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Oncogenomics

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https://www.readbyqxmd.com/read/28067315/kank1-inhibits-cell-growth-by-inducing-apoptosis-though-regulating-cxxc5-in-human-malignant-peripheral-nerve-sheath-tumors
#1
Zhibin Cui, Yingjia Shen, Kenny H Chen, Suresh K Mittal, Jer-Yen Yang, GuangJun Zhang
Malignant peripheral nerve sheath tumors (MPNSTs) are a type of rare sarcomas with a poor prognosis due to its highly invasive nature and limited treatment options. Currently there is no targeted-cancer therapy for this type of malignancy. Thus, it is important to identify more cancer driver genes that may serve as targets of cancer therapy. Through comparative oncogenomics, we have found that KANK1 was a candidate tumor suppressor gene (TSG) for human MPNSTs. Although KANK1 is known as a cytoskeleton regulator, its tumorigenic function in MPNSTs remains largely unknown...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28067031/informed-consent-the-case-of-%C3%A2-omics%C3%A2-literacy
#2
Marilyn Hammer
The world of “-omics” is vastly changing the landscape of accelerated research and its translation to patient care. Understanding this complex science, particularly in the world of oncogenomics, can be daunting. Questions arise pertaining to how nurses can best educate patients who are forced to make difficult decisions without fully understanding to what they are consenting. This article follows a patient story that drives home the need to improve -omics literacy.
6, 2017: Oncology Nursing Forum
https://www.readbyqxmd.com/read/28050146/personalized-oncogenomics-in-the-management-of-gastrointestinal-carcinomas-early-experiences-from-a-pilot-study
#3
B S Sheffield, B Tessier-Cloutier, H Li-Chang, Y Shen, E Pleasance, K Kasaian, Y Li, S J M Jones, H J Lim, D J Renouf, D G Huntsman, S Yip, J Laskin, M Marra, D F Schaeffer
BACKGROUND: Gastrointestinal carcinomas are genomically complex cancers that are lethal in the metastatic setting. Whole-genome and transcriptome sequencing allow for the simultaneous characterization of multiple oncogenic pathways. METHODS: We report 3 cases of metastatic gastrointestinal carcinoma in patients enrolled in the Personalized Onco-Genomics program at the BC Cancer Agency. Real-time genomic profiling was combined with clinical expertise to diagnose a carcinoma of unknown primary, to explore treatment response to bevacizumab in a colorectal cancer, and to characterize an appendiceal adenocarcinoma...
December 2016: Current Oncology
https://www.readbyqxmd.com/read/27997009/-genomics-of-lung-adenocarcinoma-pathogenetic-significance-and-clinical-applications
#4
Raffaele Palmirotta, Silvana Acquafredda, Antonella Argentiero, Claudia Carella, Laura Lanotte, Nicla Pappagallo, Davide Quaresmini, Franco Silvestris
Diagnostic and therapeutic approaches to non small cell lung cancer (NSCLC), especially adenocarcinoma, have recently undergone dramatic evolution according to the tremendous amount of molecular data collected on this cancer. In fact, the application of oncogenomics has identified novel molecular subtypes of NSCLC and led the way to diagnostic criteria based on the expression of specific genetic alterations that can provide prognostic and specific indications to the molecular targeted therapies. In NSCLC, several genes show "driver" molecular alterations that confer oncogenic potential to progenitor cells through the enrollment of metabolic pathways critical for cell proliferation and tumor development...
December 2016: Recenti Progressi in Medicina
https://www.readbyqxmd.com/read/27798239/phosphatidylinositol-4-kinase-ii%C3%AE-negatively-regulates-invadopodia-formation-and-suppresses-an-invasive-cellular-phenotype
#5
Ganiyu Olabanji Alli-Balogun, Christina A Gewinner, Ruth Jacobs, Janos Kriston-Vizi, Mark G Waugh, Shane Minogue
The type II phosphatidylinositol 4-kinase (PI4KII) enzymes synthesize the lipid phosphatidylinositol 4-phosphate (PI(4)P), which has been detected at the Golgi complex and endosomal compartments and recruits clathrin adaptors. Despite common mechanistic similarities between the isoforms, the extent of their redundancy is unclear. We found that depletion of PI4KIIα and PI4KIIβ using small interfering RNA led to actin remodeling. Depletion of PI4KIIβ also induced the formation of invadopodia containing membrane type I matrix metalloproteinase (MT1-MMP)...
