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Mutation analysis biomarkers cancer

Haruyoshi Tanaka, Mitsuro Kanda, Dai Shimizu, Chie Tanaka, Daisuke Kobayashi, Masamichi Hayashi, Naoki Iwata, Suguru Yamada, Tsutomu Fujii, Goro Nakayama, Hiroyuki Sugimoto, Michitaka Fujiwara, Yukiko Niwa, Yasuhiro Kodera
BACKGROUND: Gastric cancer (GC) relapse can occur even if curative resection is achieved. Biomarkers predicting recurrence are needed to provide appropriate postoperative surveillance and perioperative therapeutic strategy. METHODS: A global expression profiling was performed using tissues from GC patients with synchronous liver-confined metastasis. Family with sequence similarity 46, member C (FAM46C), was identified as a candidate biomarker. mRNA expression analysis, direct nucleotide sequencing, bisulfite sequencing and copy number assays for FAM46C were performed with eleven GC cell lines...
October 21, 2016: Annals of Surgical Oncology
Ashton A Connor, Robert E Denroche, Gun Ho Jang, Lee Timms, Sangeetha N Kalimuthu, Iris Selander, Treasa McPherson, Gavin W Wilson, Michelle A Chan-Seng-Yue, Ivan Borozan, Vincent Ferretti, Robert C Grant, Ilinca M Lungu, Eithne Costello, William Greenhalf, Daniel Palmer, Paula Ghaneh, John P Neoptolemos, Markus Buchler, Gloria Petersen, Sarah Thayer, Michael A Hollingsworth, Alana Sherker, Daniel Durocher, Neesha Dhani, David Hedley, Stefano Serra, Aaron Pollett, Michael H A Roehrl, Prashant Bavi, John M S Bartlett, Sean Cleary, Julie M Wilson, Ludmil B Alexandrov, Malcolm Moore, Bradly G Wouters, John D McPherson, Faiyaz Notta, Lincoln D Stein, Steven Gallinger
Importance: Outcomes for patients with pancreatic ductal adenocarcinoma (PDAC) remain poor. Advances in next-generation sequencing provide a route to therapeutic approaches, and integrating DNA and RNA analysis with clinicopathologic data may be a crucial step toward personalized treatment strategies for this disease. Objective: To classify PDAC according to distinct mutational processes, and explore their clinical significance. Design, Setting, and Participants: We performed a retrospective cohort study of resected PDAC, using cases collected between 2008 and 2015 as part of the International Cancer Genome Consortium...
October 20, 2016: JAMA Oncology
Piera Rizzolo, Anna Sara Navazio, Valentina Silvestri, Virginia Valentini, Veronica Zelli, Ines Zanna, Giovanna Masala, Simonetta Bianchi, Marco Scarnò, Stefania Tommasi, Domenico Palli, Laura Ottini
Male breast cancer (MBC) is a rare disease. Due to its rarity, MBC research and clinical approach are mostly based upon data derived from its largely known female counterpart. We aimed at investigating whether MBC cases harbor somatic alterations of genes known as prognostic biomarkers and molecular therapeutic targets in female breast cancer.We examined 103 MBC cases, all characterized for germ-line BRCA1/2 mutations, for somatic alterations in PIK3CA, EGFR, ESR1 and CCND1 genes.Pathogenic mutations of PIK3CA were detected in 2% of MBCs...
September 27, 2016: Oncotarget
Ha Young Park, Hyung Joo Oh, Ki-Hyun Kim, Tae-Ok Kim, Cheol-Kyu Park, Hong-Jun Shin, Jung-Hwan Lim, Yong-Soo Kwon, In-Jae Oh, Yu-Il Kim, Sung-Chul Lim, Young-Chul Kim, Yoo-Duk Choi
BACKGROUND: Epidermal growth factor receptor (EGFR) gene mutation is a reliable predictive factor for response to EGFR-tyrosine kinase inhibitors (TKIs). The quantified EGFR value may also predict response and survival within an EGFR mutated group. METHODS: We conducted a retrospective study of 836 lung cancer patients. The patient sample was divided into two groups based on the mean delta cycle threshold (∆Ct) value. EGFR mutation tests using peptide nucleic acid (PNA)-mediated clamping polymerase chain reaction (PCR) were performed...
