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https://www.readbyqxmd.com/read/28106345/blood-based-detection-of-ras-mutations-to-guide-anti-egfr-therapy-in-colorectal-cancer-patients-concordance-of-results-from-circulating-tumor-dna-and-tissue-based-ras-testing
#1
Wolff Schmiegel, Rodney J Scott, Susan Dooley, Wendy Lewis, Cliff J Meldrum, Peter Pockney, Brian Draganic, Steve Smith, Chelsee Hewitt, Hazel Philimore, Amanda Lucas, Elva Shi, Kateh Namdarian, Timmy Chan, Danilo Acosta, Su Ping-Chang, Andrea Tannapfel, Anke Reinacher-Schick, Waldemar Uhl, Christian Teschendorf, Heiner Wolters, Josef Stern, Richard Viebahn, Helmut Friess, Klaus-Peter Janssen, Ulrich Nitsche, Julia Slotta-Huspenina, Michael Pohl, Deepak Vangala, Alexander Baraniskin, Barbara Dockhorn-Dworniczak, Susanne Hegewisch-Becker, Philippe Ronga, Daniel L Edelstein, Frederick S Jones, Stephan Hahn, Stephen B Fox
An accurate blood-based RAS mutation assay to determine eligibility of metastatic colorectal cancer (mCRC) patients for anti-EGFR therapy would benefit clinical practice by better informing decisions to administer treatment independent of tissue availability. The objective of this study was to determine the level of concordance between plasma and tissue RAS mutation status in patients with mCRC to gauge whether blood-based RAS mutation testing is a viable alternative to standard-of-care RAS tumor testing. RAS testing was performed on plasma samples from newly diagnosed metastatic patients, or from recurrent mCRC patients using the highly sensitive digital PCR technology, BEAMing (beads, emulsions, amplification, and magnetics), and compared with DNA sequencing data of respective FFPE (formalin-fixed paraffin-embedded) tumor samples...
November 16, 2016: Molecular Oncology
https://www.readbyqxmd.com/read/28102487/assessment-of-vascularity-in-glioblastoma-and-its-implications-on-patient-outcomes
#2
Ben G McGahan, Beth K Neilsen, David L Kelly, Rodney D McComb, S A Jaffar Kazmi, Matt L White, Yan Zhang, Michele R Aizenberg
There is little data on why glioblastomas (GBM) hemorrhage and how it may affect patient outcomes. The aim of this study was to investigate the mechanisms of hemorrhage in glioblastoma by examining molecular and genetic features by immunohistochemistry (IHC) and mRNA expression profiles in association with imaging and clinical outcomes. An observational retrospective cohort analysis was performed on 43 FFPE GBM tissue samples. MR images were assessed for the presence of hemorrhage and extent of resection. Specimens were examined for CD34 and CD105 expression using IHC...
January 19, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28098202/superresolution-imaging-of-clinical-formalin-fixed-paraffin-embedded-breast-cancer-with-single-molecule-localization-microscopy
#3
Matthew K Creech, Jing Wang, Xiaolin Nan, Summer L Gibbs
Millions of archived formalin-fixed, paraffin-embedded (FFPE) specimens contain valuable molecular insight into healthy and diseased states persevered in their native ultrastructure. To diagnose and treat diseases in tissue on the nanoscopic scale, pathology traditionally employs electron microscopy (EM), but this platform has significant limitations including cost and painstaking sample preparation. The invention of single molecule localization microscopy (SMLM) optically overcame the diffraction limit of light to resolve fluorescently labeled molecules on the nanoscale, leading to many exciting biological discoveries...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28097440/prevalence-of-nras-pten-and-akt1-gene-mutations-in-the-central-nervous-system-metastases-of-non-small-cell-lung-cancer
#4
Marcin Nicoś, Paweł Krawczyk, Bożena Jarosz, Marek Sawicki, Tomasz Trojanowski, Janusz Milanowski
Somatic mutations in NRAS, PTEN and AKT1 genes are rarely (~1%) reported in primary NSCLC, but their role in carcinogenesis have been proven. Therefore, we assessed the frequency of them in 145 FFPE tissue samples from CNS metastases of NSCLC using the real-time PCR technique. We identified four (two NRAS and single AKT1 and PTEN) mutations in CNS metastases of NSCLC. All mutations were observed in current male smokers (4% out of the male group; 4/100 and 4.25% out of smokers; 4/94). Three mutations have been detected in patients with SqCC (10...