December 15, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27783941/mek-inhibitors-reverse-growth-of-embryonal-brain-tumors-derived-from-oligoneural-precursor-cells
#6
Katarzyna Modzelewska, Elena F Boer, Timothy L Mosbruger, Daniel Picard, Daniela Anderson, Rodney R Miles, Mitchell Kroll, William Oslund, Theodore J Pysher, Joshua D Schiffman, Randy Jensen, Cicely A Jette, Annie Huang, Rodney A Stewart
Malignant brain tumors are the leading cause of cancer-related deaths in children. Primitive neuroectodermal tumors of the CNS (CNS-PNETs) are particularly aggressive embryonal tumors of unknown cellular origin. Recent genomic studies have classified CNS-PNETs into molecularly distinct subgroups that promise to improve diagnosis and treatment; however, the lack of cell- or animal-based models for these subgroups prevents testing of rationally designed therapies. Here, we show that a subset of CNS-PNETs co-express oligoneural precursor cell (OPC) markers OLIG2 and SOX10 with coincident activation of the RAS/MAPK (mitogen-activated protein kinase) pathway...
October 25, 2016: Cell Reports
https://www.readbyqxmd.com/read/27746730/using-pharmacogenomic-databases-for-discovering-patient-target-genes-and-small-molecule-candidates-to-cancer-therapy
#7
José E Belizário, Beatriz A Sangiuliano, Marcela Perez-Sosa, Jennifer M Neyra, Dayson F Moreira
With multiple omics strategies being applied to several cancer genomics projects, researchers have the opportunity to develop a rational planning of targeted cancer therapy. The investigation of such numerous and diverse pharmacogenomic datasets is a complex task. It requires biological knowledge and skills on a set of tools to accurately predict signaling network and clinical outcomes. Herein, we describe Web-based in silico approaches user friendly for exploring integrative studies on cancer biology and pharmacogenomics...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/27697861/sik2-restricts-autophagic-flux-to-support-triple-negative-breast-cancer-survival
#8
Kimberly E Maxfield, Jennifer Macion, Hariprasad Vankayalapati, Angelique W Whitehurst
Triple-negative breast cancer (TNBC) is a highly heterogeneous disease with multiple, distinct molecular subtypes that exhibit unique transcriptional programs and clinical progression trajectories. Despite knowledge of the molecular heterogeneity of the disease, most patients are limited to generic, indiscriminate treatment options: cytotoxic chemotherapy, surgery, and radiation. To identify new intervention targets in TNBC, we used large-scale, loss-of-function screening to identify molecular vulnerabilities among different oncogenomic backgrounds...
December 15, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27611943/novel-tumor-suppressor-microrna-at-frequently-deleted-chromosomal-region-8p21-regulates-epidermal-growth-factor-receptor-in-prostate-cancer
#9
Nathan Bucay, Kirandeep Sekhon, Shahana Majid, Soichiro Yamamura, Varahram Shahryari, Z Laura Tabatabai, Kirsten Greene, Yuichiro Tanaka, Rajvir Dahiya, Guoren Deng, Sharanjot Saini
Genomic loss of chromosome (chr) 8p21 region, containing prostate-specific NKX3.1 gene, is a frequent alteration of the prostate cancer (PCa) oncogenome. We propose a novel, paradigm shifting hypothesis that this frequently deleted locus is also associated with a cluster of microRNA genes- miR-3622a/b- that are lost in PCa and play an important mechanistic role in progression and metastasis. In this study, we demonstrate the role of miR-3622b in prostate cancer. Expression analyses in a cohort of PCa clinical specimens and cell lines show that miR-3622b expression is frequently lost in prostate cancer...
