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https://www.readbyqxmd.com/read/28735509/diagnostic-utility-of-automated-surefish-dako-omnis-in-the-diagnosis-of-musculoskeletal-translocation-related-sarcomas
#1
Shintaro Sugita, Tomoyuki Aoyama, Yoshimasa Ito, Hiroko Asanuma, Taro Sugawara, Keiko Segawa, Yumika Ito, Noriaki Kikuchi, Mitsuhiro Tsujiwaki, Hiromi Fujita, Yusuke Ono, Tadashi Hasegawa
Fluorescence in situ hybridization (FISH) is an essential tool for genetic diagnosis in daily pathological work. Almost full automation of FISH can be achieved with the recently released automated SureFISH platform (Dako Omnis, Agilent Technologies, Santa Clara, CA, USA). Its utility has been reported in HER2 amplification of breast and gastric carcinoma and ALK-rearranged lung cancer. Here, we examined the utility of automated SureFISH for the identification of rearrangement signals in translocation-related sarcomas (TRSs), including 11 EWSR1-rearranged and 10 synovial sarcoma cases, compared with non-automated conventional FISH using the same specimens...
July 22, 2017: Pathology International
https://www.readbyqxmd.com/read/28735488/bioinformatics-data-analysis-of-next-generation-sequencing-data-from-heterogeneous-tumor-samples
#2
Sean R Landman, Tae Hyun Hwang
Tumor heterogeneity is a major challenge when it comes to treating cancer and also complicates research aimed at determining genetic sources for tumorigenesis. Leveraging high-throughput sequencing technology has been an effective approach for advancing our understanding of genetic diseases, and this type of data can also be used to better understand and make inferences about tumor heterogeneity. Here we describe the basics of genomics data analysis, as well as analysis pipelines for investigating tumor heterogeneity with next-generation sequencing data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735299/identification-of-the-first-dominant-mutation-of-lama5-gene-causing-a-complex-multisystem-syndrome-due-to-dysfunction-of-the-extracellular-matrix
#3
Simone Sampaolo, Filomena Napolitano, Alfonsina Tirozzi, Mafalda Giovanna Reccia, Luca Lombardi, Olimpia Farina, Adriano Barra, Ferdinando Cirillo, Mariarosa Anna Beatrice Melone, Fernando Gianfrancesco, Giuseppe Di Iorio, Teresa Esposito
BACKGROUND: The laminin alpha 5 gene (LAMA5) plays a master role in the maintenance and function of the extracellular matrix (ECM) in mammalian tissues, which is critical in developmental patterning, stem cell niches, cancer and genetic diseases. Its mutations have never been reported in human disease so far. The aim of this study was to associate the first mutation in LAMA5 gene to a novel multisystem syndrome. METHODS: A detailed characterisation of a three-generation family, including clinical, biochemical, instrumental and morphological analysis, together with genetics and expression (WES and RNAseq) studies, was performed...
July 22, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28734786/clinical-usefulness-of-tools-to-support-decision-making-for-palliative-treatment-of%C3%A2-metastatic-colorectal-cancer-a-systematic-review
#4
Ellen G Engelhardt, Dóra Révész, Hans J Tamminga, Cornelis J A Punt, Mirjam Koopman, Bregje D Onwuteaka-Philipsen, Ewout W Steyerberg, Ilse P Jansma, Henrica C W De Vet, Veerle M H Coupé
BACKGROUND: Decision-making regarding palliative treatment for patients with metastatic colorectal cancer (mCRC) is complex and comprises numerous decisions. Decision-making should be guided by the premise of maintaining and/or improving patients' quality of life, by patient preference, and by the trade-off between treatment benefits and harm. Decision support systems (DSSs) for clinicians (eg, nomograms) can assist in this process. The present systematic review aimed to provide a comprehensive overview of the available DSSs for incurable mCRC and to assess their clinical usefulness...
June 24, 2017: Clinical Colorectal Cancer
https://www.readbyqxmd.com/read/28733542/use-of-a-genome-wide-haploid-genetic-screen-to-identify-treatment-predicting-factors-a-proof-of-principle-study-in-pancreatic-cancer
#5
Yuk Ting Ma, Sarah M Leonard, Naheema Gordon, Jennifer Anderton, Claire James, David Huen, Ciaran B Woodman, Daniel H Palmer
The ability to develop a comprehensive panel of treatment predicting factors would significantly improve our ability to stratify patients for cytotoxic or targeted therapies, and prevent patients receiving ineffective treatments. We have investigated if a recently developed genome-wide haploid genetic screen can be used to reveal the critical mediators of response to anticancer therapy. Pancreatic cancer is known to be highly resistant to systemic therapy. Recently epigenetic changes have been shown to be a key determinant in the maintenance of subpopulations of cancer cells with high-level resistance to cytotoxic therapy...
