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Cancer gene panel

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https://www.readbyqxmd.com/read/28337746/thymidylate-synthase-is-functionally-associated-with-zeb1-and-contributes-to-the-epithelial-to-mesenchymal-transition-of-cancer-cells
#1
Aarif Siddiqui, Maria Eleni Vazakidou, Annemarie Schwab, Francesca Napoli, Cristina Fernandez-Molina, Ida Rapa, Marc P Stemmler, Marco Volante, Thomas Brabletz, Paolo Ceppi
Thymidylate synthase (TS) is a fundamental enzyme of nucleotide metabolism and one of the oldest anti-cancer targets. Beginning from the analysis of gene array data from the NCI-60 panel of cancer cell lines, we identified a significant correlation at both gene and protein level between TS and the markers of epithelial-to-mesenchymal transition (EMT), a developmental process that allows cancer cells to acquire features of aggressiveness, like motility and chemoresistance. TS levels were found to be significantly augmented in mesenchymal-like compared to epithelial-like cancer cells, to be regulated by EMT induction, and to negatively correlate with micro-RNAs (miRNAs) usually expressed in epithelial-like cells and known to actively suppress EMT...
March 24, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28333958/targeted-deep-sequencing-of-plasma-circulating-cell-free-dna-reveals-vimentin-and-fibulin-1-as-potential-epigenetic-biomarkers-for-hepatocellular-carcinoma
#2
Reetta Holmila, Athena Sklias, David C Muller, Davide Degli Esposti, Paule Guilloreau, James Mckay, Suleeporn Sangrajrang, Petcharin Srivatanakul, Pierre Hainaut, Philippe Merle, Zdenko Herceg, Andre Nogueira da Costa
Hepatocellular carcinoma (HCC) is the second most common cause of cancer death worldwide, but is still lacking sensitive and specific biomarkers for early diagnosis and prognosis. In this study, we applied targeted massively parallel semiconductor sequencing to assess methylation on a panel of genes (FBLN1, HINT2, LAMC1, LTBP1, LTBP2, PSMA2, PSMA7, PXDN, TGFB1, UBE2L3, VIM and YWHAZ) in plasma circulating cell-free DNA (cfDNA) and to evaluate the potential of these genes as HCC biomarkers in two different series, one from France (42 HCC cases and 42 controls) and one from Thailand (42 HCC cases, 26 chronic liver disease cases and 42 controls)...
2017: PloS One
https://www.readbyqxmd.com/read/28331560/introducing-crucial-protein-panel-of-gastric-adenocarcinoma-disease
#3
Mostafa Rezaei-Tavirani, Majid Rezaei-Tavirani, Vahid Mansouri, Seyed Mohammad Mahdavi, Reza Valizadeh, Mohammad Rostami-Nejad, Mohammad Reza Zali
AIM: Since interactome analysis of diseases can provide candidate biomarker panel related to the diseases, in this research, protein-protein interaction (PPI) network analysis is used to introduce the involved crucial proteins in Gastric adenocarcinoma (GA). BACKGROUND: Gastric adenocarcinoma (GA) is the most common type of stomach cancer. There is no efficient diagnostic molecular method for GA. METHOD: Applying Cytoscape software 3.4.0 and String Database, the PPI network was constructed for 200 genes...
2017: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28327201/detecting-gene-signature-activation-in-breast-cancer-in-an-absolute-single-patient-manner
#4
E R Paquet, R Lesurf, A Tofigh, V Dumeaux, M T Hallett
BACKGROUND: The ability to reliably identify the state (activated, repressed, or latent) of any molecular process in the tumor of a patient from an individual whole-genome gene expression profile obtained from microarray or RNA sequencing (RNA-seq) promises important clinical utility. Unfortunately, all previous bioinformatics tools are only applicable in large and diverse panels of patients, or are limited to a single specific pathway/process (e.g. proliferation). METHODS: Using a panel of 4510 whole-genome gene expression profiles from 10 different studies we built and selected models predicting the activation status of a compendium of 1733 different biological processes...