September 6, 2016: Oncotarget
https://www.readbyqxmd.com/read/27165352/genomic-approaches-to-zebrafish-cancer
#10
REVIEW
Richard M White
The zebrafish has emerged as an important model for studying cancer biology. Identification of DNA, RNA and chromatin abnormalities can give profound insight into the mechanisms of tumorigenesis and the there are many techniques for analyzing the genomes of these tumors. Here, I present an overview of the available technologies for analyzing tumor genomes in the zebrafish, including array based methods as well as next-generation sequencing technologies. I also discuss the ways in which zebrafish tumor genomes can be compared to human genomes using cross-species oncogenomics, which act to filter genomic noise and ultimately uncover central drivers of malignancy...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27148575/lessons-learned-from-the-application-of-whole-genome-analysis-to-the-treatment-of-patients-with-advanced-cancers
#11
Janessa Laskin, Steven Jones, Samuel Aparicio, Stephen Chia, Carolyn Ch'ng, Rebecca Deyell, Peter Eirew, Alexandra Fok, Karen Gelmon, Cheryl Ho, David Huntsman, Martin Jones, Katayoon Kasaian, Aly Karsan, Sreeja Leelakumari, Yvonne Li, Howard Lim, Yussanne Ma, Colin Mar, Monty Martin, Richard Moore, Andrew Mungall, Karen Mungall, Erin Pleasance, S Rod Rassekh, Daniel Renouf, Yaoqing Shen, Jacqueline Schein, Kasmintan Schrader, Sophie Sun, Anna Tinker, Eric Zhao, Stephen Yip, Marco A Marra
Given the success of targeted agents in specific populations it is expected that some degree of molecular biomarker testing will become standard of care for many, if not all, cancers. To facilitate this, cancer centers worldwide are experimenting with targeted "panel" sequencing of selected mutations. Recent advances in genomic technology enable the generation of genome-scale data sets for individual patients. Recognizing the risk, inherent in panel sequencing, of failing to detect meaningful somatic alterations, we sought to establish processes to integrate data from whole-genome analysis (WGA) into routine cancer care...
October 2015: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27022066/response-to-angiotensin-blockade-with-irbesartan-in-a-patient-with-metastatic-colorectal-cancer
#12
M R Jones, K A Schrader, Y Shen, E Pleasance, C Ch'ng, N Dar, S Yip, D J Renouf, J E Schein, A J Mungall, Y Zhao, R Moore, Y Ma, B S Sheffield, T Ng, S J M Jones, M A Marra, J Laskin, H J Lim
BACKGROUND: A patient suffering from metastatic colorectal cancer, treatment-related toxicity and resistance to standard chemotherapy and radiation was assessed as part of a personalized oncogenomics initiative to derive potential alternative therapeutic strategies. PATIENTS AND METHODS: Whole-genome and transcriptome sequencing was used to interrogate a metastatic tumor refractory to standard treatments of a patient with mismatch repair-deficient metastatic colorectal cancer...
May 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/27006499/sleeping-beauty-transposon-mutagenesis-identifies-genes-that-cooperate-with-mutant-smad4-in-gastric-cancer-development
#13
Haruna Takeda, Alistair G Rust, Jerrold M Ward, Christopher Chin Kuan Yew, Nancy A Jenkins, Neal G Copeland
Mutations in SMAD4 predispose to the development of gastrointestinal cancer, which is the third leading cause of cancer-related deaths. To identify genes driving gastric cancer (GC) development, we performed a Sleeping Beauty (SB) transposon mutagenesis screen in the stomach of Smad4(+/-) mutant mice. This screen identified 59 candidate GC trunk drivers and a much larger number of candidate GC progression genes. Strikingly, 22 SB-identified trunk drivers are known or candidate cancer genes, whereas four SB-identified trunk drivers, including PTEN, SMAD4, RNF43, and NF1, are known human GC trunk drivers...
April 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26716509/integrative-bioinformatic-analyses-of-an-oncogenomic-profile-reveal-the-biology-of-endometrial-cancer-and-guide-drug-discovery
#14
Henry Sung-Ching Wong, Yung-Shun Juan, Mei-Shin Wu, Yan-Feng Zhang, Yu-Wen Hsu, Huang-Hui Chen, Wei-Min Liu, Wei-Chiao Chang
A major challenge in personalized cancer medicine is to establish a systematic approach to translate huge oncogenomic datasets to clinical situations and facilitate drug discovery for cancers such as endometrial carcinoma. We performed a genome-wide somatic mutation-expression association study in a total of 219 endometrial cancer patients from TCGA database, by evaluating the correlation between ~5,800 somatic mutations to ~13,500 gene expression levels (in total, ~78, 500, 000 pairs). A bioinformatics pipeline was devised to identify expression-associated single nucleotide variations (eSNVs) which are crucial for endometrial cancer progression and patient prognoses...
