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FFPE prostate cancer

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
Shun Xiao, Jingshu Guo, Byeong Hwa Yun, Peter W Villalta, Suprita Krishna, Resha Tejpaul, Paari Murugan, Christopher J Weight, Robert J Turesky
Epidemiologic studies have reported an association between frequent consumption of well-done cooked meats and prostate cancer risk. However, unambiguous physiochemical markers of DNA damage from carcinogens derived from cooked meats, such as DNA adducts, have not been identified in human samples to support this paradigm. We have developed a highly sensitive nano-LC-Orbitrap MS (n) method to measure DNA adducts of several carcinogens originating from well-done cooked meats, tobacco smoke, and environmental pollution, including 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-9H-pyrido[2,3-b]indole (AαC), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), benzo[a]pyrene (B[a]P), and 4-aminobiphenyl (4-ABP)...
December 20, 2016: Analytical Chemistry
Gunes Guner, Paul Sirajuddin, Qizhi Zheng, Baoyan Bai, Alexandra Brodie, Hester Liu, Taija Af Hallstrom, Ibrahim Kulac, Marikki Laiho, Angelo M De Marzo
This report develops an analytically validated chromogenic in situ hybridization (CISH) assay using branched DNA signal amplification (RNAscope) for detecting the expression of the 5' external transcribed spacer (ETS) of the 45S ribosomal (r) RNA precursor in formalin fixed and paraffin embedded (FFPE) human tissues. 5'ETS/45S CISH was performed on standard clinical specimens and tissue microarrays (TMAs) from untreated prostate carcinomas, high-grade prostatic intraepithelial neoplasia (PIN) and matched benign prostatic tissues...
January 23, 2017: Molecular Cancer Research: MCR
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. A total of 352 and 460 metabolites were profiled in human tissues and cell lines, respectively...
April 2017: Molecular Cancer Research: MCR
Irene Panderi, Evgeny Yakirevich, Silvana Papagerakis, Lelia Noble, Kara Lombardo, Dionysios Pantazatos
RATIONALE: Many patients with adenocarcinoma of the prostate present with advanced and metastatic cancer at the time of diagnosis. There is an urgent need to detect biomarkers that will improve the diagnosis and prognosis of this disease. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) is playing a key role in cancer research and it can be useful to unravel the molecular profile of prostate cancer biopsies. METHODS: MALDI imaging data sets are highly complex and their interpretation requires the use of multivariate statistical methods...
January 30, 2017: Rapid Communications in Mass Spectrometry: RCM
Claire S Zhu, Wen-Yi Huang, Paul F Pinsky, Christine D Berg, Mark Sherman, Kelly J Yu, Danielle M Carrick, Amanda Black, Robert Hoover, Petra Lenz, Craig Williams, Laura Hawkins, Matthew Chaloux, Susan Yurgalevitch, Sunitha Mathew, Amy Miller, Vanessa Olivo, Asia Khan, Shannon M Pretzel, Deborah Multerer, Patricia Beckmann, Karen G Broski, Neal D Freedman
BACKGROUND: Pathology tissue specimens with associated epidemiologic and clinical data are valuable for cancer research. The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial undertook a large-scale effort to create a public resource of pathology tissues from PLCO participants who developed a cancer during the trial. METHODS: Formalin-fixed paraffin-embedded tissue blocks were obtained from pathology laboratories on a loan basis for central processing of tissue microarrays, with additional free-standing tissue cores collected for nucleic acid extraction...
December 2016: Cancer Epidemiology, Biomarkers & Prevention
Vlastimil Kulda, Ondrej Topolcan, Radek Kucera, Michaela Kripnerova, Kristyna Srbecka, Milan Hora, Ondrej Hes, Jiri Klecka, Vaclav Babuska, Milena Rousarova, Veronika Benson, Martin Pesta
BACKGROUND/AIM: Current research of prostate cancer (PCa) offers a promising way of identifying patients with adverse prognosis who do benefit from radical treatment that can affect quality of life as resections are associated with numerous side-effects. The aim of our study was to evaluate the relationship of TMPRSS2-ERG fusion gene status, tumor tissue prostate-specific antigen (PSA), prostate cancer antigen 3 (PCA3), miR-23b, miR-26a and miR-221 expression levels in combination with preoperative serum PSA level to the risk of PCa recurrence after radical prostatectomy...
2016: Anticancer Research
Maisarah Mohamad, Norhazlina Abdul Wahab, Rosna Yunus, Nor Azian Abdul Murad, Zulkifli Md Zainuddin, Murali Sundaram, Norfilza Mohd Mokhtar
BACKGROUND: There is an increasing concern in the role of microRNA (miRNA) in the pathogenesis of bone metastasis (BM) secondary to prostate cancer (CaP). In this exploratory study, we hypothesized that the expression of vinculin (VCL) and chemokine X3C ligand 1 (CX3CL1) might be downregulated in clinical samples, most likely due to the posttranscriptional modification by microRNAs. Targeted genes would be upregulated upon transfection of the bone metastatic prostate cancer cell line, PC3, with specific microRNA inhibitors...