March 21, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28324944/biclustering-strategies-for-genetic-marker-selection-in-gynecologic-tumor-cell-lines
#5
A Alevyzaki, S Sfakianakis, E S Bei, E Obermayr, R Zeillinger, D Fotiadis, M Zervakis
Over the past few decades great interest has been focused on cell lines derived from tumors, because of their usability as models to understand the biology of cancer. At the same time, advanced technologies such as DNA-microarrays have been broadly used to study the expression level of thousands of genes in primary tumors or cancer cell lines in a single experiment. Results from microarray analysis approaches have provided valuable insights into the underlying biology and proven useful for tumor classification, prognostication and prediction...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28317894/swim-a-computational-tool-to-unveiling-crucial-nodes-in-complex-biological-networks
#6
Paola Paci, Teresa Colombo, Giulia Fiscon, Aymone Gurtner, Giulio Pavesi, Lorenzo Farina
SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called "fight-club hubs", characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called "switch genes", appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28315379/magnetic-nanoparticles-for-efficient-cell-transduction-with-semliki-forest-virus
#7
Baiba Kurena, Aleksandra Vežāne, Dace Skrastiņa, Olga Trofimova, Anna Zajakina
Semliki Forest virus (SFV) is a potential cancer gene therapy vector capable of providing high and transient expression of heterologous proteins in mammalian cells. However, SFV has shown suboptimal transduction levels in several cancer cell types as well as wide biodistribution of SFV has been observed after in vivo applications. Magnetic nanoparticles (MNPs) have been shown to increase cell transduction with several viral vectors in vitro under an external magnetic field and enhance magnetically guided viral vector delivery...
March 14, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28306219/characterization-of-a-novel-pold1-missense-founder-mutation-in-a-spanish-population
#8
Rosario Ferrer-Avargues, Virginia Díez-Obrero, Ester Martín-Tomás, Eva Hernández-Illán, María-Isabel Castillejo, Alan Codoñer-Alejos, Víctor-Manuel Barberá, Ana-Beatriz Sánchez-Heras, Ángel Segura, María-José Juan, Isabel Tena, Adela Castillejo, José-Luis Soto
BACKGROUND: We identified a new and a recurrent POLD1 mutation associated with predisposition to colorectal cancer (CRC). We characterized the molecular and clinical nature of the potential POLD1 founder mutation in families from Valencia (Spain). METHODS: Clinical and molecular data were collected from 4 independent families known to have a POLD1 Leu474Pro mutation. To establish its founder effect, haplotype construction was performed using 14 flanking POLD1 polymorphic markers...
March 17, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28301456/prediction-of-breast-cancer-risk-based-on-flow-variant-analysis-of-circulating-peripheral-blood-b-cells
#9
Mahrukh M Syeda, Kinnari Upadhyay, Johnny Loke, Alexander Pearlman, Susan Klugman, Yongzhao Shao, Harry Ostrer
PURPOSE: Identifying women at high risk for breast cancer can trigger a personal program of annual mammograms and magnetic resonance imaging scans for early detection, prophylactic surgery, or chemoprevention to reduce the risk of cancer. Yet, current strategies to identify high-risk mutations based on sequencing panels of genes have significant false-positive and false-negative results, suggesting the need for alternative approaches. METHODS: Flow-variant assays (FVAs) that assess the effects of mutations in the double-strand break (DSB) repair genetic pathway in lymphoblastoid cells in response to treatment with radiomimetic agents were assessed for sensitivity, specificity, and accuracy both alone and as part of a logistic regression classification score...
March 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28301252/identification-of-optimal-reference-genes-for-normalization-of-rt-qpcr-data-in-cancerous-and-non-cancerous-tissues-of-human-uterine-cervix
#10
COMPARATIVE STUDY
Shing Cheng Tan, Mohd Pazudin Ismail, Daniel Roza Duski, Nor Hayati Othman, Venkata Murali Krishna Bhavaraju, Ravindran Ankathil
This study aimed to identify the most stably expressed reference genes from a panel of 32 candidate genes for normalization of reverse transcription-quantitative real-time polymerase chain reaction data in cancerous and non-cancerous tissues of human uterine cervix. Overall, PUM1, YWHAZ, and RPLP0 were identified as the most stably expressed genes in paired cancerous and non-cancerous tissues. The results were further stratified by the state of malignancy of the tissues, histopathological type of the cancer, and the human papillomavirus-type...
March 16, 2017: Cancer Investigation
https://www.readbyqxmd.com/read/28294295/breast-cancer-major-changes-in-the-american-joint-committee-on-cancer-eighth-edition-cancer-staging-manual
#11
Armando E Giuliano, James L Connolly, Stephen B Edge, Elizabeth A Mittendorf, Hope S Rugo, Lawrence J Solin, Donald L Weaver, David J Winchester, Gabriel N Hortobagyi
Answer questions and earn CME/CNE The revision of the eighth edition of the primary tumor, lymph node, and metastasis (TNM) classification of the American Joint Commission of Cancer (AJCC) for breast cancer was determined by a multidisciplinary team of breast cancer experts. The panel recognized the need to incorporate biologic factors, such as tumor grade, proliferation rate, estrogen and progesterone receptor expression, human epidermal growth factor 2 (HER2) expression, and gene expression prognostic panels into the staging system...