June 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28733541/a-validated-transitional-and-translational-porcine-model-of-hepatocellular-carcinoma
#6
Kyle M Schachtschneider, Regina M Schwind, Kwame A Darfour-Oduro, Arun K De, Lauretta A Rund, Kuldeep Singh, Daniel R Principe, Grace Guzman, Charles E Ray, Howard Ozer, Ron C Gaba, Lawrence B Schook
Difficult questions are confronting clinicians attempting to improve hepatocellular carcinoma (HCC) outcomes. A large animal model with genetic, anatomical, and physiological similarities to humans is required to transition from mouse models to human clinical trials to address unmet clinical needs. To validate our previously reported inducible porcine cancer model (Oncopig) as a transitional HCC model, Oncopig hepatocyte cultures were transformed using Cre recombinase. The resulting porcine HCC cells (pHCC) expressed oncogenic TP53R167H and KRASG12D, and displayed nuclear pleomorphisms with pale to granular cytoplasm arranged in expanded plates similar to human HCC histopathology...
June 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28733453/a-novel-functional-splice-variant-of-akt3-defined-by-analysis-of-alternative-splice-expression-in-hpv-positive-oropharyngeal-cancers
#7
Theresa Guo, Akihiro Sakai, Bahman Afsari, Michael Considine, Ludmila Danilova, Alexander V Favorov, Srinivasan Yegnasubramanian, Dylan Z Kelley, Emily Flam, Patrick K Ha, Zubair Khan, Sarah J Wheelan, J Silvio Gutkind, Elana J Fertig, Daria A Gaykalova, Joseph Califano
The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples...
July 21, 2017: Cancer Research
https://www.readbyqxmd.com/read/28733441/molecular-screening-for-cancer-treatment-optimization-moscato-01-in-pediatric-patients-a-single-institutional-prospective-molecular-stratification-trial
#8
Anne Catherine Harttrampf, Ludovic Lacroix, Marc Deloger, Frederic Deschamps, Stéphanie Puget, Nathalie Auger, Philippe Vielh, Pascale Varlet, Zsofia Balogh, Samuel Abbou, Adrien Allorant, Dominique Valteau-Couanet, Sabine Sarnacki, Louise Galmiche, Guillaume Meurice, Véronique Minard-Colin, Jacques Grill, Laurence Brugières, Christelle Dufour, Nathalie Gaspar, Stefan Michiels, Gilles Vassal, Jean-Charles Soria, Birgit Geoerger
This single institutional feasibility study prospectively characterized genomic alterations in recurrent or refractory solid tumors of pediatric patients in order to select a targeted therapy.<br /><br />Experimental Design: Following treatment failure patients with signed consent and aged above 6 months, underwent tumor biopsy or surgical resection of primary or metastatic tumor site.  These newly acquired samples were analyzed by comparative genomic hybridization array, next generation sequencing for 75 target genes, whole exome and RNA sequencing...
July 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28733143/mechanisms-of-nlrp1-mediated-autoinflammatory-disease-in-humans-and-mice
#9
REVIEW
Chien-Hsiung Yu, Jonas Moecking, Matthias Geyer, Seth L Masters
NLRP1 was the first NLR protein described to form an inflammasome, recruiting ASC to activate caspase-1, which processes interleukin-1β and interleukin-18 to their active form. A wealth of new genetic information has now redefined our understanding of this innate immune sensor. Specifically, rare loss-of-function variants in the N-terminal pyrin domain (PYD) indicate that this part of NLRP1 is autoinhibitory, and normally acts to prevent a familial autoinflammatory skin disease associated with cancer. In the absence of a ligand to trigger human NLRP1, these mutations have now confirmed the requirement of NLRP1 autolytic cleavage within the FIIND domain, which had previously been implicated in NLRP1 activation...
July 18, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28732364/a-novel-heterozygous-germline-deletion-in-msh2-gene-in-a-five-generation-chinese-family-with-lynch-syndrome
#10
Bin Wu, Wuyang Ji, Shengran Liang, Chao Ling, Yan You, Lai Xu, Min-Er Zhong, Yi Xiao, Hui-Zhong Qiu, Jun-Yang Lu, Santasree Banerjee
Lynch syndrome (LS) is one of the most common familial forms of colorectal cancer predisposing syndrome with an autosomal dominant mode of inheritance. LS is caused by the germline mutations in DNA mismatch repair (MMR) genes including MSH2, MLH1, MSH6and PMS2. Clinically, LS is characterized by high incidence of early-onset colorectal cancer as well as endometrial, small intestinal and urinary tract cancers, usually occur in the third to fourth decade of the life. Here we describe a five generation Chinese family with LS clinically diagnosed according to the Amsterdam II criteria...
