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https://www.readbyqxmd.com/read/28649946/choline-transporter-immunohistochemistry
#1
Raj P Kapur, Philipp W Raess, Samuel Hwang, Conrad Winter
Acetylcholinesterase enzymatic histochemistry (AChE EHC), which highlights abnormal cholinergic nerves in the mucosa of aganglionic bowel, has been used for decades to evaluate rectal biopsies for Hirschsprung disease (HSCR). While useful diagnostically, AChE EHC is not compatible with conventional formalin-fixed and paraffin-embedded (FFPE) tissues and is not widely available. The choline transporter (ChT) is a putative alternative marker of cholinergic nerves. ChT immunohistochemistry (IHC) was investigated using FFPE biopsies and resections from patients with confirmed HSCR, as well as appropriate non-HSCR controls...
January 1, 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28646562/argininosuccinate-synthase-1-ass1-a-marker-of-unclassified-hepatocellular-adenoma-and-high-bleeding-risk
#2
Elodie Henriet, Aya Abou Hammoud, Jean-William Dupuy, Benjamin Dartigues, Zakaria Ezzoukry, Nathalie Dugot-Senant, Thierry Leste-Lasserre, Nestor Pallares-Lupon, Macha Nikolski, Brigitte Le Bail, Jean-Frédéric Blanc, Charles Balabaud, Paulette Bioulac-Sage, Anne-Aurélie Raymond, Frédéric Saltel
Hepatocellular adenomas (HCA) are rare benign tumors divided into three main subgroups defined by patho-molecular features, HNF1A (H-HCA), mutated β-catenin (b-HCA) and inflammatory (IHCA). In the case of unclassified HCA (UHCA), which are currently identified by default, a high risk of bleeding remains a clinical issue. The objective of this study was to explore UHCA proteome with the aim to identify specific biomarkers. Following dissection of the tumoral (T) and non-tumoral (NT) tissue on formalin-fixed paraffin-embedded (FFPE) from HCA tissue sections using laser capture methodology, we performed mass spectrometry analysis to compare T and NT protein expression levels in HCA, H-HCA, IHCA, b-HCA, UHCA and focal nodular hyperplasia...
June 23, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28644855/comparison-of-the-mirna-expression-profiles-in-fresh-frozen-and-formalin-fixed-paraffin-embedded-tonsillar-tumors
#3
Zuzana Vojtechova, Jiri Zavadil, Jan Klozar, Marek Grega, Ruth Tachezy
MicroRNAs are considered as promising prognostic and diagnostic biomarkers of human cancer since their profiles differ between tumor types. Most of the tumor profiling studies were performed on rarely available fresh frozen (FF) samples. Alternatively, archived formalin-fixed paraffin-embedded (FFPE) tissue samples are also well applicable to larger-scale retrospective miRNA profiling studies. The aim of this study was to perform systematic comparison of the miRNA expression profiles between FF and macrodissected FFPE tonsillar tumors using the TaqMan Low Density Array system, with the data processed by different software programs and two types of normalization methods...
2017: PloS One
https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#4
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642331/diagnosis-and-risk-stratification-of-barrett-s-dysplasia-by-flow-cytometric-dna-analysis-of-paraffin-embedded-tissue
#5
Won-Tak Choi, Jia-Huei Tsai, Peter S Rabinovitch, Thomas Small, Danning Huang, Aras N Mattis, Sanjay Kakar
OBJECTIVE: The diagnosis of dysplasia in Barrett's oesophagus (BO) can be challenging, and reliable ancillary techniques are not available. This study examines if DNA content abnormality detected by flow cytometry can serve as a diagnostic marker of dysplasia and facilitate risk stratification of low-grade dysplasia (LGD) and indefinite for dysplasia (IND) patients using formalin-fixed paraffin-embedded (FFPE) BO samples with varying degrees of dysplasia. DESIGN: DNA flow cytometry was performed on 80 FFPE BO samples with high-grade dysplasia (HGD), 38 LGD, 21 IND and 14 negative for dysplasia (ND)...