2016: Asian Pacific Journal of Cancer Prevention: APJCP
Mathias Stiller, Antje Sucker, Klaus Griewank, Daniela Aust, Gustavo Bruno Baretton, Dirk Schadendorf, Susanne Horn
DNA derived from formalin-fixed and paraffin-embedded (FFPE) tissue has been a challenge to large-scale genomic sequencing, due to its low quality and quantities. Improved techniques enabling the genome-wide analysis of FFPE material would be of great value, both from a research and clinical perspective.Comparing a single-strand DNA library preparation method originally developed for ancient DNA to conventional protocols using double-stranded DNA derived from FFPE material we obtain on average 900-fold more library molecules and improved sequence complexity from as little as 5 ng input DNA...
September 13, 2016: Oncotarget
Armelle Meunier, Angela Nilda Flores, Niamh McDermott, Karla Rivera-Figueroa, Antoinette Perry, Thomas Lynch, Kathrine Røe Redalen, Laure Marignol
The Notch-3 receptor is a recognized key regulator of vascular responses and is increasingly associated with tumorigenesis. Hypoxia-inducible factors activate specific signaling pathways such as Notch in a number of cellular models. This study aimed to evaluate the regulation of Notch-3 by hypoxia in prostate cancer cells. Notch-3 gene and protein expression was established in a panel of aerobic and hypoxic prostate cell lines in vitro, the CWR22 xenograft model and RNA extracted from low grade (Gleason score < = 6); high grade (Gleason score > = 7); non-hypoxic (low HIF, low VEGF); hypoxic (high HIF, high VEGF) patient FFPE specimens...
May 2016: Heliyon
Thomas Mandel Clausen, Marina Ayres Pereira, Htoo Zarni Oo, Mafalda Resende, Tobias Gustavson, Yang Mao, Nobuo Sugiura, Janet Liew, Ladan Fazli, Thor G Theander, Mads Daugaard, Ali Salanti
In clinical oncology, diagnosis and evaluation of optimal treatment strategies are mostly based on histopathological examination combined with immunohistochemical (IHC) expression analysis of cancer-associated antigens in formalin fixed paraffin-embedded (FFPE) tissue biopsies. However, informative IHC analysis depends on both the specificity and affinity of the binding reagent, which are inherently difficult to quantify in situ. Here we describe a label-free method that allows for the direct and real-time assessment of molecular binding kinetics in situ on FFPE tissue specimens using quartz crystal microbalance (QCM) enabled biosensor technology...
July 2016: Sensing and Bio-Sensing Research
Philip J Saylor, Richard J Lee, Kshitij S Arora, Vikram Deshpande, Rong Hu, Kara Olivier, Erika Meneely, Miguel N Rivera, David T Ting, Chin-Lee Wu, David T Miyamoto
PURPOSE: The androgen receptor (AR) mRNA splice variant AR-V7 has emerged as a predictive biomarker for response to AR-targeted therapies. There are currently no commercially available assays to detect AR splice variants. The branched chain RNA in situ hybridization (ISH) platform enables the highly sensitive detection of RNA transcripts in formalin-fixed, paraffin-embedded (FFPE) tissues. EXPERIMENTAL DESIGN: We designed a branched chain RNA ISH probe to target the unique cryptic exon CE3 of AR-V7 using multiple tiling probes...
July 20, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Satu Luhtala, Synnöve Staff, Mark Barok, Minna Tanner, Jorma Isola
BACKGROUND: Growth factor receptor HER3 (ErbB3) lacks standardized immunohistochemistry (IHC)-based methods for formalin-fixed paraffin-embedded (FFPE) tissue samples. We compared 4 different anti-HER3 antibodies to explain the differences found in the staining results reported in the literature. MATERIALS AND METHODS: Four commercial HER3 antibodies were tested on FFPE samples including mouse monoclonal antibody clones, DAK-H3-IC and RTJ1, rabbit monoclonal antibody clone SP71, and rabbit polyclonal antibody (SAB4500793)...
July 6, 2016: Applied Immunohistochemistry & Molecular Morphology: AIMM
Martin E van Royen, Esther I Verhoef, Charlotte F Kweldam, Wiggert A van Cappellen, Gert-Jan Kremers, Adriaan B Houtsmuller, Geert J L H van Leenders
AIMS: Microscopic evaluation of prostate specimens for both clinical and research purposes is generally performed on 5-μm-thick tissue sections. Because cross-sections give a two-dimensional (2D) representation, little is known about the actual underlying three-dimensional (3D) architectural features of benign prostate tissue and prostate cancer (PCa). The aim of this study was to show that a combination of tissue-clearing protocols and confocal microscopy can successfully be applied to investigate the 3D architecture of human prostate tissue...
