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https://www.readbyqxmd.com/read/28523502/maldi-ms-imaging-in-the-study-of-glomerulonephritis
#1
Andrew Smith, Manuel Galli, Vincenzo L'Imperio, Fabio Pagni, Fulvio Magni
Glomerulonephritis (GNs) are one of the most frequent causes of chronic kidney disease (CKD), a renal condition that often leads to end-stage renal failure, and a careful assessment of these diseases is essential for prognostic and therapeutic purposes. The application of MALDI-MSI directly on bioptic renal tissue represents a new stimulating perspective and facilitates the detection of specific proteomic indicators that are directly correlated with the pathological alterations that occur within the glomeruli during the development of glomerulonephritis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28523495/fresh-frozen-versus-formalin-fixed-paraffin-embedded-for-mass-spectrometry-imaging
#2
Ekta Patel
Matrix-Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry Imaging (MSI) is fast becoming an industry leading technique as a means of investigating the distributions of protein and peptide molecules directly from sections of tissue. Developing protocols for the analysis of FFPE tissue opens up numerous opportunities for novel biomarker discovery, due to the large number of tissue banks containing FFPE biopsy samples. This chapter reports the analysis of both fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues using such protocols...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28523030/detection-and-genotyping-of-helicobacter-pylori-among-gastric-ulcer-and-cancer-patients-from-saudi-arabia
#3
Fehmida Bibi, Sana Akhtar Alvi, Sara Ali Sawan, Muhammad Yasir, Ali Sawan, Asif A Jiman-Fatani, Esam I Azhar
BACKGROUND AND OBJECTIVES: Helicobacter pylori (H. pylori) infection is cause of several gastrointestinal diseases in humans. Virulence genes of H. pylori are associated with severity of disease and vary geographically. The aim of present study was to detect H. pylori in formalin-fixed paraffin-embedded (FFPE) tissues and further investigate prevalence of babA2, cagA, iceA1, iceA2, vacA s1/s2 and vacA m1/m2 genotypes in H. pylori from gastric cancer (GC) and gastric ulcer (GU) patients' biopsy samples...
March 2017: Pakistan Journal of Medical Sciences Quarterly
https://www.readbyqxmd.com/read/28512868/metastasis-associated-microrna-expression-in-canine-uveal-melanoma
#4
M P Starkey, L Compston-Garnett, P Malho, K Dunn, R Dubielzig
BACKGROUND: Uveal melanoma (UM) is the most common primary intraocular tumour in dogs. There is no effective means of predicting whether a tumour will metastasize. microRNA (miRNA) metastasis signatures have been identified for several human cancers, including UM. AIMS: In this study we investigated whether metastasizing and non-metastasizing canine UMs can be distinguished by miRNA expression levels. MATERIALS AND METHODS: miRNA microarray profiling was used to compare miRNA expression in 8 metastasizing and 12 non-metastasizing formalin-fixed, paraffin-embedded (FFPE) primary UM biopsies...
May 17, 2017: Veterinary and Comparative Oncology
https://www.readbyqxmd.com/read/28502006/fluorescence-in-situ-hybridization-of-cells-chromosomes-and-formalin-fixed-paraffin-embedded-tissues
#5
Ahmad Alamri, Jun Yeb Nam, Jan K Blancato
Fluorescence in situ hybridization (FISH) with DNA probes allows the visualization of gene copy number and localization of specific DNA targets with fluorescence microscopy. Cells in culture, metaphase chromosomes, and tissue sections are fixed and prepared on glass slides. Both the DNA in the cells and fluorescently labeled probe are denatured, and the labeled probe is allowed to hybridize to the cellular DNA. The slides are washed, counterstained, and viewed via fluorescence microscopy. We describe the basic method for preparing slides and probes for studies involving DNA copy number changes and structural chromosome rearrangements in formalin-fixed paraffin-embedded (FFPE) tissue sections and cell culture preparations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28502004/somatic-dna-mutation-analysis
#6
Anthony O'Grady, Robert Cummins
Somatic mutations in patient tumor DNA samples can be readily detected based on mass spectrometry. The MassARRAY system is a high-throughput matrix-assisted laser desorption time-of-flight (MALDI) mass spectrometer for detection of nucleic acids. The technique is based on single-nucleotide base extension. A series of PCR assays amplify specific DNA regions of interest harboring mutations. A third primer is then introduced into the reaction which corresponds to the DNA template immediately in front of the mutation site...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28498833/assessment-of-the-quality-of-dna-from-various-formalin-fixed-paraffin-embedded-ffpe-tissues-and-the-use-of-this-dna-for-next-generation-sequencing-ngs-with-no-artifactual-mutation
#7
Naoki Einaga, Akio Yoshida, Hiroko Noda, Masaaki Suemitsu, Yuki Nakayama, Akihisa Sakurada, Yoshiko Kawaji, Hiromi Yamaguchi, Yasushi Sasaki, Takashi Tokino, Mariko Esumi
Formalin-fixed, paraffin-embedded (FFPE) tissues used for pathological diagnosis are valuable for studying cancer genomics. In particular, laser-capture microdissection of target cells determined by histopathology combined with FFPE tissue section immunohistochemistry (IHC) enables precise analysis by next-generation sequencing (NGS) of the genetic events occurring in cancer. The result is a new strategy for a pathological tool for cancer diagnosis: 'microgenomics'. To more conveniently and precisely perform microgenomics, we revealed by systematic analysis the following three details regarding FFPE DNA compared with paired frozen tissue DNA...
