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Fiona Taylor, James Bradford, Penella J Woll, Dawn Teare, Angela Cox
Molecular profiling using low coverage whole genome sequencing of cell free DNA (cfDNA) represents a non-targeted approach to identify multiple somatic copy number alterations (SCNA) across different lung cancer subtypes. We aim to establish that SCNA can be detected in cfDNA of lung cancer cases.Standard protocols were followed to process matched cfDNA, formalin-fixed paraffin embedded (FFPE) tumour and lymphocyte DNA. Copy number profiles for cfDNA or FFPE DNA were normalised to profiles from matched lymphocyte DNA with the software CNAnorm...
2016: Advances in Experimental Medicine and Biology
Xiu Chen, Peng Lu, Dan-Dan Wang, Su-Jin Yang, Ying Wu, Hong-Yu Shen, Shan-Liang Zhong, Jian-Hua Zhao, Jin-Hai Tang
PURPOSE: Chemoresistance mediated by miRNAs in breast cancer have been already validated by previous studies in vitro, while little is known concerning the expression of them in vivo. The aim of this study was to investigate the role of miR-222, miR-29a, miR-34a, miR-130a, miR-90b, miR-200b, miR-452, miR-197, miR-138, miR-210, miR-423, miR-4298, miR-4644, miR-139, miR-1246, miR-1268a, miR-140, miR-149, miR-3178, miR-3613, miR-4258, miR-574, miR-671, miR-6780b, miR-7107, miR-744 and miR-7847 linked to drug resistance in breast cancer formalin-fixed paraffin-embedded tissues and the association of prognosis with miRNAs, thus providing effective targets in chemotherapy, as well as potential biomarkers for guiding effective treatments of breast cancer...
October 13, 2016: Gene
Jezkova Eva, Kajo Karol, Zubor Pavol, Grendar Marian, Malicherova Bibiana, Mendelova Andrea, Dokus Karol, Lasabova Zora, Plank Lukas, Danko Jan
Breast cancer is a heterogeneous disease with very different responses to therapy and different length of survival. In many cases, however, the determination of the stage and histopathological characteristics of breast cancer is insufficient to predict prognosis and response to treatment for the vast heterogeneity of the disease. To understand the molecular signature of subtypes of breast cancer, we attempted to identify the methylation status of key tumour suppressor gene Ras association (RalGDS/AF-6) domain family member 1 isoform a (RASSF1A) and a member of the paired-like homeodomain transcription factor family which functions in left-right asymmetry development (PITX2) and to correlate results with known clinicopathological features of breast cancer...
October 15, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
Cristina Silva Meira-Strejevitch, Vera Lucia Pereira-Chioccola, Marta Marques Maia, Daise Damaris Carnietto de Hipólito, Hui-Tzu Lin Wang, Gabriela Motoie, Aparecida Helena de Souza Gomes, Cristina Takami Kanamura, Roosecelis Brasil Martines, Cinara Cássia Brandão de Mattos, Fábio Batista Frederico, Luiz Carlos de Mattos, Cinara Cássia Brandão de Mattos, Fábio Batista Frederico, Rubens Camargo Siqueira, Mariana Previato, Amanda Pires Barbosa, Fernando Henrique Antunes Murata
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at
October 12, 2016: Gene
Emily Han-Chung Hsiue, Jih-Hsiang Lee, Chia-Chi Lin, James Chih-Hsin Yang
Gefitinib is recently approved by the US Food and Drug Administration as a first-line treatment for non-small cell lung cancer (NSCLC) patients harboring EGFR mutations. The therascreen® EGFR RGQ PCR Kit is approved as a companion diagnostic to select patients with EGFR exon 19 deletions and L858R mutation for treatment with gefitinib. Areas covered: This article reviews the methods for detecting EGFR mutations, the technology and indication of the therascreen® kit, and the clinical utility of the assay in phase 3 and phase 4 clinical trials...
October 13, 2016: Expert Review of Molecular Diagnostics
Koichiro Muromachi, Hiroshi Sugiya, Nobuyuki Tani-Ishii
In postnatal dentin formation, odontoblast differentiation occurs in the pulp tissue regenerative process under pathological condition. Odontoblasts and newly differentiated odontoblast-like cells beneath the caries lesion form tertiary dentin and are highly odontogenic. To observe the activity of dentinogenesis occur within the hard tissue, a combination of immunohistological analysis and immunodetection of dentinogenesis specific molecules, such as dentin sialophosphoprotein (DSPP) and/or its cleaved products dentin sialoprotein (DSP) and dentin phosphoprotein (DPP), is a reliable approach...
2017: Methods in Molecular Biology
Alan J Simmons, Cherié R Scurrah, Eliot T McKinley, Charles A Herring, Jonathan M Irish, M Kay Washington, Robert J Coffey, Ken S Lau
Cellular heterogeneity poses a substantial challenge to understanding tissue-level phenotypes and confounds conventional bulk analyses. To analyze signaling at the single-cell level in human tissues, we applied mass cytometry using cytometry time of flight to formalin-fixed, paraffin-embedded (FFPE) normal and diseased intestinal specimens. This technique, called FFPE-DISSECT (disaggregation for intracellular signaling in single epithelial cells from tissue), is a single-cell approach to characterizing signaling states in embedded tissue samples...