September 1, 2016: Thoracic Cancer
Seong-Jin Kim, Tae Hyeong Lee, Sang Hee Nam, Ji-Hong Kim, Sangho Oh, Yeon Sook Cho, Myeong Sup Lee, Sehoon Choi, Peter C W Lee
BACKGROUND: The UBA6-specific E2 conjugating enzyme 1 (USE1) ubiquitin enzyme cascade is a poorly characterized arm of the ubiquitin-proteasome system. We investigated whether the UBA6-USE1 enzyme cascade plays a role in lung cancer tumorigenesis. METHODS: USE1 expression was assessed in tumor-normal paired samples from 106 lung cancer patients by immunoblot. USE1 was stably overexpressed and knocked down in lung cancer cell lines to evaluate cell proliferation, colony formation, and invasion...
March 2017: Journal of the National Cancer Institute
Manojkumar Bupathi, Christina Wu
Colorectal cancer (CRC) is a heterogeneous disease for which the treatment backbone has primarily been cytotoxic chemotherapy. With better understanding of the involved molecular mechanisms, it is now known that there are a number of epigenetic and genetic events, which are involved in CRC pathogenesis. Specific biomarkers have been identified which can be used to determine the clinical outcome of patients beyond tumor staging and predict for treatment efficacy. Molecular testing is now routinely performed to select for patients that will benefit the most from targeted agents and immunotherapy...
October 2016: Journal of Gastrointestinal Oncology
Michelangelo Fiorentino, Elisa Gruppioni, Francesco Massari, Francesca Giunchi, Annalisa Altimari, Chiara Ciccarese, Davide Bimbatti, Aldo Scarpa, Roberto Iacovelli, Camillo Porta, Sarhadi Virinder, Giampaolo Tortora, Walter Artibani, Riccardo Schiavina, Andrea Ardizzoni, Matteo Brunelli, Sakari Knuutila, Guido Martignoni
Renal cell cancer (RCC) is characterized by histological and molecular heterogeneity that may account for variable response to targeted therapies. We evaluated retrospectively with a next generation sequencing (NGS) approach using a pre-designed cancer panel the mutation burden of 32 lesions from 22 metastatic RCC patients treated with at least one tyrosine kinase or mTOR inhibitor. We identified mutations in the VHL, PTEN, JAK3, MET, ERBB4, APC, CDKN2A, FGFR3, EGFR, RB1, TP53 genes. Somatic alterations were correlated with response to therapy...
October 10, 2016: Oncotarget
Wanjun Zhu, Xiao-Yan Zhang, Sadie L Marjani, Jialing Zhang, Wengeng Zhang, Shixiu Wu, Xinghua Pan
Single-cell sequencing (SCS) is a fast-growing, exciting field in genomic medicine. It enables the high-resolution study of cellular heterogeneity, and reveals the molecular basis of complicated systems, which facilitates the identification of new biomarkers for diagnosis and for targeting therapies. It also directly promotes the next generation of genomic medicine because of its ultra-high resolution and sensitivity that allows for the non-invasive and early detection of abnormalities, such as aneuploidy, chromosomal translocation, and single-gene disorders...
October 13, 2016: Cellular and Molecular Life Sciences: CMLS
Bryan P Schneider, Dongbing Lai, Fei Shen, Guanglong Jiang, Milan Radovich, Lang Li, Laura Gardner, Kathy D Miller, Anne O'Neill, Joseph A Sparano, Gloria Xue, Tatiana Foroud, George W Sledge
PURPOSE: Taxane-induced peripheral neuropathy (TIPN) is one of the most important survivorship issues for cancer patients. African Americans (AA) have previously been shown to have an increased risk for this toxicity. Germline predictive biomarkers were evaluated to help identify a priori which patients might be at extraordinarily high risk for this toxicity. EXPERIMENTAL DESIGN: Whole exome sequencing was performed using germline DNA from 213 AA patients who received a standard dose and schedule of paclitaxel in the adjuvant, randomized phase III breast cancer trial, E5103...
October 9, 2016: Oncotarget
Viviana De Rosa, Francesca Iommelli, Marcello Monti, Ciro Gabriele Mainolfi, Rosa Fonti, Silvana Del Vecchio
BACKGROUND: The two main mechanisms of resistance to EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) are the occurrence of T790M secondary mutation in the kinase domain of EGFR and MET amplification. The aim of the present study was to test whether early changes of (18)F-fluorodeoxyglucose ((18)F-FDG) uptake in animal models bearing erlotinib-resistant NSCLC may have different imaging patterns of response to erlotinib depending on the molecular mechanisms underlying resistance...