January 17, 2017: Brain Tumor Pathology
https://www.readbyqxmd.com/read/28095352/the-relationship-of-rel-proto-oncogene-to-pathobiology-and-chemoresistance-in-follicular-and-transformed-follicular-lymphoma
#5
Xiaozhou Hu, Esra Baytak, Jinnan Li, Burcu Akman, Kaan Okay, Genfu Hu, Anna Scuto, Wenyan Zhang, Can Küçük
Follicular lymphoma (FL) is a common type of indolent lymphoma that occasionally transforms to more aggressive B-cell lymphomas. These transformed follicular lymphomas (tFL) are often associated with chemoresistance whose mechanisms are currently unknown. REL, a proto-oncogene located on frequently amplified 2p16.1-p15 locus, promotes tumorigenesis in many cancer types through deregulation of the NF-κB pathway; however, its role in FL pathobiology or chemoresistance has not been addressed. Here, we evaluated REL gene copy number by q-PCR on FFPE FL tumor samples, and observed REL amplification in 30...
January 9, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28093271/characterization-and-clinical-validation-of-mcm2-and-top2a-monoclonal-antibodies-in-the-bd-proex%C3%A2-c-assay-an-immunoassay-which-detects-aberrant-s-phase-induction-in-cervical-tissue
#6
Eric P Dixon, Lorraine M King, Ramona Nelson, Stephen G Simkins, Steven L Knapp, George H Brough, Karen L Lenz, Dorian T Henderson, Clark M Whitehead, Janice Hessling, Charlotte A Brown, Douglas P Malinowski
BACKGROUND: The Papanicolaou (Pap) screen has been successful in reducing cervical cancer; but exhibits low sensitivity when detecting cervical dysplasia. Use of molecular biomarkers in Pap tests may improve diagnostic accuracy. DESIGN: Monoclonal antibodies to Minichromosome Maintenance Protein 2 (MCM2) and DNA Topoisomerase II α (TOP2A) were selected for use in IHC based on their ability to differentiate normal from diseased cervical tissues in tissue microarrays...
January 16, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28089901/over-expression-of-proteins-that-alter-the-intracellular-signaling-pathways-in-the-cytoplasm-of-the-liver-cells-forming-mallory-denk-bodies
#7
N Afifiyan, B Tillman, B A French, M Masouminia, S Samadzadeh, S W French
In this study, liver biopsy sections fixed in formalin and embedded in paraffin (FFPE) from patients with alcoholic hepatitis (AH) were used. The results showed that the expression of the SYK protein was up regulated by RNA-seq and real time PCR analyses in the alcoholic hepatitis patients compared to controls. The results were supported by using the IHC fluorescent antibody staining intensity morphometric quantitation. Morphometric quantification of fluorescent intensity measurement showed a two fold increase in SYK protein in the cytoplasm of the cells forming MDBs compared to surrounding normal hepatocytes...
January 13, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28088345/phenotypic-characterization-of-perivascular-myoid-cell-neoplasms-using-myosin-1b-a-newly-identified-human-pericyte-marker
#8
Shiori Meguro, Taisuke Akamatsu, Sayomi Matsushima, Isao Kosugi, Hideya Kawasaki, Yosifumi Arai, Satoshi Baba, Takashi Tsuchida, Youji Shido, Takafumi Suda, Toshihide Iwashita
Our aim was to identify pericyte-specific markers for the analysis of formalin-fixed paraffin-embedded (FFPE) human tissue samples, and to characterize perivascular myoid cell neoplasms phenotypically. Previously identified pericyte markers failed to distinguish pericytes from other cellular types, such as vascular smooth muscle cells (vSMCs) and fibroblasts, in immunohistochemical (IHC) analysis. However, we compared gene expression profiles between pericytes, vSMCs, and fibroblasts, and performed human skin vasculature IHC analysis, which led to the identification of myosin 1B (MYO1B) as a novel pericyte marker...
January 11, 2017: Human Pathology
https://www.readbyqxmd.com/read/28088229/clinicopathologic-significance-of-trap1-expression-in-colorectal-cancer-a-large-scale-study-of-human-colorectal-adenocarcinoma-tissues
#9
Min Gyoung Pak, Hyong Jong Koh, Mee Sook Roh
BACKGROUND: Colorectal cancer is the major cause of cancer mortality, despite development of therapeutic strategies. The novel marker tumor necrosis factor receptor-associated protein 1 (TRAP1) is a mitochondrial heat shock protein that has been related to drug resistance and protection from apoptosis in colorectal cancer. This study aims to delineate the clinicopathologic significance of TRAP1 expression in colorectal cancer. METHODS: Seven-hundred and fourteen FFPE tissues were collected from colorectal cancer patients who underwent surgery from February 2002 to July 2011 at Dong-A University Medical Center, Busan, South Korea...