October 11, 2016: Science Signaling
Jinhyuk Choi, Chungyeul Kim, Hye Seung Lee, Yoo Jin Choi, Ha Yeon Kim, Jinhwan Lee, Hyeyoon Chang, Aeree Kim
Background: Human papillomavirus (HPV) is a well-established oncogenic virus of cervical, anogenital, and oropharyngeal cancer. Various subtypes of HPV have been detected in 0% to 60% of breast cancers. The roles of HPV in the carcinogenesis of breast cancer remain controversial. This study was performed to determine the prevalence of HPV-positive breast cancer in Korean patients and to evaluate the possibility of carcinogenic effect of HPV on breast. Materials and Methods: Meta-analysis was performed in 22 case-control studies for HPV infection in breast cancer...
October 10, 2016: Journal of Pathology and Translational Medicine
Romina Barani, Gholamreza Motalleb, Hossein Maghsoudi
BACKGROUND: Esophageal cancer is a public health concern around the world; this cancer is the sixth leading cause of death of cancer in the world with about 386,000 deaths per year. Its risk factors include environmental factors such as tobacco smoke, gastroesophageal reflux and genetic changes. iNOS is stated by the effect of various inflammatory factors and is thus called inducible NOS. Investigating iNOS expression is a powerful tool for understanding effective molecular parameters at tissue and cellular responses to external factors...
September 2016: Gastrointestinal Tumors
Lori D Racsa, Marlene DeLeon-Carnes, Matthew Hiskey, Jeannette Guarner
16S sequencing on formalin-fixed paraffin-embedded (FFPE) material has been used to identify bacteria when culture-based phenotyping techniques have not worked. The objective of this study was to determine how frequently 16S sequencing used in FFPE material was helpful to clinicians in the diagnosis and treatment of infectious diseases. Requests for testing occurred upon consultation between an infectious disease pathologist and a surgical pathologist or an infectious disease physician. A selected paraffin block from each case was referred for 16S sequencing...
October 4, 2016: Human Pathology
Marlon C Rebelatto, Anita Midha, Amita Mistry, Constantine Sabalos, Nicole Schechter, Xia Li, Xiaoping Jin, Keith E Steele, Paul B Robbins, John A Blake-Haskins, Jill Walker
BACKGROUND: A high-quality programmed cell-death ligand 1 (PD-L1) diagnostic assay may help predict which patients are more likely to respond to anti-programmed cell death-1 (PD-1)/PD-L1 antibody-based cancer therapy. Here we describe a PD-L1 immunohistochemical (IHC) staining protocol developed by Ventana Medical Systems Inc. and key analytical parameters of its use in formalin-fixed, paraffin-embedded (FFPE) samples of non-small cell lung cancer (NSCLC) and head and neck squamous cell carcinoma (HNSCC)...
October 8, 2016: Diagnostic Pathology
Verena Sailer, Emily Eva Holmes, Heidrun Gevensleben, Diane Goltz, Freya Dröge, Luka de Vos, Alina Franzen, Friederike Schröck, Friedrich Bootz, Glen Kristiansen, Andreas Schröck, Dimo Dietrich
BACKGROUND: Squamous cell carcinoma of the head and neck region (HNSCC) is a common malignant disease accompanied by a high risk of local or distant recurrence after curative-intent treatment. Biomarkers that allow for the prediction of disease outcome can guide clinicians with respect to treatment and surveillance strategies. Here, the methylation status of PITX2 and an adjacent lncRNA (PANCR) were evaluated for their ability to predict overall survival in HNSCC patients. RESULTS: PITX2 hypermethylation was associated with a better overall survival (hazard ratio, HR = 0...
October 3, 2016: Oncotarget
Christopher S Hughes, Melissa K McConechy, Dawn R Cochrane, Tayyebeh Nazeran, Anthony N Karnezis, David G Huntsman, Gregg B Morin
Although re-sequencing of gene panels and mRNA expression profiling are now firmly established in clinical laboratories, in-depth proteome analysis has remained a niche technology, better suited for studying model systems rather than challenging materials such as clinical trial samples. To address this limitation, we have developed a novel and optimized platform called SP3-Clinical Tissue Proteomics (SP3-CTP) for in-depth proteome profiling of practical quantities of tumour tissues, including formalin fixed and paraffin embedded (FFPE)...
October 7, 2016: Scientific Reports
Koji Arihiro, Miyo Oda, Katsunari Ogawa, Yoshie Kaneko, Tomomi Shimizu, Yuna Tanaka, Yukari Marubashi, Katsunari Ishida, Chikako Takai, Chie Taoka, Shuji Kimura, Noriyuki Shiroma
OBJECTIVES: Although updated HER2 testing guidelines have been improved by a collaboration between the American Society of Clinical Oncology (ASCO) and the College of American Pathologists (CAP) in 2013, HER2 evaluation is still problematic because of issues involving CEP17 polysomy, heterogeneity, and HER2 score 2+ cases. The aim of this retrospective study was to evaluate the relationship between HER2 gene heterogeneity, or so called CEP17 polysomy, using breast carcinoma cells sampled by scraping and the IHC score graded by automated image analysis using whole slide image...