June 22, 2017: Gut
https://www.readbyqxmd.com/read/28640876/reliability-and-performance-of-commercial-rna-and-dna-extraction-kits-for-ffpe-tissue-cores
#6
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/28640798/evaluation-of-placental-and-fetal-tissue-specimens-for-zika-virus-infection-50-states-and-district-of-columbia-january-december-2016
#7
Sarah Reagan-Steiner, Regina Simeone, Elizabeth Simon, Julu Bhatnagar, Titilope Oduyebo, Rebecca Free, Amy M Denison, Demi B Rabeneck, Sascha Ellington, Emily Petersen, Joy Gary, Gillian Hale, M Kelly Keating, Roosecelis B Martines, Atis Muehlenbachs, Jana Ritter, Ellen Lee, Alexander Davidson, Erin Conners, Sarah Scotland, Kayleigh Sandhu, Andrea Bingham, Elizabeth Kassens, Lou Smith, Kirsten St George, Nina Ahmad, Mary Tanner, Suzanne Beavers, Brooke Miers, Kelley VanMaldeghem, Sumaiya Khan, Ingrid Rabe, Carolyn Gould, Dana Meaney-Delman, Margaret A Honein, Wun-Ju Shieh, Denise J Jamieson, Marc Fischer, Sherif R Zaki
Zika virus infection during pregnancy can cause congenital microcephaly and brain abnormalities (1), and detection of Zika virus RNA in clinical and tissue specimens can provide definitive laboratory evidence of recent Zika virus infection. Whereas duration of viremia is typically short, prolonged detection of Zika virus RNA in placental, fetal, and neonatal brain tissue has been reported and can provide key diagnostic information by confirming recent Zika virus infection (2). In accordance with recent guidance (3,4), CDC provides Zika virus testing of placental and fetal tissues in clinical situations where this information could add diagnostic value...
June 23, 2017: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/28638728/gene-expression-analysis-in-cutaneous-t-cell-lymphomas-ctcl-highlights-disease-heterogeneity-and-potential-diagnostic-and-prognostic-indicators
#8
Ivan V Litvinov, Michael T Tetzlaff, Philippe Thibault, Pamela Gangar, Linda Moreau, Andrew K Watters, Elena Netchiporouk, Kevin Pehr, Victor G Prieto, Elham Rahme, Nathalie Provost, Martin Gilbert, Denis Sasseville, Madeleine Duvic
Cutaneous T-Cell Lymphomas (CTCL) are rare, but potentially devastating malignancies, whose pathogenesis remains poorly elucidated. Unfortunately, currently it is not possible to predict based on the available criteria in which patients the cancer will progress and which patients will experience an indolent disease course. Furthermore, at early stages this malignancy often masquerades as psoriasis, chronic eczema or other benign inflammatory dermatoses. As a result, it takes on average 6 y to diagnose this lymphoma since its initial presentation...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28638726/downregulation-of-antigen-presentation-associated-pathway-proteins-is-linked-to-poor-outcome-in-triple-negative-breast-cancer-patient-tumors
#9
Martin H Pedersen, Brian L Hood, Hans Christian Beck, Thomas P Conrads, Henrik J Ditzel, Rikke Leth-Larsen
Triple-negative breast cancer (TNBC) is a heterogeneous subtype with varying disease outcomes. Tumor-infiltrating lymphocytes (TILs) are frequent in TNBC and have been shown to correlate with outcome, suggesting an immunogenic component in this subtype. However, other factors intrinsic to the cancer cells may also influence outcome. To identify proteins and molecular pathways associated with recurrence in TNBC, 34 formalin-fixed paraffin-embedded (FFPE) primary TNBC tumors were investigated by global proteomic profiling using mass spectrometry...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28632792/identification-of-cell-proliferation-immune-response-and-cell-migration-as-critical-pathways-in-a-prognostic-signature-for-her2-er%C3%AE-breast-cancer
#10
Jeffrey C Liu, Miriam Zacksenhouse, Andrea Eisen, Sharon Nofech-Mozes, Eldad Zacksenhaus
BACKGROUND: Multi-gene prognostic signatures derived from primary tumor biopsies can guide clinicians in designing an appropriate course of treatment. Identifying genes and pathways most essential to a signature performance may facilitate clinical application, provide insights into cancer progression, and uncover potentially new therapeutic targets. We previously developed a 17-gene prognostic signature (HTICS) for HER2+:ERα- breast cancer patients, using genes that are differentially expressed in tumor initiating cells (TICs) versus non-TICs from MMTV-Her2/neu mammary tumors...