March 14, 2017: CA: a Cancer Journal for Clinicians
https://www.readbyqxmd.com/read/28292937/disruption-of-tcf-%C3%AE-catenin-binding-impairs-wnt-signalling-and-induces-apoptosis-in-soft-tissue-sarcoma-cells
#12
Esther Martinez-Font, Irene Felipe-Abrio, Silvia Calabuig-Fariñas, Rafael F Ramos, Josefa Terrasa, Oliver Vögler, Regina Alemany, Javier Martín-Broto, Antònia Obrador-Hevia
Soft tissue sarcomas (STS) are malignant tumours of mesenchymal origin and represent around 1% of adult cancers, being a very heterogeneous group of tumours with more than 50 different subtypes. The Wnt signalling pathway is involved in the development and in the regulation, self-renewal and differentiation of mesenchymal stem cells and plays a role in sarcomagenesis. In this study we have tested pharmacological inhibition of Wnt signalling mediated by disruption of TCF/β-catenin binding and AXIN stabilization, being the first strategy more efficient in reducing cell viability and downstream effects...
March 14, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28283864/lower-gastrointestinal-neuroendocrine-neoplasms-associated-with-hereditary-cancer-syndromes-a-case-series
#13
Trilokesh D Kidambi, Christina Pedley, Amie Blanco, Emily K Bergsland, Jonathan P Terdiman
Lower gastrointestinal (GI) neuroendocrine neoplasms (NENs) of the colon and rectum are uncommon and not traditionally associated with hereditary GI cancer syndromes. However, with widespread implementation of colorectal cancer screening programs, lower GI NENs are being identified with increasing frequency. We report the first case series of six patients with lower GI NENs who were diagnosed with hereditary GI cancer syndromes by germline testing. Two patients presented with poorly differentiated rectal neuroendocrine carcinoma (NECs) with colonic polyposis and were found to have Familial Adenomatous Polyposis and MYH-Associated Polyposis, respectively...
March 10, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28283079/molecular-investigation-of-the-direct-anti-tumour-effects-of-nonsteroidal-anti-inflammatory-drugs-in-a-panel-of-canine-cancer-cell-lines
#14
R Yoshitake, K Saeki, M Watanabe, N Nakaoka, S M Ong, M Hanafusa, N Choisunirachon, N Fujita, R Nishimura, T Nakagawa
Nonsteroidal anti-inflammatory drugs (NSAIDs) have been suggested as effective adjunctive anti-tumour agents in human and veterinary medicine. However, the molecular mechanisms associated with their anti-tumour effects and correlations with the expression of cyclooxygenase (COX) and related molecules in tumours remain controversial. The objective of this study was to compare the expression profiles of COX and related molecules with NSAID sensitivity and to explore the molecular mechanisms of anti-tumour effects...
March 2017: Veterinary Journal
https://www.readbyqxmd.com/read/28281553/ctnnb1-beta-catenin-mutation-identifies-low-grade-early-stage-endometrial-cancer-patients-at-increased-risk-of-recurrence
#15
Katherine C Kurnit, Grace N Kim, Bryan M Fellman, Diana L Urbauer, Gordon B Mills, Wei Zhang, Russell R Broaddus
Although the majority of low grade, early stage endometrial cancer patients will have good survival outcomes with surgery alone, those patients who do recur tend to do poorly. Optimal identification of the subset of patients who are at high risk of recurrence and would benefit from adjuvant treatment has been difficult. The purpose of this study was to evaluate the impact of somatic tumor mutation on survival outcomes in this patient population. For this study, low grade was defined as endometrioid FIGO grades 1 or 2, while early stage was defined as endometrioid stages I or II (disease confined to the uterus)...
March 10, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28281552/reaching-the-limits-of-prognostication-in-non-small-cell-lung-cancer-an-optimized-biomarker-panel-fails-to-outperform-clinical-parameters
#16
Marianna Grinberg, Dijana Djureinovic, Hans Rr Brunnström, Johanna Sm Mattsson, Karolina Edlund, Jan G Hengstler, Linnea La Fleur, Simon Ekman, Hirsh Koyi, Eva Branden, Elisabeth Ståhle, Karin Jirström, Derek K Tracy, Fredrik Pontén, Johan Botling, Jörg Rahnenführer, Patrick Micke
Numerous protein biomarkers have been analyzed to improve prognostication in non-small cell lung cancer, but have not yet demonstrated sufficient value to be introduced into clinical practice. Here, we aimed to develop and validate a prognostic model for surgically resected non-small cell lung cancer. A biomarker panel was selected based on (1) prognostic association in published literature, (2) prognostic association in gene expression data sets, (3) availability of reliable antibodies, and (4) representation of diverse biological processes...