December 2016: EJNMMI Research
Zhaomei Mu, Naoual Benali-Furet, Georges Uzan, Anaëlle Znaty, Zhong Ye, Carmela Paolillo, Chun Wang, Laura Austin, Giovanna Rossi, Paolo Fortina, Hushan Yang, Massimo Cristofanilli
The availability of blood-based diagnostic testing using a non-invasive technique holds promise for real-time monitoring of disease progression and treatment selection. Circulating tumor cells (CTCs) have been used as a prognostic biomarker for the metastatic breast cancer (MBC). The molecular characterization of CTCs is fundamental to the phenotypic identification of malignant cells and description of the relevant genetic alterations that may change according to disease progression and therapy resistance. However, the molecular characterization of CTCs remains a challenge because of the rarity and heterogeneity of CTCs and technological difficulties in the enrichment, isolation and molecular characterization of CTCs...
September 30, 2016: International Journal of Molecular Sciences
Patrick H Lizotte, Elena V Ivanova, Mark M Awad, Robert E Jones, Lauren Keogh, Hongye Liu, Ruben Dries, Christina Almonte, Grit S Herter-Sprie, Abigail Santos, Nora B Feeney, Cloud P Paweletz, Meghana M Kulkarni, Adam J Bass, Anil K Rustgi, Guo-Cheng Yuan, Donald W Kufe, Pasi A Jänne, Peter S Hammerman, Lynette M Sholl, F Stephen Hodi, William G Richards, Raphael Bueno, Jessie M English, Mark A Bittinger, Kwok-Kin Wong
BACKGROUND. Immune checkpoint blockade improves survival in a subset of patients with non-small-cell lung cancer (NSCLC), but robust biomarkers that predict response to PD-1 pathway inhibitors are lacking. Furthermore, our understanding of the diversity of the NSCLC tumor immune microenvironment remains limited. METHODS. We performed comprehensive flow cytometric immunoprofiling on both tumor and immune cells from 51 NSCLCs and integrated this analysis with clinical and histopathologic characteristics, next-generation sequencing, mRNA expression, and PD-L1 immunohistochemistry (IHC)...
September 8, 2016: JCI Insight
Elizabeth H Stover, Panagiotis A Konstantinopoulos, Ursula A Matulonis, Elizabeth M Swisher
Drugs targeting DNA damage repair (DDR) pathways are exciting new agents in cancer therapy. Many of these drugs exhibit synthetic lethality with defects in DNA repair in cancer cells. For example, ovarian cancers with impaired homologous recombination DNA repair show increased sensitivity to poly- (ADP-ribose) polymerase (PARP) inhibitors. Understanding the activity of different DNA repair pathways in individual tumors, and the correlations between DNA repair function and drug response, will be critical to patient selection for DNA repair targeted agents...
September 27, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
A Patnaik, L J Appleman, A W Tolcher, K P Papadopoulos, M Beeram, D W Rasco, G J Weiss, J C Sachdev, M Chadha, M Fulk, S Ejadi, J M Mountz, M T Lotze, F G S Toledo, E Chu, M Jeffers, C Peña, C Xia, S Reif, I Genvresse, R K Ramanathan
BACKGROUND: To evaluate the safety, tolerability, pharmacokinetics, and maximum tolerated dose (MTD) of copanlisib, a phosphatidylinositol 3-kinase inhibitor, in patients with advanced solid tumors or non-Hodgkin's lymphoma (NHL). PATIENTS AND METHODS: Phase I dose-escalation study including patients with advanced solid tumors or NHL, and a cohort of patients with type 2 diabetes mellitus. Patients received three weekly intravenous infusions of copanlisib per 28-day cycle over the dose range 0...