2017: PloS One
https://www.readbyqxmd.com/read/28498805/foxm1-predicts-overall-and-disease-specific-survival-in-muscle-invasive-urothelial-carcinoma-and-presents-a-differential-expression-between-bladder-cancer-subtypes
#8
Sebastien Rinaldetti, Ralph Markus Wirtz, Thomas Stefan Worst, Markus Eckstein, Cleo Aaron Weiss, Johannes Breyer, Wolfgang Otto, Christian Bolenz, Arndt Hartmann, Philipp Erben
Forkhead box M1 (FOXM1) is a late cell cycle gene that plays a crucial role in carcinogenesis and chemotherapeutic drug resistance. In this study, the impact of FOXM1 expression on patient outcome was investigated for the first time in formalin fixed and paraffin embedded (FFPE) samples of chemotherapy naïve muscle-invasive bladder cancer (MIBC) patients. Expression analyses were performed on the Mannheim cohort (n=84) and validated on the independent Chungbuk cohort (n=61). In a Cox' proportional hazards model, a distinct FOXM1 expression cut-off dividing both cohorts in a 'high-risk' and 'low-risk' group has been determined...
April 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28493979/tissue-lithography-microscale-dewaxing-to-enable-retrospective-studies-on-formalin-fixed-paraffin-embedded-ffpe-tissue-sections
#9
Julien F Cors, Aditya Kashyap, Anna Fomitcheva Khartchenko, Peter Schraml, Govind V Kaigala
We present a new concept, termed tissue lithography (TL), and its implementation which enables retrospective studies on formalin-fixed paraffin-embedded tissue sections. Tissue lithography uses a microfluidic probe to remove microscale areas of the paraffin layer on formalin-fixed paraffin-embedded biopsy samples. Current practices in sample utilization for research and diagnostics require complete deparaffinization of the sample prior to molecular testing. This imposes strong limitations in terms of the number of tests as well as the time when they can be performed on a single sample...
2017: PloS One
https://www.readbyqxmd.com/read/28489587/ngs-based-identification-of-mutational-hotspots-for-targeted-therapy-in-anaplastic-thyroid-carcinoma
#10
Vera Tiedje, Saskia Ting, Thomas Herold, Sarah Synoracki, Soeren Latteyer, Lars C Moeller, Denise Zwanziger, Martin Stuschke, Dagmar Fuehrer, Kurt Werner Schmid
CONTEXT: Anaplastic thyroid carcinoma (ATC) represents one of the most aggressive carcinomas with no consistent survival benefit when treated with conventional radiochemotherapy. Approaches targeting "oncogene addiction" of ATC are increasingly explored and first promising results have been reported in single case studies. OBJECTIVE: To determine the prevalence of mutations in known thyroid oncogenes and signalling pathways amendable to targeted therapy in a large cohort of ATC...
April 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28489571/analysis-of-stat3-post-translational-modifications-ptms-in-human-prostate-cancer-with-different-gleason-scores
#11
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...