March 10, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28281021/multi-gene-panel-testing-for-hereditary-cancer-predisposition-in-unsolved-high-risk-breast-and-ovarian-cancer-patients
#17
Beth Crawford, Sophie B Adams, Taylor Sittler, Jeroen van den Akker, Salina Chan, Ofri Leitner, Lauren Ryan, Elad Gil, Laura van 't Veer
PURPOSE: Many women with an elevated risk of hereditary breast and ovarian cancer have previously tested negative for pathogenic mutations in BRCA1 and BRCA2. Among them, a subset has hereditary susceptibility to cancer and requires further testing. We sought to identify specific groups who remain at high risk and evaluate whether they should be offered multi-gene panel testing. METHODS: We tested 300 women on a multi-gene panel who were previously enrolled in a long-term study at UCSF...
March 9, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28279308/detection-of-somatic-variants-in-peripheral-blood-lymphocytes-using-a-next-generation-sequencing-multigene-pan-cancer-panel
#18
Bradford Coffee, Hannah C Cox, John Kidd, Scott Sizemore, Krystal Brown, Susan Manley, Debora Mancini-DiNardo
Next Generation Sequencing (NGS) multigene panels, which are routinely used to assess hereditary cancer risk, can detect both inherited germline variants and somatic variants in cancer-risk genes. We evaluated the frequency and distribution of likely somatic Pathogenic and Likely Pathogenic variants (PVs) detected in >220,000 individuals who underwent clinical testing with a 25-gene panel between September 2013 and March 2016. Likely somatic PVs are defined as variants with NGS read frequencies from 10% to 30%...
February 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28275007/gene-expression-profiling-of-patient-derived-pancreatic-cancer-xenografts-predicts-sensitivity-to-the-bet-bromodomain-inhibitor-jq1-implications-for-individualized-medicine-efforts
#19
Benjamin Bian, Martin Bigonnet, Odile Gayet, Celine Loncle, Aurélie Maignan, Marine Gilabert, Vincent Moutardier, Stephane Garcia, Olivier Turrini, Jean-Robert Delpero, Marc Giovannini, Philippe Grandval, Mohamed Gasmi, Mehdi Ouaissi, Veronique Secq, Flora Poizat, Rémy Nicolle, Yuna Blum, Laetitia Marisa, Marion Rubis, Jean-Luc Raoul, James E Bradner, Jun Qi, Gwen Lomberk, Raul Urrutia, Andres Saul, Nelson Dusetti, Juan Iovanna
c-MYC controls more than 15% of genes responsible for proliferation, differentiation, and cellular metabolism in pancreatic as well as other cancers making this transcription factor a prime target for treating patients. The transcriptome of 55 patient-derived xenografts show that 30% of them share an exacerbated expression profile of MYC transcriptional targets (MYC-high). This cohort is characterized by a high level of Ki67 staining, a lower differentiation state, and a shorter survival time compared to the MYC-low subgroup...
March 8, 2017: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/28273451/interrogation-of-functional-cell-surface-markers-identifies-cd151-dependency-in-high-grade-serous-ovarian-cancer
#20
Mauricio Medrano, Laudine Communal, Kevin R Brown, Marcin Iwanicki, Josee Normand, Joshua Paterson, Fabrice Sircoulomb, Paul Krzyzanowski, Marian Novak, Sasha A Doodnauth, Fernando Suarez Saiz, Jane Cullis, Rima Al-Awar, Benjamin G Neel, John McPherson, Ronny Drapkin, Laurie Ailles, Anne-Marie Mes-Massons, Robert Rottapel
The degree of genetic aberrations characteristic of high-grade serous ovarian cancer (HGSC) makes identification of the molecular features that drive tumor progression difficult. Here, we perform genome-wide RNAi screens and comprehensive expression analysis of cell-surface markers in a panel of HGSC cell lines to identify genes that are critical to their survival. We report that the tetraspanin CD151 contributes to survival of a subset of HGSC cell lines associated with a ZEB transcriptional program and supports the growth of HGSC tumors...
March 7, 2017: Cell Reports
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