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FFPE prostate cancer

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https://www.readbyqxmd.com/read/29132337/gene-expression-signatures-of-neuroendocrine-prostate-cancer-and-primary-small-cell-prostatic-carcinoma
#1
Harrison K Tsai, Jonathan Lehrer, Mohammed Alshalalfa, Nicholas Erho, Elai Davicioni, Tamara L Lotan
BACKGROUND: Neuroendocrine prostate cancer (NEPC) may be rising in prevalence as patients with advanced prostate cancer potentially develop resistance to contemporary anti-androgen treatment through a neuroendocrine phenotype. While prior studies comparing NEPC and prostatic adenocarcinoma have identified important candidates for targeted therapy, most have relied on few NEPC patients due to disease rarity, resulting in thousands of differentially expressed genes collectively and offering an opportunity for meta-analysis...
November 13, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28984675/feasibility-of-prostate-paxgene-fixation-for-molecular-research-and-diagnostic-surgical-pathology-comparison-of-matched-fresh-frozen-ffpe-and-pfpe-tissues
#2
Gunilla Högnäs, Kati Kivinummi, Heini M L Kallio, Reija Hieta, Pekka Ruusuvuori, Antti Koskenalho, Juha Kesseli, Teuvo L J Tammela, Jarno Riikonen, Joanna Ilvesaro, Saara Kares, Pasi P Hirvikoski, Marita Laurila, Tuomas Mirtti, Matti Nykter, Paula M Kujala, Tapio Visakorpi, Teemu Tolonen, G Steven Bova
Advances in prostate cancer biology and diagnostics are dependent upon high-fidelity integration of clinical, histomorphologic, and molecular phenotypic findings. In this study, we compared fresh frozen, formalin-fixed paraffin-embedded (FFPE), and PAXgene-fixed paraffin-embedded (PFPE) tissue preparation methods in radical prostatectomy prostate tissue from 36 patients and performed a preliminary test of feasibility of using PFPE tissue in routine prostate surgical pathology diagnostic assessment. In addition to comparing histology, immunohistochemistry, and general measures of DNA and RNA integrity in each fixation method, we performed functional tests of DNA and RNA quality, including targeted Miseq RNA and DNA sequencing, and implemented methods to relate DNA and RNA yield and quality to quantified DNA and RNA picogram nuclear content in each tissue volume studied...
October 3, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28640876/reliability-and-performance-of-commercial-rna-and-dna-extraction-kits-for-ffpe-tissue-cores
#3
Palak G Patel, Shamini Selvarajah, Karl-Philippe Guérard, John M S Bartlett, Jacques Lapointe, David M Berman, John B A Okello, Paul C Park
Cancer biomarker studies often require nucleic acid extraction from limited amounts of formalin-fixed, paraffin-embedded (FFPE) tissues, such as histologic sections or needle cores. A major challenge is low quantity and quality of extracted nucleic acids, which can limit our ability to perform genetic analyses, and have a significant influence on overall study design. This study was aimed at identifying the most reliable and reproducible method of obtaining sufficient high-quality nucleic acids from FFPE tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28545426/insulin-like-growth-factor-1-receptor-affects-the-survival-of-primary-prostate-cancer-patients-depending-on-tmprss2-erg-status
#4
Caterina Mancarella, Irene Casanova-Salas, Ana Calatrava, Maria García-Flores, Cecilia Garofalo, Andrea Grilli, José Rubio-Briones, Katia Scotlandi, José Antonio López-Guerrero
BACKGROUND: Prostate cancer (PCa) is characterized by clinical and biological heterogeneity and has differential outcomes and mortality rates. Therefore, it is necessary to identify molecular alterations to define new therapeutic strategies based on the risk of progression. In this study, the prognostic relevance of the insulin-like growth factor (IGF) system was examined in molecular subtypes defined by TMPRSS2-ERG (T2E) gene fusion within a series of patients with primary localized PCa...
May 25, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28489571/analysis-of-stat3-post-translational-modifications-ptms-in-human-prostate-cancer-with-different-gleason-score
#5
Rossana Cocchiola, Donatella Romaniello, Caterina Grillo, Fabio Altieri, Marcello Liberti, Fabio Massimo Magliocca, Silvia Chichiarelli, Ilaria Marrocco, Giuseppe Borgoni, Giacomo Perugia, Margherita Eufemi
Prostate Cancer (PCa) is a complex and heterogeneous disease. The androgen receptor (AR) and the signal transducer and activator of transcription 3 (STAT3) could be effective targets for PCa therapy. STAT3, a cytoplasmatic latent transcription factor, is a hub protein for several oncogenic signalling pathways and up-regulates the expression of numerous genes involved in tumor cell proliferation, angiogenesis, metastasis and cell survival. STAT3 activity can be modulated by several Post-Translational Modifications (PTMs) which reflect particular cell conditions and may be implicated in PCa development and progression...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28446506/analytic-preanalytic-and-clinical-validation-of-p53-ihc-for-detection-of-tp53-missense-mutation-in-prostate-cancer
#6
Liana B Guedes, Fawaz Almutairi, Michael C Haffner, Gaurav Rajoria, Zach Liu, Szczepan Klimek, Roberto Zoino, Kasra Yousefi, Rajni Sharma, Angelo M De Marzo, George J Netto, William B Isaacs, Ashley E Ross, Edward M Schaeffer, Tamara L Lotan
Purpose:TP53 missense mutations may help to identify prostate cancer with lethal potential. Here, we preanalytically, analytically, and clinically validated a robust IHC assay to detect subclonal and focal TP53 missense mutations in prostate cancer.Experimental Design: The p53 IHC assay was performed in a CLIA-accredited laboratory on the Ventana Benchmark immunostaining system. p53 protein nuclear accumulation was defined as any p53 nuclear labeling in >10% of tumor cells. Fifty-four formalin-fixed paraffin embedded (FFPE) cell lines from the NCI-60 panel and 103 FFPE prostate cancer tissues (88 primary adenocarcinomas, 15 metastases) with known TP53 mutation status were studied...
August 15, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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
#7
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...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28139123/biomonitoring-dna-adducts-of-cooked-meat-carcinogens-in-human-prostate-by-nano-liquid-chromatography-high-resolution-tandem-mass-spectrometry-identification-of-2-amino-1-methyl-6-phenylimidazo-4-5-b-pyridine-dna-adduct
#8
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
https://www.readbyqxmd.com/read/28119429/novel-assay-to-detect-rna-polymerase-i-activity-in-vivo
#9
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
https://www.readbyqxmd.com/read/28074002/metabolic-profiling-in-formalin-fixed-and-paraffin-embedded-prostate-cancer-tissues
#10
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
https://www.readbyqxmd.com/read/27791282/differentiating-tumor-heterogeneity-in-formalin-fixed-paraffin-embedded-ffpe-prostate-adenocarcinoma-tissues-using-principal-component-analysis-of-matrix-assisted-laser-desorption-ionization-imaging-mass-spectral-data
#11
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
https://www.readbyqxmd.com/read/27635065/the-prostate-lung-colorectal-and-ovarian-cancer-plco-screening-trial-pathology-tissue-resource
#12
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
#13
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
https://www.readbyqxmd.com/read/27509989/roles-of-microrna21-and-microrna29a-in-regulating-cell-adhesion-related-genes-in-bone-metastasis-secondary-to-prostate-cancer
#14
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
#15
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
https://www.readbyqxmd.com/read/27441277/hypoxia-regulates-notch-3-mrna-and-receptor-activation-in-prostate-cancer-cells
#16
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
#17
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
#18
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
#19
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
#20
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
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