April 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28488345/patterns-of-pd-1-pd-l1-and-pd-l2-expression-in-pediatric-solid-tumors
#12
Navin Pinto, Julie R Park, Erin Murphy, Jennifer Yearley, Terri McClanahan, Lakshmanan Annamalai, Douglas S Hawkins, Erin R Rudzinski
BACKGROUND: Significant antitumor effects have been observed in a variety of malignancies via blockade of immune checkpoints. Interaction of programmed death 1 (PD-1) with its ligands PD-L1 and PD-L2 suppresses T-cell function and restricts immune-mediated tumor killing. We examined expression of these proteins in children with solid tumors, as expression may serve as biomarkers of response to this class of drugs. METHODS: Sections cut from formalin-fixed paraffin-embedded (FFPE) tissue blocks were processed and evaluated for PD-1, PD-L1, and PD-L2 by immunohistochemistry (IHC) as well as by mRNA expression...
May 10, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28487100/differential-expression-of-pd-l1-in-high-grade-t1-vs-muscle-invasive-bladder-carcinoma-and-its-prognostic-implications
#13
Stephanie A M Wankowicz, Lillian Werner, Anna Orsola, Jesse Novak, Michaela Bowden, Toni K Choueiri, Inés de Torres, Juan Morote, Gordon J Freeman, Sabina Signoretti, Joaquim Bellmunt
PURPOSE: PD-1 ligand (PD-L1) is expressed on both tumor cells (TCs) and tumor immune cell infiltrates (TIMC). In metastatic bladder cancer, increased TIMC PD-L1 positivity (PD-L1+) was correlated with better overall survival, however, in high grade T1 bladder tumors (HGT1) PD-L1+ on TCs and TIMCs, and correlation with outcome or pathological features remain unknown. MATERIALS AND METHODS: Formalin-fixed paraffin embedded (FFPE) tumor samples from 140 clinically annotated HGT1patients (pts) were retrieved...
May 6, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28484924/development-of-mammary-hyperplasia-dysplasia-and-invasive-ductal-carcinoma-in-transgenic-mice-expressing-the-8p11-amplicon-oncogene-nsd3
#14
Brittany Turner-Ivey, Ericka L Smith, Alex C Rutkovsky, Laura S Spruill, Jamie N Mills, Stephen P Ethier
PURPOSE: NSD3 has been implicated as a candidate driver oncogene from the 8p11-p12 locus, and we have previously published evidence for its amplification and overexpression in human breast cancer. This aim of this study was to further characterize the transforming function of NSD3 in vivo. METHODS: We generated a transgenic mouse model in which NSD3 gene expression was driven by the MMTV promoter and expressed in mammary epithelium of FVB mice. Mammary glands were fixed and whole mounts were stained with carmine to visualize gland structure...
May 8, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28481046/human-neural-stem-cell-biodistribution-and-predicted-tumor-coverage-by-a-diffusible-therapeutic-in-a-mouse-glioma-model
#15
Michael E Barish, Kelsey Herrmann, Yang Tang, Siranush Argalian Herculian, Marianne Metz, Soraya Aramburo, Revathiswari Tirughana, Margarita Gutova, Alexander Annala, Rex A Moats, Leanne Goldstein, Russell C Rockne, Jennifer Gutierrez, Christine E Brown, Lucy Ghoda, Karen S Aboody
Engineered neural stem cells (NSCs) intrinsically migrating to brain tumors offer a promising mechanism for local therapeutic delivery. However, difficulties in quantitative assessments of NSC migration and in estimates of tumor coverage by diffusible therapeutics have impeded development and refinement of NSC-based therapies. To address this need, we developed techniques by which conventional serial-sectioned formalin-fixed paraffin-embedded (FFPE) brains can be analyzed in their entirety across multiple test animals...
May 8, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28480996/the-pd-1-pd-l1-axis-and-human-papilloma-virus-in-patients-with-head-and-neck-cancer-after-adjuvant-chemoradiotherapy-a-multicentre-study-of-the-german-cancer-consortium-radiation-oncology-group-dktk-rog
#16
Panagiotis Balermpas, Franz Rödel, Mechthild Krause, Annett Linge, Fabian Lohaus, Michael Baumann, Inge Tinhofer, Volker Budach, Ali Sak, Martin Stuschke, Eleni Gkika, Anca-Ligia Grosu, Amir Abdollahi, Jürgen Debus, Stefan Stangl, Ute Ganswindt, Claus Belka, Steffi Pigorsch, Gabriele Multhoff, Stephanie E Combs, Stefan Welz, Daniel Zips, Su Yin Lim, Claus Rödel, Emmanouil Fokas
We examined the prognostic role of PD-1+ and CD8+ tumor infiltrating lymphocytes (TILs), and PD-L1+ cells in patients with squamous cell carcinoma of the head and neck (SCCHN) treated with surgery and postoperative chemoradiotherapy (CRT). FFPE samples from 161 patients were immunohistochemically stained for PD-1, CD8 and PD-L1. The immune marker expression was correlated with clinicopathologic characteristics, and overall survival (OS), local progression-free survival (LPFS) and distant metastases free-survival (DMFS), also in the context of HPV16 DNA/p16 status...
