keyword
MENU ▼
Read by QxMD icon Read
search

Integrative genomics cancer

keyword
https://www.readbyqxmd.com/read/29444297/draft-genomes-of-two-blister-beetles-genus-hycleus-harvested-for-the-potent-blistering-agent-cantharidin
#1
Yuan-Ming Wu, Jiang Li, Xiang-Sheng Chen
Background: Commonly known as blister beetles or Spanish fly, there are more than 1,500 species in the Meloidae family (Hexapoda: Coleoptera: Tenebrionoidea) that produce the potent defensive blistering agent cantharidin. Cantharidin and its derivatives have been used to treat cancers, such as liver, stomach, lung and esophageal cancers. Hycleus cichorii and Hycleus phaleratus are the most commercially important blister beetles in China due to their ability to biosynthesize this potent vesicant...
February 10, 2018: GigaScience
https://www.readbyqxmd.com/read/29443391/human-papillomavirus-genome-integration-in-squamous-carcinogenesis-what-have-next-generation-sequencing-studies-taught-us
#2
REVIEW
Ian J Groves, Nicholas Coleman
Human papillomavirus (HPV) infection is associated with ~5% of all human cancers, including a range of squamous cell carcinomas (SCCs). Persistent infection by high-risk HPVs (HRHPVs) is associated with the integration of virus genomes (which are usually stably maintained as extrachromosomal episomes) into host chromosomes. Although HRHPV integration rates differ across human sites of infection, this process appears to be an integral event in HPV-associated neoplastic progression, leading to deregulation of virus oncogene expression, host gene expression modulation and further genomic instability...
February 14, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29441649/assessing-the-genome-integrity-of-human-induced-pluripotent-stem-cells-what-quality-control-metrics
#3
REVIEW
Said Assou, Julien Bouckenheimer, John De Vos
Human induced pluripotent stem cells (hiPSCs) have the potential to differentiate virtually into any cell type in unlimited quantities. Therefore, they are ideal for in vitro tissue modeling or to produce cells for clinical use. Importantly, and differently from immortalized and cancer cell lines, the hiPSC genome scrupulously reproduces that of the cell from which they were derived. However, hiPSCs can develop genetic abnormalities during reprogramming or prolonged cell culture, such as aneuploidies or oncogenic mutations (e...
February 14, 2018: Stem Cells
https://www.readbyqxmd.com/read/29440447/a-human-genome-wide-rnai-screen-reveals-diverse-modulators-that-mediate-ire1%C3%AE-xbp1-activation
#4
Zhifen Yang, Jing Zhang, Dadi Jiang, Purvesh Khatri, David E Solow-Cordero, Diego A S Toesca, Constantinos Koumenis, Nicholas C Denko, Amato J Giaccia, Quynh-Thu Le, Albert C Koong
Activation of the unfolded protein response (UPR) signaling pathways is linked to multiple human diseases including cancer. The inositol-requiring kinase 1 (IRE1)-X-box binding protein 1 (XBP1) pathway is the most evolutionarily conserved of the three major signaling branches of the UPR. Here, we performed a genome-wide siRNA screen to obtain a systematic assessment of genes integrated in the IRE1-XBP1 axis. We monitored the expression of an XBP1-luciferase chimeric protein in which luciferase was fused in-frame with the spliced (active) form of XBP1...
February 9, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29440233/comprehensive-characterisation-of-compartment-specific-long-non-coding-rnas-associated-with-pancreatic-ductal-adenocarcinoma
#5
Luis Arnes, Zhaoqi Liu, Jiguang Wang, Hans Carlo Maurer, Irina Sagalovskiy, Marta Sanchez-Martin, Nikhil Bommakanti, Diana C Garofalo, Dina A Balderes, Lori Sussel, Kenneth P Olive, Raul Rabadan
OBJECTIVE: Pancreatic ductal adenocarcinoma (PDA) is a highly metastatic disease with limited therapeutic options. Genome and transcriptome analyses have identified signalling pathways and cancer driver genes with implications in patient stratification and targeted therapy. However, these analyses were performed in bulk samples and focused on coding genes, which represent a small fraction of the genome. DESIGN: We developed a computational framework to reconstruct the non-coding transcriptome from cross-sectional RNA-Seq, integrating somatic copy number alterations (SCNA), common germline variants associated to PDA risk and clinical outcome...
February 10, 2018: Gut
https://www.readbyqxmd.com/read/29439884/a-quantitative-ct-imaging-signature-predicts-survival-and-complements-established-prognosticators-in-stage-i-non-small-cell-lung-cancer
#6
Juheon Lee, Bailiang Li, Yi Cui, Xiaoli Sun, Jia Wu, Hui Zhu, Jinming Yu, Michael F Gensheimer, Billy W Loo, Maximilian Diehn, Ruijiang Li
PURPOSE: Prognostic biomarkers are needed to guide the management of early-stage non-small cell lung cancer (NSCLC). This work aims to develop an image-based prognostic signature and assess its complementary value to existing biomarkers. METHODS AND MATERIALS: We retrospectively analyzed data of stage I NSCLC in 8 cohorts. On the basis of an analysis of 39 computed tomography (CT) features characterizing tumor and its relation to neighboring pleura, we developed a prognostic signature in an institutional cohort (n = 117) and tested it in an external cohort (n = 88)...