2017: PloS One
https://www.readbyqxmd.com/read/28627450/impact-of-fixation-artifacts-and-threshold-selection-on-high-resolution-melting-analysis-for-kras-mutation-screening
#11
Wendy Pérez-Báez, Ethel A Garcia-Latorre, Hector Aquiles Maldonado-Martinez, Iris Coronado-Martinez, Leonardo Flores-Garcia, Lucía Taja-Chayeb
INTRODUCTION: Treatment in the metastatic colorectal cancer has expanded with monoclonal antibodies targeting Epidermal Growth Factor Receptor, but is restricted to patients with a wild-type (WT) KRAS mutational status. The most sensitive assays for KRAS mutation detection in formalin-fixed paraffin embedded (FFPE) tissues are based on Real-time PCR. Among them, high resolution melting analysis (HRMA), is a simple, fast, highly sensitive, specific and cost-effective method, proposed as adjunct for KRAS mutation detection...
June 13, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28625575/overexpression-of-stmn1-is-associated-with-the-prognosis-of-meningioma-patients
#12
Haifeng Wang, Wenchen Li, Guangming Wang, Shuyan Zhang, Li Bie
There is a small part of the pathological type of the meningioma has a malignant tendency and patients have the poor prognosis. Looking for effective biomarkers to predict the degree of malignancy of the tumors, will help us to better manage the patient and guide the treatment. The present study aims at investigating the prognostic value of the expression of Stathmin in a series of meningiomas of different grade. We integrated eight published microarray datasets of meningiomas to screen grade biomarkers in meningiomas patients using the WebArrayDB platform...
June 16, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28625519/multiplex-ultrasensitive-genotyping-of-patients-with-non-small-cell-lung-cancer-for-epidermal-growth-factor-receptor-egfr-mutations-by-means-of-picodroplet-digital-pcr
#13
Masaru Watanabe, Tomoya Kawaguchi, Shun-Ichi Isa, Masahiko Ando, Akihiro Tamiya, Akihito Kubo, Hideo Saka, Sadanori Takeo, Hirofumi Adachi, Tsutomu Tagawa, Osamu Kawashima, Motohiro Yamashita, Kazuhiko Kataoka, Yukito Ichinose, Yukiyasu Takeuchi, Katsuya Watanabe, Akihide Matsumura, Yasuhiro Koh
Epidermal growth factor receptor (EGFR) mutations have been used as the strongest predictor of effectiveness of treatment with EGFR tyrosine kinase inhibitors (TKIs). Three most common EGFR mutations (L858R, exon 19 deletion, and T790M) are known to be major selection markers for EGFR-TKIs therapy. Here, we developed a multiplex picodroplet digital PCR (ddPCR) assay to detect 3 common EGFR mutations in 1 reaction. Serial-dilution experiments with genomic DNA harboring EGFR mutations revealed linear performance, with analytical sensitivity ~0...
June 7, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28624956/dicer1-mutations-in-twelve-chinese-patients-with-pleuropulmonary-blastoma
#14
Siyu Cai, Xisi Wang, Wen Zhao, Libing Fu, Xiaoli Ma, Xiaoxia Peng
Our aim is to examine the impact of DICER1 mutations on the pathogenesis of pleuropulmonary blastoma (PPB) by evaluating the mutation frequency and investigating the family history of Chinese patients with PPB. The family histories of 12 children with PPB recruited consecutively were surveyed. Blood samples from patients and their first-degree relatives were tested for DICER1 mutations. Whole-genome sequencing of blood samples and formalin-fixed and paraffin-embedded (FFPE) tumor tissue was performed in one family with twins...
June 14, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28624625/a-formalin-fixed-paraffin-embedded-ffpe-based-prognostic-signature-to-predict-metastasis-in-clinically-low-risk-stage-i-ii-microsatellite-stable-colorectal-cancer
#15
Yee Syuen Low, Christopher Blöcker, John R McPherson, See Aik Tang, Ying Ying Cheng, Joyner Y S Wong, Clarinda Chua, Tony K H Lim, Choong Leong Tang, Min Hoe Chew, Patrick Tan, Iain B Tan, Steven G Rozen, Peh Yean Cheah
Approximately 20% early-stage (I/II) colorectal cancer (CRC) patients develop metastases despite curative surgery. We aim to develop a formalin-fixed and paraffin-embedded (FFPE)-based predictor of metastases in early-stage, clinically-defined low risk, microsatellite-stable (MSS) CRC patients. We considered genome-wide mRNA and miRNA expression and mutation status of 20 genes assayed in 150 fresh-frozen tumours with known metastasis status. We selected 193 genes for further analysis using NanoString nCounter arrays on corresponding FFPE tumours...