January 14, 2017: Diagnostic Pathology
https://www.readbyqxmd.com/read/28075488/generating-exome-enriched-sequencing-libraries-from-formalin-fixed-paraffin-embedded-tissue-dna-for-next-generation-sequencing
#10
Beth A Marosy, Brian D Craig, Kurt N Hetrick, P Dane Witmer, Hua Ling, Sean M Griffith, Benjamin Myers, Elaine A Ostrander, Janet L Stanford, Lawrence C Brody, Kimberly F Doheny
This unit describes a technique for generating exome-enriched sequencing libraries using DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Utilizing commercially available kits, we present a low-input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution-targeted selection for exons, followed by sequencing using the Illumina next-generation short-read sequencing platform...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28074285/t-cell-receptor-repertoire-usage-in-cancer-as-a-surrogate-marker-for-immune-responses
#11
REVIEW
David Schrama, Cathrin Ritter, Jürgen C Becker
Characterizing the interaction of cancer cells with the host adaptive immune system is critical for understanding tumor immunology and the modus operandi of immunotherapeutic interventions to treat cancer. As the key cellular effectors of adaptive immunity, T cells are endowed with specialized receptors (the T cell receptor; TCR), to recognize and to eliminate cancer cells. The diversity of the TCR repertoire results from specialized genetic diversification mechanisms that generate an incredible variability allowing recognizing extensive collections of antigens...
January 10, 2017: Seminars in Immunopathology
https://www.readbyqxmd.com/read/28074276/in-stage-pt1-non-muscle-invasive-bladder-cancer-nmibc-high-krt20-and-low-krt5-mrna-expression-identify-the-luminal-subtype-and-predict-recurrence-and-survival
#12
Johannes Breyer, Ralph M Wirtz, Wolfgang Otto, Philipp Erben, Maximilian C Kriegmair, Robert Stoehr, Markus Eckstein, Sebastian Eidt, Stefan Denzinger, Maximilian Burger, Arndt Hartmann
Differential expression of cytokeratins (CK) is a characteristic feature of chemoresistant luminal (KRT20) and chemosensitive intrinsic aggressive basal (KRT5) subtypes in muscle-invasive bladder cancer (MIBC). We investigated mRNA expression of KRT5 and KRT20 and its predictive value in stage pT1 bladder cancer. In retrospective analysis of clinical data and formalin-fixed paraffin-embedded tissues (FFPE) of patients with stage pT1 NMIBC who underwent transurethral resection of the bladder, a single-step RT-qPCR was used to measure mRNA expression...
January 10, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28074002/metabolic-profiling-in-formalin-fixed-and-paraffin-embedded-prostate-cancer-tissues
#13
Stefano Cacciatore, Giorgia Zadra, Clyde Bango, Kathryn L Penney, Svitlana Tyekucheva, Oscar Yanes, Massimo Loda
: Metabolite profiling has significantly contributed to a deeper understanding of the biochemical metabolic networks and pathways in cancer cells. Metabolomics-based biomarker discovery would greatly benefit from the ability to interrogate retrospective annotated clinical specimens archived as formalin-fixed paraffin-embedded (FFPE) material. Mass spectrometry-based metabolomic analysis was performed in matched frozen and FFPE human prostate cancers as well as isogenic prostate cancer cell lines...
January 10, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28073897/identification-of-alk-ros1-and-ret-fusions-by-a-multiplexed-mrna-based-assay-in-formalin-fixed-paraffin-embedded-samples-from-advanced-non-small-cell-lung-cancer-patients
#14
Noemí Reguart, Cristina Teixidó, Ana Giménez-Capitán, Laia Paré, Patricia Galván, Santiago Viteri, Sonia Rodríguez, Vicente Peg, Erika Aldeguer, Nuria Viñolas, Jordi Remon, Niki Karachaliou, Esther Conde, Fernando Lopez-Rios, Ernest Nadal, Sabine Merkelbach-Bruse, Reinhard Büttner, Rafael Rosell, Miguel A Molina-Vila, Aleix Prat
BACKGROUND: Anaplastic lymphoma receptor tyrosine kinase (ALK), ROS protooncogene 1, receptor tyrosine kinase (ROS1), and ret protooncogene (RET) fusions are present in 5%-7% of patients with advanced non-small-cell lung cancer (NSCLC); their accurate identification is critical to guide targeted therapies. FISH and immunohistochemistry (IHC) are considered the gold standards to determine gene fusions, they have limitations. The nCounter platform is a potentially useful genomic tool for multiplexed detection of gene fusions, but has not been validated in the clinical setting...