May 8, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28477007/tissue-recommendations-for-precision-cancer-therapy-using-next-generation-sequencing-a-comprehensive-single-cancer-center-s-experiences
#17
Minho Cho, Soomin Ahn, Mineui Hong, Heejin Bang, Michael Van Vrancken, Seungtae Kim, Jeeyun Lee, Se Hoon Park, Joon Oh Park, Young Suk Park, Ho Yeong Lim, Won Ki Kang, Jong-Mu Sun, Se Hoon Lee, Myung-Ju Ahn, Keunchil Park, Duk Hwan Kim, Seunggwan Lee, Woongyang Park, Kyoung-Mee Kim
To generate accurate next-generation sequencing (NGS) data, the amount and quality of DNA extracted is critical. We analyzed 1564 tissue samples from patients with metastatic or recurrent solid tumor submitted for NGS according to their sample size, acquisition method, organ, and fixation to propose appropriate tissue requirements.Of the 1564 tissue samples, 481 (30.8%) consisted of fresh-frozen (FF) tissue, and 1,083 (69.2%) consisted of formalin-fixed paraffin-embedded (FFPE) tissue. We obtained successful NGS results in 95...
April 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28472036/accurate-detection-of-low-prevalence-akt1-e17k-mutation-in-tissue-or-plasma-from-advanced-cancer-patients
#18
Elza C de Bruin, Jessica L Whiteley, Claire Corcoran, Pauline M Kirk, Jayne C Fox, Javier Armisen, Justin P O Lindemann, Gaia Schiavon, Helen J Ambrose, Alexander Kohlmann
Personalized healthcare relies on accurate companion diagnostic assays that enable the most appropriate treatment decision for cancer patients. Extensive assay validation prior to use in a clinical setting is essential for providing a reliable test result. This poses a challenge for low prevalence mutations with limited availability of appropriate clinical samples harboring the mutation. To enable prospective screening for the low prevalence AKT1 E17K mutation, we have developed and validated a competitive allele-specific TaqMan® PCR (castPCR™) assay for mutation detection in formalin-fixed paraffin-embedded (FFPE) tumor tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28470955/phenotypic-characterisation-of-cell-populations-in-the-brains-of-horses-experimentally-infected-with-west-nile-virus
#19
G H Delcambre, J Liu, W J Streit, G P J Shaw, K Vallario, J Herrington, N Wenzlow, K L Barr, M T Long
BACKGROUND: West Nile Virus (WNV), a mosquito borne member of the Flaviviridae, is one of the most commonly diagnosed agents of viral encephalitis in horses and people worldwide. OBJECTIVE: A cassette of markers for formalin-fixed paraffin-embedded (FFPE) tissue and an archive of tissues from experimental infections in the horse were used to investigate the equine neuroimmune response to WNV meningoencephalomyelitis to phenotype the early response to WNV infection in the horse...
May 4, 2017: Equine Veterinary Journal
https://www.readbyqxmd.com/read/28469400/real-time-reverse-transcription-quantitative-polymerase-chain-reaction-assay-is-a-feasible-method-for-the-relative-quantification-of-heregulin-expression-in-non-small-cell-lung-cancer-tissue
#20
Jessica Kristof, Kellen Sakrison, Xiaoping Jin, Kenji Nakamaru, Matthias Schneider, Robert A Beckman, Daniel Freeman, Cindy Spittle, Wenqin Feng
In preclinical studies, heregulin (HRG) expression was shown to be the most relevant predictive biomarker for response to patritumab, a fully human anti-epidermal growth factor receptor 3 monoclonal antibody. In support of a phase 2 study of erlotinib ± patritumab in non-small cell lung cancer (NSCLC), a reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay for relative quantification of HRG expression from formalin-fixed paraffin-embedded (FFPE) NSCLC tissue samples was developed and validated and described herein...
2017: Biomarker Insights
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