December 2016: Histopathology
Heather H Cheng, Nola Klemfuss, Bruce Montgomery, Celestia S Higano, Michael T Schweizer, Elahe A Mostaghel, Lisa G McFerrin, Evan Y Yu, Peter S Nelson, Colin C Pritchard
BACKGROUND: Targeted next generation sequencing (tNGS) is increasingly used in oncology for therapeutic decision-making, but is not yet widely used for prostate cancer. The objective of this study was to determine current clinical utility of tNGS for prostate cancer management. METHODS: Seven academic genitourinary medical oncologists recruited and consented patients with prostate cancer, largely with unusual clinical and/or pathologic features, from 2013 to 2015...
October 2016: Prostate
Liana B Guedes, Carlos L Morais, Fawaz Almutairi, Michael C Haffner, Qizhi Zheng, John T Isaacs, Emmanuel S Antonarakis, Changxue Lu, Harrison Tsai, Jun Luo, Angelo M De Marzo, Tamara L Lotan
PURPOSE: RNA expression of androgen receptor splice variants may be a biomarker of resistance to novel androgen deprivation therapies in castrate-resistant prostate cancer (CRPC). We analytically validated an RNA in situ hybridization (RISH) assay for total AR and AR-V7 for use in formalin-fixed paraffin-embedded (FFPE) prostate tumors. EXPERIMENTAL DESIGN: We used prostate cell lines and xenografts to validate chromogenic RISH to detect RNA containing AR exon 1 (AR-E1, surrogate for total AR RNA species) and cryptic exon 3 (AR-CE3, surrogate for AR-V7 expression)...
September 15, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Chendil Damodaran, Trinath P Das, A M Sashi Papu John, Suman Suman, Venkatesh Kolluru, Targhee J Morris, Erin N Faber, Shesh N Rai, Jamie C Messer, Houda Alatassi, Murali K Ankem
PURPOSE: The diagnosis and treatment of prostate cancer (CaP) continues to be challenging, as prostate-specific antigen (PSA) appears to be overly sensitive and biopsy is the only reliable method for confirmation. Hence, the goal of the study is to identify a biomarker that could distinguish malignant cancer from benign prostatic hyperplasia (BPH) during the early diagnosis of the disease. MATERIALS AND METHODS: A total of 75 formalin fixed paraffin embedded (FFPE) with matching controls, 4 paired metastatic tumors, 6 fresh tumor tissues and BPH (13 cases) with their clinical diagnosis were selected for this study...
August 2016: Urologic Oncology
Tibor Szarvas, Henning Reis, Frank Vom Dorp, Stephan Tschirdewahn, Christian Niedworok, Peter Nyirady, Kurt W Schmid, Herbert Rübben, Ilona Kovalszky
BACKGROUND: PSA-screening detects many cases of clinically non-aggressive prostate cancer (PC) leading to significant overtreatment. Therefore, pre-operatively available prognostic biomarkers are needed to help therapy decisions. Syndecan-1 (SDC1) is a promising prognostic tissue marker in several cancers including PC but serum levels of shedded SDC1-ectodomain (sSDC1) have not been assessed in PC. METHODS: A total of 150 patients with PC were included in this study (n = 99 serum samples, n = 103 paraffin-embedded samples (FFPE), n = 52 overlap)...
August 2016: Prostate
Zhuochun Peng, Karl Andersson, Johan Lindholm, Olga Dethlefsen, Setia Pramana, Yudi Pawitan, Monica Nistér, Sten Nilsson, Chunde Li
BACKGROUND: A previously reported expression signature of three genes (IGFBP3, F3 and VGLL3) was shown to have potential prognostic value in estimating overall and cancer-specific survivals at diagnosis of prostate cancer in a pilot cohort study using freshly frozen Fine Needle Aspiration (FNA) samples. METHODS: We carried out a new cohort study with 241 prostate cancer patients diagnosed from 2004-2007 with a follow-up exceeding 6 years in order to verify the prognostic value of gene expression signature in formalin fixed paraffin embedded (FFPE) prostate core needle biopsy tissue samples...
2016: PloS One
Adrian Mihala, Andreea Anda Alexa, Corina Samoilă, Alis Dema, Anda Cornelia Vizitiu, Andrei Anghel, Liviu Tămaş, Cătălin Valer Marian, Ioan Ovidiu Sîrbu
The tremendous research effort of the last decades added a new, epigenetic layer of complexity to the already complex image of prostate cancer pathogenesis. Here we use quantitative real-time polymerase chain reaction (qRT-PCR) to investigate the expression of the microRNAs resident on chromosome 21 (miR-ch21) in laser capture microdissected (LCM) tissues from formalin-fixed paraffin-embedded (FFPE) archived, prostate adenocarcinoma samples. We show a strong, specific down-regulation of miR-ch21 in tumoral epithelia and stromae as compared to normal counterparts, results at odd with the current paradigm on the involvement of these microRNAs in prostate oncogenesis...
2015: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
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