February 2, 2016: Oncotarget
https://www.readbyqxmd.com/read/26506113/mirna-182-and-the-regulation-of-the-glioblastoma-phenotype-toward-mirna-based-precision-therapeutics
#15
Fotini M Kouri, Carissa Ritner, Alexander H Stegh
Glioblastoma (GBM) is an incurable cancer, with survival rates of just 14-16 months after diagnosis. (1) Functional genomics have identified numerous genetic events involved in GBM development. One of these, the deregulation of microRNAs (miRNAs), has been attracting increasing attention due to the multiple biologic processes that individual miRNAs influence. Our group has been studying the role of miR-182 in GBM progression, therapy resistance, and its potential as GBM therapeutic. Oncogenomic analyses revealed that miR-182 is the only miRNA, out of 470 miRNAs profiled by The Cancer Genome Atlas (TCGA) program, which is associated with favorable patient prognosis, neuro-developmental context, temozolomide (TMZ) susceptibility, and most significantly expressed in the least aggressive oligoneural subclass of GBM...
2015: Cell Cycle
https://www.readbyqxmd.com/read/26433552/genetic-testing-and-tissue-banking-for-personalized-oncology-analytical-and-institutional-factors
#16
REVIEW
George Miles, James Rae, Suresh S Ramalingam, John Pfeifer
Personalized oncology, or more aptly precision oncogenomics, refers to the identification and implementation of clinically actionable targets tailored to an individual patient's cancer genomic information. Banking of human tissue and other biospecimens establishes a framework to extract and collect the data essential to our understanding of disease pathogenesis and treatment. Cancer cooperative groups in the United States have led the way in establishing robust biospecimen collection mechanisms to facilitate translational research, and combined with technological advances in molecular testing, tissue banking has expanded from its traditional base in academic research and is assuming an increasingly pivotal role in directing the clinical care of cancer patients...
October 2015: Seminars in Oncology
https://www.readbyqxmd.com/read/26376888/transcriptomic-heterogeneity-in-cancer-as-a-consequence-of-dysregulation-of-the-gene-gene-interaction-network
#17
Wessel N van Wieringen, Aad W van der Vaart
Many pathways are dysregulated in cancer. Dysregulation of the regulatory network results in less control of transcript levels in the cell. Hence, dysregulation is reflected in the heterogeneity of the transcriptome: the more dysregulated the pathway, the more the transcriptomic heterogeneity. We identify four scenarios for a transcriptomic heterogeneity increase (i.e., pathway dysregulation) in cancer: (1) activation of a molecular switch, (2) a structural change in a regulator, (3) a temporal change in a regulator, and (4) weakening of gene-gene interactions...
September 2015: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/26276717/integrated-proteo-genomic-approach-for-early-diagnosis-and-prognosis-of-cancer
#18
REVIEW
Hem D Shukla, Javed Mahmood, Zeljko Vujaskovic
Cancer is the leading cause of mortality among men and women worldwide. Despite the availability of numerous diagnostic techniques for various cancers, the overall survival rate remains low and the majority of patients die due to late diagnosis and advanced stage of the disease. Diagnosing and treating cancer at its early stages ideally during the precancerous phase could significantly increase survival rate with the possibility of cure and prolong survival. Cancer is a genetic disease and it is illicitly activated by the acquisition of somatic DNA lesions and aberrations in genome structure and defects in maintenance and repair...
December 1, 2015: Cancer Letters
https://www.readbyqxmd.com/read/26257864/liver-cancer-oncogenomics-opportunities-and-dilemmas-for-clinical-applications
#19
Jens U Marquardt, Jesper B Andersen
Primary liver cancers are among the most rapidly evolving malignant tumors worldwide. An underlying chronic inflammatory liver disease, which precedes liver cancer development for several decades and frequently creates a pro-oncogenic microenvironment, impairs progress in therapeutic approaches. Molecular heterogeneity of liver cancer is potentiated by a crosstalk between epithelial tumor and stromal cells that complicate translational efforts to unravel molecular mechanisms of hepatocarcinogenesis with a drugable intend...
2015: Hepatic Oncology
https://www.readbyqxmd.com/read/26190583/rna-interference-for-multiple-myeloma-therapy-targeting-signal-transduction-pathways
#20
REVIEW
Jianfeng Guo, Sharon L McKenna, Michael E O'Dwyer, Mary R Cahill, Caitriona M O'Driscoll
INTRODUCTION: Multiple myeloma (MM) is a hematological malignancy characterized by infiltration of malignant plasma cells in the bone marrow (BM) and end-organ damage to the bone, BM, kidney and immune system. Although current treatments have improved the treatment of MM, it still remains an incurable disease. RNA interference (RNAi) effectors such as microRNAs and small interference RNAs have shown potential to selectively downregulate genes implicated in the pathology of a range of diseases...
2016: Expert Opinion on Therapeutic Targets
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