January 10, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28073359/whole-transcriptome-analysis-of-pre-invasive-and-invasive-early-squamous-lung-carcinoma-in-archival-laser-microdissected-samples
#15
Andre Koper, Leo A H Zeef, Leena Joseph, Keith Kerr, John Gosney, Mark A Lindsay, Richard Booton
BACKGROUND: Preinvasive squamous cell cancer (PSCC) are local transformations of bronchial epithelia that are frequently observed in current or former smokers. Their different grades and sizes suggest a continuum of dysplastic change with increasing severity, which may culminate in invasive squamous cell carcinoma (ISCC). As a consequence of the difficulty in isolating cancerous cells from biopsies, the molecular pathology that underlies their histological variability remains largely unknown...
January 10, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28070496/utility-of-the-succinate-fumarate-ratio-for-assessing-sdh-dysfunction-in-different-tumor-types
#16
Edward Kim, Michael Jp Wright, Loretta Sioson, Talia Novos, Anthony J Gill, Diana E Benn, Christopher White, Trisha Dwight, Roderick J Clifton-Bligh
OBJECTIVE: Mutations of genes encoding the four subunits of succinate dehydrogenase (SDH) have been associated with pheochromocytoma and paraganglioma (PPGLs), gastrointestinal stromal tumors (GISTs) and renal cell carcinomas (RCCs). These tumors have not been characterized in a way that reflects severity of SDH dysfunction. Mass spectrometric analysis now allows measurement of metabolites extracted from formalin fixed paraffin embedded (FFPE) specimens. We assess whether SDH deficiency in various tumor types characterized by loss of SDHB protein expression correlates with SDH dysfunction as assessed by the ratio of succinate:fumarate in FFPE specimens...
March 2017: Molecular Genetics and Metabolism Reports
https://www.readbyqxmd.com/read/28061773/differential-long-term-stability-of-micrornas-and-rnu6b-snrna-in-12-20-year-old-archived-formalin-fixed-paraffin-embedded-specimens
#17
Sarah B Peskoe, John R Barber, Qizhi Zheng, Alan K Meeker, Angelo M De Marzo, Elizabeth A Platz, Shawn E Lupold
BACKGROUND: The quantitative analysis of microRNA (miRNA) gene expression in archived formalin-fixed, paraffin embedded (FFPE) tissues has been instrumental to identifying their potential roles in cancer biology, diagnosis, and prognosis. However, it remains unclear whether miRNAs remain stable in FFPE tissues stored for long periods of time. METHODS: Here we report Taqman real-time RT-PCR quantification of miR-21, miR-141, miR-221, and RNU6B small nuclear RNA (snRNA) levels from 92 radical prostatectomy specimens stored for 12-20 years in FFPE blocks...
January 6, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28049581/validation-of-a-next-generation-sequencing-panel-for-detection-of-hotspot-cancer-mutations-in-a-clinical-laboratory
#18
Reza Shahsiah, Jenefer DeKoning, Saeed Samie, Seyed Ziaeddin Latifzadeh, Zahra Mehdizadeh Kashi
Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform...
December 16, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28039034/development-and-evaluation-of-a-novel-rt-qpcr-based-test-for-the-quantification-of-her2-gene-expression-in-breast-cancer
#19
Hicham El Hadi, Imane Abdellaoui-Maane, Denise Kottwitz, Manal El Amrani, Nadia Bouchoutrouch, Zineb Qmichou, Mehdi Karkouri, Hicham ElAttar, Hassan Errihani, Pedro L Fernandez, Youssef Bakri, Hassan Sefrioui, Abdeladim Moumen
Accurate measurement of Human epidermal growth factor receptor (HER2) gene expression is central for breast or stomach cancer therapy orientation and prognosis. The current standards testing methods for HER2 expression are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). In the current study, we explored the use of quantitative real time reverse transcription-PCR (RT-qPCR) as a potential method for the accurate relative quantification of the HER2 gene using formalin fixed paraffin embedded (FFPE) breast cancer biopsy samples...
December 28, 2016: Gene
https://www.readbyqxmd.com/read/28036302/high-expression-of-mir-181c-as-a-predictive-marker-of-recurrence-in-stage-ii-colorectal-cancer
#20
Nobuyoshi Yamazaki, Yoshikatsu Koga, Hirokazu Taniguchi, Motohiro Kojima, Yukihide Kanemitsu, Norio Saito, Yasuhiro Matsumura
INTRODUCTION: A standard treatment for stage II colorectal cancer (CRC) is surgical resection without adjuvant chemotherapy. However, the recurrence rate of these patients is approximately 20%. To date, there are no robust biomarkers suitable for predicting recurrence in stage II CRC patients. In this study, microRNAs (miRNAs) extracted from CRC tissues were examined for a possible biomarker to predict recurrence in stage II CRC patients. RESULTS: From the comprehensive analysis, 15 miRNAs were selected as candidates for further study...
December 28, 2016: Oncotarget
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