June 15, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28622584/stmn1-as-a-candidate-gene-associated-with-atypical-meningioma-progression
#16
Haiyu Liu, Ye Li, Yunbo Li, Lixiang Zhou, Li Bie
OBJECTIVES: Meningiomas are the most common type of primary intracranial tumor. Atypical meningiomas are especially difficult to manage due to frequent disease recurrence. This study aimed to examine the role of stathmin (coded by the gene STMN1) as a factor in atypical meningioma recurrence. PATIENTS AND METHODS: A total of 59 sporadic atypical meningioma formalin-fixed paraffin-embedded (FFPE) samples were collected. The mRNA levels of the biomarker gene STMN1 were tested using quantitative RT-PCR...
June 10, 2017: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/28618047/focal-b-catenin-mutation-identified-on-formalin-fixed-and-paraffin-embedded-inflammatory-hepatocellular-adenomas
#17
Joan Saldarriaga, Bettina Bisig, Gabrielle Couchy, Claire Castain, Jessica Zucman-Rossi, Charles Balabaud, Christine Sempoux, Paulette Bioulac-Sage
The identification of hepatocellular adenoma (HCA) with mutation in exon 3 of the CTNNB1 gene encoding for b-catenin is clinically relevant due to higher risk of malignant transformation. Inflammatory HCA (IHCA) can exhibit b-catenin activation (b-IHCA). We report 2 cases with multiple IHCA in which focal b-catenin activation has been found in one of the IHCA. In both cases, the diagnosis of IHCA was confirmed on the resected nodules by routine stains, immunohistochemical detection of C-reactive protein (CRP), and molecular biology on frozen material...
June 15, 2017: Histopathology
https://www.readbyqxmd.com/read/28612287/methylation-markers-differentiate-thyroid-cancer-from-benign-nodules
#18
J K Stephen, K M Chen, J Merritt, D Chitale, G Divine, M J Worsham
PURPOSE: The incidence of thyroid cancer (TC) is increasing. Cytology by itself cannot distinguish TC from some benign nodules especially in certain subtypes of TC. Our immediate goal is to identify DNA methylation markers for early detection of TC and to molecularly differentiate TC subtypes from benign nodules. METHODS: Promoter methylation status of 21 candidate genes was examined on formalin-fixed paraffin-embedded tissue (FFPE) utilizing quantitative methylation-specific polymerase chain reaction (QMSP) in a retrospective cohort of 329 patients (56% white, 29% African American, 61% female) comprising 71 normal thyroid, 83 benign nodules [follicular adenomas (FA)], 90 follicular TC (FTC) and 85 papillary TC (PTC)...
June 13, 2017: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/28611940/involvement-of-chromatin-remodeling-genes-and-the-rho-gtpases-rhob-and-cdc42-in-ovarian-clear-cell-carcinoma
#19
Nicolai Skovbjerg Arildsen, Jenny-Maria Jönsson, Katarina Bartuma, Anna Ebbesson, Sofia Westbom-Fremer, Anna Måsbäck, Susanne Malander, Mef Nilbert, Ingrid A Hedenfalk
OBJECTIVE: Ovarian clear cell carcinomas (OCCCs) constitute a rare ovarian cancer subtype with distinct clinical features, but may nonetheless be difficult to distinguish morphologically from other subtypes. There is limited knowledge of genetic events driving OCCC tumorigenesis beyond ARID1A, which is reportedly mutated in 30-50% of OCCCs. We aimed to further characterize OCCCs by combined global transcriptional profiling and targeted deep sequencing of a panel of well-established cancer genes...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28611295/assessment-of-concordance-between-fresh-frozen-and-formalin-fixed-paraffin-embedded-tumor-dna-methylation-using-a-targeted-sequencing-approach
#20
Bruce Moran, Sudipto Das, Dominiek Smeets, Gillian Peutman, Rut Klinger, Bozena Fender, Kate Connor, Matthias Ebert, Timo Gaiser, Jochen Hm Prehn, Orna Bacon, Elaine Kay, Bryan Hennessy, Verena Murphy, Bauke Ylstra, Diether Lambrechts, Annette T Byrne, William M Gallagher, Darran P O'Connor
DNA methylation is altered in many types of disease, including metastatic colorectal cancer. However, the methylome has not yet been fully described in archival formalin-fixed paraffin embedded (FFPE) samples in the context of matched fresh-frozen (FF) tumor material at base-pair resolution using a targeted approach. Using next-generation sequencing, we investigated three pairs of matched FFPE and FF samples to determine the extent of their similarity. We identified a 'bowing' pattern specific to FFPE samples categorized by a lower CG proportion at the start of sequence reads...
May 30, 2017: Oncotarget
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