October 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
I-Shou Chang, Shih Sheng Jiang, James Chih-Hsin Yang, Wu-Chou Su, Li-Hsin Chien, Chin-Fu Hsiao, Jih-Hsiang Lee, Chih-Yi Chen, Chung-Hsing Chen, Gee-Chen Chang, Zhaoming Wang, Fang-Yi Lo, Kuan-Yu Chen, Wen-Chang Wang, Yuh-Min Chen, Ming-Shyan Huang, Ying-Huang Tsai, Yu-Chun Su, Wan-Shan Hsieh, Wen-Chi Shih, Shwn-Huey Shieh, Tsung-Ying Yang, Qing Lan, Nathaniel Rothman, Chien-Jen Chen, Stephen J Chanock, Pan-Chyr Yang, Chao A Hsiung
RATIONALE: Patients of NSCLC with mutated EGFR are relatively sensitive to EGFR-TKI treatment and have longer progression-free survival (PFS) when treated with EGFR-TKI, compared with platinum-based chemotherapy. However, many advanced NSCLC patients with mutated EGFR do not response to first-line EGFR-TKI treatment and still have shorter PFS. OBJECTIVES: The aim of this study was to identify genetic variants associated PFS among lung adenocarcinoma (ADC) patients treated with first-line EGFR-TKIs...
September 26, 2016: American Journal of Respiratory and Critical Care Medicine
Reshma Shinde, Xiting Cao, Smita Kothari
BACKGROUND: Epidermal growth factor receptor (EGFR) gene mutations and anaplastic lymphoma kinase (ALK) gene rearrangements are key therapeutic targets for biomarker-driven treatment with an EGFR or ALK tyrosine kinase inhibitor (TKI) in patients with metastatic non-small cell lung cancer (NSCLC). To appropriately guide treatment decisions, since 2011, the National Comprehensive Cancer Network and the American Society of Clinical Oncology therefore recommend EGFR and ALK analysis in tumor samples obtained at the time of diagnosis in patients with non-squamous NSCLC...
October 2016: Journal of Managed Care & Specialty Pharmacy
Pamela Norton, Mary Ann Comunale, Harmin Herrera, Mengjun Wang, Josef Houser, Michaela Wimmerova, Patrick R Romano, Anand Mehta
The Aleuria aurantia lectin (AAL) derived from orange peel fungus contains five fucose-binding sites that recognizes fucose bound in α-1,2, α-1,3, α-1,4 and α-1,6 linkages to N-acetylglucosamine (GlcNAc) and galactose. Recently, we have created several recombinant AAL (rAAL) proteins that had altered binding affinity to fucose linkages. In this report we further characterize the binding specificity of one of the mutated lectins, N224Q lectin. This lectin was characterized by lectin western blotting, surface plasmon resonance and glycan microarray and shown to have increased binding to fucosylated glycan...
September 21, 2016: Proteomics
Bo Kong, Philipp Bruns, Nora A Behler, Ligong Chang, Anna Melissa Schlitter, Jing Cao, Andreas Gewies, Jürgen Ruland, Sina Fritzsche, Nataliya Valkovskaya, Ziying Jian, Ivonne Regel, Susanne Raulefs, Martin Irmler, Johannes Beckers, Helmut Friess, Mert Erkan, Nikola S Mueller, Susanne Roth, Thilo Hackert, Irene Esposito, Fabian J Theis, Jörg Kleeff, Christoph W Michalski
OBJECTIVE: The initial steps of pancreatic regeneration versus carcinogenesis are insufficiently understood. Although a combination of oncogenic Kras and inflammation has been shown to induce malignancy, molecular networks of early carcinogenesis remain poorly defined. DESIGN: We compared early events during inflammation, regeneration and carcinogenesis on histological and transcriptional levels with a high temporal resolution using a well-established mouse model of pancreatitis and of inflammation-accelerated Kras(G12D)-driven pancreatic ductal adenocarcinoma...
September 19, 2016: Gut
Laetitia Borsu, Julie Intrieri, Linta Thampi, Helena Yu, Gregory Riely, Khedoudja Nafa, Raghu Chandramohan, Marc Ladanyi, Maria E Arcila
Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR mutant lung adenocarcinomas (LADs) with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples...
September 12, 2016: Journal of Molecular Diagnostics: JMD
Hisae Iinuma, Noriyuki Matsutani, Hirofumi Uehara, Masafumi Kawamura
The superior therapeutic effects of antibodies targeting immune checkpoints have been reported in the treatment of various cancers including non-small cell lung cancer(NSCLC)and malignant melanoma. However, the risk of reactivity against selfantigens and the high prices of these drugs are major concerns. Previously, PD-L1 protein expression and the number of infiltrating T cells in tumor tissues were investigated by immunohistochemical staining, as biomarkers for therapeutic anti-PD- 1 antibodies. However, further research into the clinical significance of PD-L1 expression in tumor tissues is still required...
September 2016: Gan to Kagaku Ryoho. Cancer & Chemotherapy
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