July 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732081/il-6-variant-is-associated-with-metastasis-in-breast-cancer-patients
#11
Chike O Abana, Brian S Bingham, Ju Hwan Cho, Amy J Graves, Tatsuki Koyama, Robert T Pilarski, A Bapsi Chakravarthy, Fen Xia
INTRODUCTION: Although tumor metastases remain significant drivers of mortality, the genetic factors that increase the risks of metastases are not fully identified. Interleukin 6 (IL-6) has emerged as an important factor in breast cancer progression with IL-6 single nucleotide polymorphism (SNP) variants shown to affect survival. We hypothesized that SNPs of the IL-6 promoter at rs1800795 in breast cancer patients are associated with distant metastases. METHODS: We performed an initial case-control study using Vanderbilt University Medical Center's BioVU, a genomic biobank linked to de-identified electronic medical records in the Synthetic Derivative database, to identify germline SNPs that may predict the development of metastatic disease to any site from any solid tumor including breast cancer...
2017: PloS One
https://www.readbyqxmd.com/read/28732012/multi-approach-metabolomics-analysis-and-artificial-simplified-phytocomplexes-reveal-cultivar-dependent-synergy-between-polyphenols-and-ascorbic-acid-in-fruits-of-the-sweet-cherry-prunus-avium-l
#12
Mauro Commisso, Martino Bianconi, Flavia Di Carlo, Stefania Poletti, Alessandra Bulgarini, Francesca Munari, Stefano Negri, Matteo Stocchero, Stefania Ceoldo, Linda Avesani, Michael Assfalg, Gianni Zoccatelli, Flavia Guzzo
Fruits of the sweet cherry (Prunus avium L.) accumulate a range of antioxidants that can help to prevent cardiovascular disease, inflammation and cancer. We tested the in vitro antioxidant activity of 18 sweet cherry cultivars collected from 12 farms in the protected geographical indication region of Marostica (Vicenza, Italy) during two growing seasons. Multiple targeted and untargeted metabolomics approaches (NMR, LC-MS, HPLC-DAD, HPLC-UV) as well as artificial simplified phytocomplexes representing the cultivars Sandra Tardiva, Sandra and Grace Star were then used to determine whether the total antioxidant activity reflected the additive effects of each compound or resulted from synergistic interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28731690/the-metal-drives-the-chemistry-dual-functions-of-acireductone-dioxygenase
#13
Aditi R Deshpande, Thomas C Pochapsky, Dagmar Ringe
Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe(2+) or Ni(2+)) in the active site. The Fe(2+)-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni(2+)-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate...
July 21, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28731463/peroxisomes-protect-lymphoma-cells-from-hdac-inhibitor-mediated-apoptosis
#14
Michael S Dahabieh, ZongYi Ha, Erminia Di Pietro, Jessica N Nichol, Alicia M Bolt, Christophe Goncalves, Daphné Dupéré-Richer, Filippa Pettersson, Koren K Mann, Nancy E Braverman, Sonia V Del Rincón, Wilson H Miller
Peroxisomes are a critical rheostat of reactive oxygen species (ROS), yet their role in drug sensitivity and resistance remains unexplored. Gene expression analysis of clinical lymphoma samples suggests that peroxisomes are involved in mediating drug resistance to the histone deacetylase inhibitor (HDACi) Vorinostat (Vor), which promotes ROS-mediated apoptosis. Vor augments peroxisome numbers in cultured lymphoma cells, concomitant with increased levels of peroxisomal proteins PEX3, PEX11B, and PMP70. Genetic inhibition of peroxisomes, using PEX3 knockdown, reveals that peroxisomes protect lymphoma cells against Vor-mediated cell death...
July 21, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28731408/defining-the-biological-basis-of-radiomic-phenotypes-in-lung-cancer
#15
Patrick Grossmann, Olya Stringfield, Nehme El-Hachem, Marilyn M Bui, Emmanuel Rios Velazquez, Chintan Parmar, Ralph Th Leijenaar, Benjamin Haibe-Kains, Philippe Lambin, Robert Gillies, Hugo Jwl Aerts
Medical imaging can visualize characteristics of human cancer noninvasively. Radiomics is an emerging field that translates these medical images into quantitative data to enable phenotypic profiling of tumors. While radiomics has been associated with several clinical endpoints, the complex relationships of radiomics, clinical factors, and tumor biology are largely unknown. To this end, we analyzed two independent cohorts of respectively 262 North American and 89 European patients with lung cancer, and consistently identified previously undescribed associations between radiomic imaging features, molecular pathways, and clinical factors...
