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FFPE prostate cancer

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https://www.readbyqxmd.com/read/27791282/differentiating-tumor-heterogeneity-in-ffpe-prostate-adenocarcinoma-tissues-using-pca-analysis-of-maldi-ims-spectral-data
#1
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. MALDI 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...
October 28, 2016: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/27635065/the-prostate-lung-colorectal-and-ovarian-cancer-plco-screening-trial-pathology-tissue-resource
#2
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
https://www.readbyqxmd.com/read/27630329/prognostic-significance-of-tmprss2-erg-fusion-gene-in-prostate-cancer
#3
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...
September 2016: Anticancer Research
https://www.readbyqxmd.com/read/27509989/roles-of-microrna21-and-microrna29a-in-regulating-cell-adhesion-related-genes-in-bone-metastasis-secondary-to-prostate-cancer
#4
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
https://www.readbyqxmd.com/read/27463017/single-strand-dna-library-preparation-improves-sequencing-of-formalin-fixed-and-paraffin-embedded-ffpe-cancer-dna
#5
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...
July 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27441277/hypoxia-regulates-notch-3-mrna-and-receptor-activation-in-prostate-cancer-cells
#6
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
https://www.readbyqxmd.com/read/27441183/real-time-and-label-free-determination-of-ligand-binding-kinetics-to-primary-cancer-tissue-specimens-a-novel-tool-for-the-assessment-of-biomarker-targeting
#7
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
https://www.readbyqxmd.com/read/27440270/branched-chain-rna-in-situ-hybridization-for-androgen-receptor-splice-variant-ar-v7-as-a-prognostic-biomarker-for-metastatic-castration-sensitive-prostate-cancer
#8
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
https://www.readbyqxmd.com/read/27389555/comparison-of-antibodies-for-immunohistochemistry-based-detection-of-her3-in-breast-cancer
#9
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
https://www.readbyqxmd.com/read/27353346/three-dimensional-microscopic-analysis-of-clinical-prostate-specimens
#10
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...
June 29, 2016: Histopathology
https://www.readbyqxmd.com/read/27324988/a-pilot-study-of-clinical-targeted-next-generation-sequencing-for-prostate-cancer-consequences-for-treatment-and-genetic-counseling
#11
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
https://www.readbyqxmd.com/read/27166397/analytic-validation-of-rna-in-situ-hybridization-rish-for-ar-and-ar-v7-expression-in-human-prostate-cancer
#12
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
https://www.readbyqxmd.com/read/27133223/mir-301a-expression-a-prognostic-marker-for-prostate-cancer
#13
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
https://www.readbyqxmd.com/read/27062540/soluble-syndecan-1-sdc1-serum-level-as-an-independent-pre-operative-predictor-of-cancer-specific-survival-in-prostate-cancer
#14
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
https://www.readbyqxmd.com/read/26731648/improving-the-prediction-of-prostate-cancer-overall-survival-by-supplementing-readily-available-clinical-data-with-gene-expression-levels-of-igfbp3-and-f3-in-formalin-fixed-paraffin-embedded-core-needle-biopsy-material
#15
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
https://www.readbyqxmd.com/read/26662140/a-pilot-study-on-the-expression-of-micrornas-resident-on-chromosome-21-in-laser-microdissected-ffpe-prostate-adenocarcinoma-samples
#16
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
https://www.readbyqxmd.com/read/26444865/comprehensive-serial-molecular-profiling-of-an-n-of-1-exceptional-non-responder-with-metastatic-prostate-cancer-progressing-to-small-cell-carcinoma-on-treatment
#17
Kunal C Kadakia, Scott A Tomlins, Saagar K Sanghvi, Andi K Cani, Kei Omata, Daniel H Hovelson, Chia-Jen Liu, Kathleen A Cooney
IMPORTANCE: Small cell carcinoma/neuroendocrine prostate cancer (NePC) is a lethal, poorly understood prostate cancer (PCa) subtype. Controversy exists about the origin of NePC in this setting. OBJECTIVE: To molecularly profile archived biopsy specimens from a case of early-onset PCa that rapidly progressed to NePC to identify drivers of the aggressive course and mechanisms of NePC origin and progression. DESIGN, SETTING, AND PARTICIPANTS: A 47-year-old patient presented with metastatic prostatic adenocarcinoma (Gleason score 9)...
2015: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/26406418/evaluation-of-two-mitochondrial-dna-biomarkers-for-prostate-cancer-detection
#18
COMPARATIVE STUDY
Samantha Maragh, Robert W Veltri, Steven P Lund, Leslie Mangold, Sumit Isharwal, Christhunesa S Christudass, Alan W Partin, Elizabeth B Humphreys, Lynn Sorbara, Sudhir Srivastava, Paul D Wagner
BACKGROUND: A 3.4kb deletion (3.4kbΔ ) in mitochondrial DNA (mtDNA) found in histologically normal prostate biopsy specimens has been reported to be a biomarker for the increased probability of prostate cancer. Increased mtDNA copy number is also reported as associated with cancer. OBJECTIVE: Independent evaluation of these two potential prostate cancer biomarkers using formalin-fixed paraffin-embedded (FFPE) prostate tissue and matched urine and serum from a high risk cohort of men with and without prostate cancer...
2015: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/26388710/proteins-from-formalin-fixed-paraffin-embedded-prostate-cancer-sections-that-predict-the-risk-of-metastatic-disease
#19
Jonathan C Dunne, David S Lamb, Brett Delahunt, Judith Murray, Peter Bethwaite, Peter Ferguson, John N Nacey, Sven Sondhauss, T William Jordan
BACKGROUND: Prostate cancer is the most frequently diagnosed cancer in men and the third leading cause of cancer related deaths among men living in developed countries. Biomarkers that predict disease outcome at the time of initial diagnosis would substantially aid disease management. RESULTS: Proteins extracted from formalin-fixed paraffin-embedded tissue were identified using nanoflow liquid chromatography-MALDI MS/MS or after separation by one- or two-dimensional electrophoresis...
2015: Clinical Proteomics
https://www.readbyqxmd.com/read/26382040/mirna-expression-analyses-in-prostate-cancer-clinical-tissues
#20
Nathan Bucay, Varahram Shahryari, Shahana Majid, Soichiro Yamamura, Yozo Mitsui, Z Laura Tabatabai, Kirsten Greene, Guoren Deng, Rajvir Dahiya, Yuichiro Tanaka, Sharanjot Saini
A critical challenge in prostate cancer (PCa) clinical management is posed by the inadequacy of currently used biomarkers for disease screening, diagnosis, prognosis and treatment. In recent years, microRNAs (miRNAs) have emerged as promising alternate biomarkers for prostate cancer diagnosis and prognosis. However, the development of miRNAs as effective biomarkers for prostate cancer heavily relies on their accurate detection in clinical tissues. miRNA analyses in prostate cancer clinical specimens is often challenging owing to tumor heterogeneity, sampling errors, stromal contamination etc...
September 8, 2015: Journal of Visualized Experiments: JoVE
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