptor-heterogeneity-in-breast-cancer-by-single-molecule-rna-fluorescence-in-situ-hybridization
#7
Laura Annaratone, Michele Simonetti, Erik Wernersson, Caterina Marchiò, Silvano Garnerone, Maria Stella Scalzo, Magda Bienko, Roberto Chiarle, Anna Sapino, Nicola Crosetto
Intra-tumor heterogeneity is a pervasive property of human cancers that poses a major clinical challenge. Here, we describe the characterization, at the transcriptional level, of the intra-tumor topography of two prominent breast cancer biomarkers and drug targets, epidermal growth factor receptor 2 (HER2) and estrogen receptor 1 (ER) in 49 archival breast cancer samples. We developed a protocol for single-molecule RNA FISH in formalin-fixed, paraffin-embedded tissue sections (FFPE-smFISH), which enabled us to simultaneously detect and perform absolute quantification of HER2 and ER mature transcripts in single cells and multiple tumor regions...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418914/met-exon-14-mutations-as-targets-in-routine-molecular-analysis-of-primary-sarcomatoid-carcinoma-of-the-lung
#8
Raphaël Saffroy, Vincent Fallet, Nicolas Girard, Julien Mazieres, Denis Moro Sibilot, Sylvie Lantuejoul, Isabelle Rouquette, Françoise Thivolet-Bejui, Thibaut Vieira, Martine Antoine, Jacques Cadranel, Antoinette Lemoine, Marie Wislez
MET exon 14 splicing mutations are new targetable oncogenic drivers reported in 3% of non-small cell lung cancer (NSCLC) cases and have been shown to be more common in pulmonary sarcomatoid carcinomas (PSCs). This study sought to screen mutations affecting MET exon 14 splice sites in a large SC cohort of Caucasian patients, with a large adenocarcinoma cohort as internal control.We tested 81 patients with SC and 150 with adenocarcinoma for splice site DNA mutations leading to RNA splicing-based skipping of MET exon 14...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418912/human-microrna-expression-in-sporadic-and-fap-associated-desmoid-tumors-and-correlation-with-beta-catenin-mutations
#9
Aldo Cavallini, Maria Teresa Rotelli, Catia Lippolis, Domenico Piscitelli, Rosa Digennaro, Claudia Covelli, Nicola Carella, Matteo Accetturo, Donato Francesco Altomare
Desmoid tumors (DT) are rare, benign, fibroblastic neoplasm with challenging histological diagnosis. DTs can occur sporadically or associated with the familial adenomatous polyposis coli (FAP). Most sporadic DTs are associated with β-catenin gene (CTNNB1) mutations, while mutated APC gene causes FAP disease. microRNAs (miRNAs) are involved in many human carcinogenesis.The miRNA profile was analyzed by microarray in formalin-fixed, paraffin-embedded (FFPE) specimens of 12 patients (8 sporadic, 4 FAP-associated) and 4 healthy controls...
March 19, 2017: Oncotarget
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
#10
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/28416765/lolopicker-detecting-low-allelic-fraction-variants-from-low-quality-cancer-samples
#11
Jian Carrot-Zhang, Jacek Majewski
INTRODUCTION: Although several programs are designed to identify variants with low allelic-fraction, further improvement is needed, especially to push the detection limit of low allelic-faction variants in low-quality, "noisy" tumor samples. RESULTS: We developed LoLoPicker, an efficient tool dedicated to calling somatic variants from next-generation sequencing (NGS) data of tumor sample against the matched normal sample plus a user-defined control panel of additional normal samples...
March 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414163/droplet-digital-pcr-ddpcr-vs-quantitative-real-time-pcr-qpcr-approach-for-detection-and-quantification-of-merkel-cell-polyomavirus-mcpyv-dna-in-formalin-fixed-paraffin-embedded-ffpe-cutaneous-biopsies
#12
Rosaria Arvia, Mauro Sollai, Federica Pierucci, Carmelo Urso, Daniela Massi, Krystyna Zakrzewska
BACKGROUND: Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma and high viral load in the skin was proposed as a risk factor for the occurrence of this tumour. MCPyV DNA was detected, with lower frequency, in different skin cancers but since the viral load was usually low, the real prevalence of viral DNA could be underestimated. OBJECTIVE: To evaluate the performance of two assays (qPCR and ddPCR) for MCPyV detection and quantification in formalin fixed paraffin embedded (FFPE) tissue samples...
April 14, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28412294/visualization-of-hepatitis-e-virus-rna-and-proteins-in-the-human-liver
#13
Daniela Lenggenhager, Jérôme Gouttenoire, Mohsen Malehmir, Marion Bawohl, Hanna Honcharova-Biletska, Susanne Kreutzer, David Semela, Jörg Neuweiler, Sandra Hürlimann, Patrick Aepli, Montserrat Fraga, Roland Sahli, Luigi Terracciano, Laura Rubbia-Brandt, Beat Müllhaupt, Christine Sempoux, Darius Moradpour, Achim Weber
BACKGROUND: / Aims: Although hepatitis E constitutes a substantial disease burden worldwide, surprisingly little is known about the localization of hepatitis E virus (HEV) in the human liver. We therefore aimed to visualize HEV RNA and proteins in situ. METHODS: A panel of 12 different antibodies against HEV open reading frame (ORF) 1-3 proteins was evaluated for immunohistochemistry (IHC) and two probes for in situ hybridization (ISH) in formalin-fixed, paraffin-embedded (FFPE) Huh-7 cells transfected with HEV ORF1-3 expression vectors...