October 3, 2016: Pathology, Research and Practice
Zhenhao Qi, Lisu Wang, Aiqing He, Manling Ma-Edmonds, John Cogswell
AIM: Formalin-fixed, paraffin-embedded (FFPE) clinical tissue samples have the potential to provide valuable gene-expression data for the development of cancer biomarkers. However, FFPE RNA is extensively fragmented, presenting a significant challenge for reliably detecting gene expression using traditional qPCR methods. RESULTS: We evaluated three novel methodologies along with the traditional qPCR method for their ability to detect Notch pathway gene expression in colorectal cancer FFPE tissue RNAs...
October 7, 2016: Bioanalysis
Rajneesh Kumar, Barbara Testoni, Judith Fresquet, Tony Kiat Hon Lim, Ying Hao, Hui Hui Tan, Wan Cheng Chow, Fabien Zoulim
: Hepatitis B is leading cause of liver related morbidity in Asia with predominant genotypes B and C in East-asia. Data on Serum, intrahepatic viral-markers and long-term follow-up of prevalent genotypes (GT) B and C in patients with biopsy proven advanced fibrosis is sparse. AIMS: To compare serum, intrahepatic viral-markers and development of Hepatocellular carcinoma(HCC) in GT-B and C in patients with advanced fibrosis (Ishak≥4) METHOD: 63 treatment-naïve patients identified with advanced fibrosis on liver-biopsy performed between 1998-2000 at Singapore-General-Hospital...
October 6, 2016: Journal of Medical Virology
Shahla Masood, Ehab El-Gabry, Chuhua Zhang, Zhiqiang Wang
BACKGROUND: It is documented that in tumor cell lines, the hTERT gene exhibits prominent methylation at a CpG island rich region about -600 bp upstream of the transcription start site, but mixed or allelically absent around ±150 bp region. Given the potential clinical implications of the findings in breast cancer diagnostics, we set out to investigate if such findings are reproducible on primary surgically resected invasive breast carcinomas. METHODS: The cohort consisted of 50 cases of freshly sampled and formalin-fixed paraffin embedded (FFPE) invasive breast cancers and normal tissue...
November 2016: Laboratory Medicine
Pedram Gerami, Zuxu Yao, David Polsky, Burkhard Jansen, Klaus Busam, Jonhan Ho, Mary Martini, Laura K Ferris
BACKGROUND: Clinical and histopathologic assessment of pigmented skin lesions remains challenging even for experts. Differentiated and accurate noninvasive diagnostic modalities are highly desirable. OBJECTIVE: We sought to provide clinicians with such a tool. METHODS: A 2-gene classification method based on LINC00518 and preferentially expressed antigen in melanoma (PRAME) gene expression was evaluated and validated in 555 pigmented lesions (157 training and 398 validation samples) obtained noninvasively via adhesive patch biopsy...
October 1, 2016: Journal of the American Academy of Dermatology
Himalaya Parajuli, Muy-Teck Teh, Siren Abrahamsen, Ingrid Christoffersen, Evelyn Neppelberg, Stein Lybak, Tarig Osman, Anne Chr Johannessen, Donald Gullberg, Kathrine Skarstein, Daniela Elena Costea
BACKGROUND: Cancer-associated fibroblasts (CAFs) were shown to be important for tumour progression in head and neck squamous cell carcinomas (HNSCCs). Their heterogeneity and lack of specific markers is increasingly recognized. Integrin α11 was recently shown to be expressed by CAFs and might serve as a specific CAF marker. AIM: To investigate integrin α11 expression and its correlation with the expression of a well-known marker of CAF, alpha smooth muscle actin (α-SMA), in HNSCC...
October 4, 2016: Journal of Oral Pathology & Medicine
Robert Fred Henry Walter, Claudia Vollbrecht, Robert Werner, Thomas Mairinger, Jan Schmeller, Elena Flom, Jeremias Wohlschlaeger, Nikolaos Barbetakis, Dimitrios Paliouras, Fotios Chatzinikolaou, Vasilis Adamidis, Kosmas Tsakiridis, Paul Zarogoulidis, Georgia Trakada, Daniel Christian Christoph, Kurt Werner Schmid, Fabian Dominik Mairinger
BACKGROUND: Malignant pleural mesothelioma (MPM) is a rare, predominantly asbestos-related and biologically highly aggressive tumour leading to a dismal prognosis. Multimodality therapy consisting of platinum-based chemotherapy is the treatment of choice. The reasons for the rather poor efficacy of platinum compounds remain largely unknown. MATERIAL AND METHODS: For this exploratory mRNA study, 24 FFPE tumour specimens were screened by digital gene expression analysis...
2016: Journal of Cancer
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