July 21, 2017: ELife
https://www.readbyqxmd.com/read/28731148/molecular-genetics-and-targeted-therapy-of-wnt-related-human-diseases-review
#16
Masuko Katoh, Masaru Katoh
Canonical WNT signaling through Frizzled and LRP5/6 receptors is transduced to the WNT/β-catenin and WNT/stabilization of proteins (STOP) signaling cascades to regulate cell fate and proliferation, whereas non-canonical WNT signaling through Frizzled or ROR receptors is transduced to the WNT/planar cell polarity (PCP), WNT/G protein-coupled receptor (GPCR) and WNT/receptor tyrosine kinase (RTK) signaling cascades to regulate cytoskeletal dynamics and directional cell movement. WNT/β-catenin signaling cascade crosstalks with RTK/SRK and GPCR-cAMP-PKA signaling cascades to regulate β-catenin phosphorylation and β-catenin-dependent transcription...
July 19, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28731048/altered-peritumoral-microrna-expression-predicts-head-and-neck-cancer-patients-with-a-high-risk-of-recurrence
#17
Federica Ganci, Andrea Sacconi, Valentina Manciocco, Renato Covello, Maria Benevolo, Francesca Rollo, Sabrina Strano, Sara Valsoni, Silvio Bicciato, Giuseppe Spriano, Paola Muti, Giulia Fontemaggi, Giovanni Blandino
Head and neck squamous cell carcinoma is typically characterized by a high incidence of local recurrences. It has been extensively shown that mucosa from head and neck squamous cell carcinoma patients carries both genetic and gene expression alterations, which are mostly attributable to major etiologic agents of head and neck squamous cell carcinoma. We previously identified a signature of microRNAs (miRNAs) whose high expression in tumors is predictive of recurrence. Here, we investigated whether the deregulation of miRNA expression in the tumor-surrounding mucosa is correlated to disease recurrence...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28731045/renal-cell-tumors-with-clear-cell-histology-and-intact-vhl-and-chromosome-3p-a-histological-review-of-tumors-from-the-cancer-genome-atlas-database
#18
Laura Favazza, Dhananjay A Chitale, Ravi Barod, Craig G Rogers, Shanker Kalyana-Sundaram, Nallasivam Palanisamy, Nilesh S Gupta, Sean R Williamson
Clear cell renal cell carcinoma is by far the most common form of kidney cancer; however, a number of histologically similar tumors are now recognized and considered distinct entities. The Cancer Genome Atlas published data set was queried (http://cbioportal.org) for clear cell renal cell carcinoma tumors lacking VHL gene mutation and chromosome 3p loss, for which whole-slide images were reviewed. Of the 418 tumors in the published Cancer Genome Atlas clear cell renal cell carcinoma database, 387 had VHL mutation, copy number loss for chromosome 3p, or both (93%)...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28730685/tex15-a-dna-repair-gene-associated-with-prostate-cancer-risk-in-han-chinese
#19
Xiaoling Lin, Zhongzhong Chen, Peng Gao, Zhimei Gao, Haitao Chen, Jun Qi, Fang Liu, Dingwei Ye, Haowen Jiang, Rong Na, Hongjie Yu, Rong Shi, Daru Lu, Siqun Lilly Zheng, Zengnan Mo, Yinghao Sun, Qiang Ding, Jianfeng Xu
BACKGROUND: Both common and rare genetic variants may contribute to risk of developing prostate cancer. Genome-wide association studies (GWASs) have identified ∼100 independent, common variants associated with prostate cancer risk. However, little is known about the association of rare variants (minor allele frequency [MAF] <1%) in the genome with prostate cancer risk. METHODS: A two-stage study was used to test the association of rare, deleterious coding variants, annotated using predictive algorithms, with prostate cancer risk in Chinese men...
July 21, 2017: Prostate
https://www.readbyqxmd.com/read/28730258/morphology-with-immunohistochemical-and-genetic-profiling-of-high-grade-neuroendocrine-carcinoma-of-colon-a-case-report-with-review-of-literature
#20
Andrzej Wincewicz, Artur Kowalik, Sebastian Zięba, Stanisław Sułkowski, Stanisław Góźdź
Here we present a challenging case of a hepatic flexure colon tumor of 61-year-old woman with no primary lesion of lung cancer. Immunohistochemistry was applied and 50 genes were analyzed by next-generation sequencing (NGS) technology. The tumor contained medium to large size neoplastic cells with evident nucleoli to be diagnosed poorly differentiated neuroendocrine predominantly large cell carcinoma of colon [G3: World Health Organization (WHO) 2010] (pT3 N0: 7th edition pTNM). Cytokeratin (CK) AE1÷AE3 staining was predominantly membranous with partial distribution in "dot-like" pattern in perinecrotic cancer fields to be reminiscent of small cell carcinoma...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
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