April 12, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28404952/high-throughput-detection-of-clinically-targetable-alterations-using-next-generation-sequencing
#14
Julie A Vendrell, David Grand, Isabelle Rouquette, Valérie Costes, Samira Icher, Janick Selves, Marion Larrieux, Aurore Barbe, Pierre Brousset, Jérôme Solassol
Next-generation sequencing (NGS) has revolutionized the therapeutic care of patients by allowing high-throughput and parallel sequencing of large numbers of genes in a single run. However, most of available commercialized cancer panels target a large number of mutations that do not have direct therapeutic implications and that are not fully adapted to low quality formalin-fixed, paraffin-embedded (FFPE) samples. Here, we designed an amplicon-based NGS panel assay of 16 currently actionable genes according to the most recent recommendations of the French National Cancer Institute (NCI)...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28404930/microrna-regulation-of-progesterone-receptor-in-breast-cancer
#15
Avital Gilam, Ayelet Shai, Itamar Ashkenazi, Liat Appel Sarid, Assi Drobot, Amitai Bickel, Noam Shomron
Hormone receptor status is of significant value when deciding on anti-estrogenic adjuvant therapy for breast cancer tumors. However, while estrogen receptor (ER) regulation was intensively studied, the regulation of progesterone receptor (PR) levels has not been extensively investigated. MicroRNAs (miRNAs, miRs) are post-transcriptional negative regulators of gene expression involved in diverse cellular processes. The aim of this study was to identify miRNAs that regulate PR in breast cancer.We mapped potential miRNA binding sites for miR-181a, miR-23a and miR-26b on PR mRNA and demonstrated a direct regulation of PR by these three miRNAs by in-vitro Luciferase binding assays...
February 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28404198/molecular-fluorescence-guided-surgery-of-peritoneal-carcinomatosis-of-colorectal-origin-a-single-centre-feasibility-study
#16
Niels J Harlaar, Marjory Koller, Steven J de Jongh, Barbara L van Leeuwen, Patrick H Hemmer, Schelto Kruijff, Robert J van Ginkel, Lukas B Been, Johannes S de Jong, Gursah Kats-Ugurlu, Matthijs D Linssen, Annelies Jorritsma-Smit, Marleen van Oosten, Wouter B Nagengast, Vasilis Ntziachristos, Gooitzen M van Dam
BACKGROUND: Optimum cytoreductive surgery combined with hyperthermic intraperitoneal chemotherapy (HIPEC) is essential for the curative treatment of peritoneal carcinomatosis of colorectal origin. At present, surgeons depend on visual inspection and palpation for tumour detection. Improved detection of tumour tissue using molecular fluorescence-guided surgery could not only help attain a complete cytoreduction of metastatic lesions, but might also prevent overtreatment by avoiding resection of benign lesions...
December 2016: Lancet. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28403882/pathobiological-investigation-of-naturally-infected-canine-rabies-cases-from-sri-lanka
#17
S Beck, P Gunawardena, D L Horton, D J Hicks, D A Marston, A Ortiz-Pelaez, A R Fooks, A Núñez
BACKGROUND: The recommended screening of rabies in 'suspect' animal cases involves testing fresh brain tissue. The preservation of fresh tissue however can be difficult under field conditions and formalin fixation provides a simple alternative that may allow a confirmatory diagnosis. The occurrence and location of histopathological changes and immunohistochemical (IHC) labelling for rabies in formalin fixed paraffin embedded (FFPE) canine brain is described in samples from 57 rabies suspect cases from Sri-Lanka...
April 12, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28392843/validation-of-the-methylationepic-beadchip-for-fresh-frozen-and-formalin-fixed-paraffin-embedded-tumours
#18
Teresia Kling, Anna Wenger, Stephan Beck, Helena Carén
DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression, and its involvement in the pathogenesis of cancer and several diseases upon aberrations in methylation. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tumours...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28380430/novel-rna-biomarkers-of-prostate-cancer-revealed-by-rna-seq-analysis-of-formalin-fixed-samples-obtained-from-russian-patients
#19
Anastasia S Nikitina, Elena I Sharova, Svetlana A Danilenko, Tatiana B Butusova, Alexandr O Vasiliev, Alexandr V Govorov, Elena A Prilepskaya, Dmitry Y Pushkar, Elena S Kostryukova
Due to heterogeneous multifocal nature of prostate cancer (PCa), there is currently a lack of biomarkers that stably distinguish it from benign prostatic hyperplasia (BPH), predict clinical outcome and guide the choice of optimal treatment. In this study RNA-seq analysis was applied to formalin-fixed paraffin-embedded (FFPE) tumor and matched normal tissue samples collected from Russian patients with PCa and BPH. We identified 3384 genes differentially expressed (DE) (FDR < 0.05) between tumor tissue of PCa patients and adjacent normal tissue as well as both tissue types from BPH patients...
March 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28376728/comparison-of-triple-negative-breast-cancer-molecular-subtyping-using-rna-from-matched-fresh-frozen-versus-formalin-fixed-paraffin-embedded-tissue
#20
Bojana Jovanović, Quanhu Sheng, Robert S Seitz, Kasey D Lawrence, Stephan W Morris, Lance R Thomas, David R Hout, Brock L Schweitzer, Yan Guo, Jennifer A Pietenpol, Brian D Lehmann
BACKGROUND: Triple negative breast cancer (TNBC) is a heterogeneous disease that lacks unifying molecular alterations that can guide therapy decisions. We previously identified distinct molecular subtypes of TNBC (TNBCtype) using gene expression data generated on a microarray platform using frozen tumor specimens. Tumors and cell lines representing the identified subtypes have distinct enrichment in biologically relevant transcripts with differing sensitivity to standard chemotherapies and targeted agents...
April 4, 2017: BMC Cancer
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