January 10, 2018: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/29438991/genetic-hitchhiking-and-population-bottlenecks-contribute-to-prostate-cancer-disparities-in-men-of-african-descent
#7
Joseph Lachance, Ali J Berens, Matthew E B Hansen, Andrew K Teng, Sarah A Tishkoff, Timothy R Rebbeck
Prostate cancer (CaP) incidence and mortality rates in African and African American men are greatly elevated compared to other ethnicities. This disparity is likely explained by a combination of social, environmental, and genetic factors. A large number of susceptibility loci have been reported by genome-wide association studies (GWAS), but the contribution of these loci to CaP disparities is unclear. Here we investigated the population structure of 68 previously reported GWAS loci and calculated Genetic Disparity Contribution (GDC) statistics to identify SNPs that contribute the most to differences in CaP risk across populations...
February 8, 2018: Cancer Research
https://www.readbyqxmd.com/read/29438696/the-integrated-genomic-landscape-of-thymic-epithelial-tumors
#8
Milan Radovich, Curtis R Pickering, Ina Felau, Gavin Ha, Hailei Zhang, Heejoon Jo, Katherine A Hoadley, Pavana Anur, Jiexin Zhang, Mike McLellan, Reanne Bowlby, Thomas Matthew, Ludmila Danilova, Apurva M Hegde, Jaegil Kim, Mark D M Leiserson, Geetika Sethi, Charles Lu, Michael Ryan, Xiaoping Su, Andrew D Cherniack, Gordon Robertson, Rehan Akbani, Paul Spellman, John N Weinstein, D Neil Hayes, Ben Raphael, Tara Lichtenberg, Kristen Leraas, Jean Claude Zenklusen, Junya Fujimoto, Cristovam Scapulatempo-Neto, Andre L Moreira, David Hwang, James Huang, Mirella Marino, Robert Korst, Giuseppe Giaccone, Yesim Gokmen-Polar, Sunil Badve, Arun Rajan, Philipp Ströbel, Nicolas Girard, Ming S Tsao, Alexander Marx, Anne S Tsao, Patrick J Loehrer
Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis...
February 12, 2018: Cancer Cell
https://www.readbyqxmd.com/read/29438472/klinefelter-syndrome-integrating-genetics-neuropsychology-and-endocrinology
#9
Claus H Gravholt, Simon Chang, Mikkel Wallentin, Jens Fedder, Philip Moore, Anne Skakkebæk
Although first identified over 70 years ago, Klinefelter syndrome (KS) continue to pose significant diagnostic challenges, as many patients are still misdiagnosed, or remain undiagnosed. In fact, as few as 25% of KS patients are accurately diagnosed, and most of these diagnoses are not made until adulthood. Classic characteristics of KS include small testes, infertility, hypergonadothropic hypogonadism, and cognitive impairment. However, the pathophysiology behind KS is not well understood, although genetic effects are also thought to play a role...
February 9, 2018: Endocrine Reviews
https://www.readbyqxmd.com/read/29436659/cholangiocarcinoma%C3%A2-associated-genes-identified-by-integrative-analysis-of-gene-expression-data
#10
Wei Zhong, Lianzhi Dai, Jing Liu, Song Zhou
Cholangiocarcinoma (CCA) is characterized by delayed diagnosis and poor survival rate. Research efforts have focused on novel diagnostic technologies for this type of cancer. Transcriptomic microarray technology is a useful research strategy for investigating the molecular properties of CCA. The objective of the present study was to identify candidate biomarkers with high potential for clinical application in CCA using a meta‑analysis‑based approach. Gene expression profiles of CCA were downloaded from the Gene Expression Omnibus database for integrated analysis...
February 12, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29435981/forty-nine-gastric-cancer-cell-lines-with-integrative-genomic-profiling-for-development-of-c-met-inhibitor
#11
Hyun Jeong Kim, Sun Kyoung Kang, Woo Sun Kwon, Tae Soo Kim, Inhye Jeong, Hei-Cheul Jeung, Michael Kragh, Ivan D Horak, Hyun Cheol Chung, Sun Young Rha
Receptor tyrosine kinase MET (c-MET) has received considerable attention as a potential target for gastric cancer (GC) therapy and a number of c-MET inhibitors have been developed. For successful drug development, proper preclinical studies especially using patient derived cancer cell lines are very important. We profiled MET and MET-related characteristics in 49 GC cell lines to utilize them as models in preclinical studies of GC. Forty-nine cell lines were analyzed for genetic, biological, and molecular status to characterize MET and MET-related molecules...
February 13, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29435938/transgene-like-animal-models-using-intronic-micrornas
#12
Shi-Lung Lin, Shin-Ju E Chang, Shao-Yao Ying
Transgenic animal models are valuable tools for testing gene functions and drug mechanisms in vivo. They are also the best similitude for a human body for etiological and pathological research of diseases. All pharmaceutically developed medicines must be proven to be safe and effective in animals before approval by the Food and Drug Administration (FDA) to be used in clinical trials. To this end, the transgenic animal models of diseases serve as the front line of drug evaluation. However, there is currently no transgenic animal model for microRNA (miRNA)-related research...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29435060/screening-of-foxd3-targets-in-lung-cancer-via-bioinformatics-analysis
#13
Wenhua Jiang, Pengfei Liu, Xiaodong Li
The purpose of the present study was to explore the targets of forkhead box D3 (FOXD3) in lung cancer, and thus contribute to the diagnosis and therapy of the disease. The gene expression profile of GSE64513 was downloaded from the Gene Expression Omnibus database. The dataset contained 3 FOXD3 knockout A549 lung cancer cell samples and 3 normal A549 cell samples. The differentially expressed genes (DEGs) between the FOXD3-knockout and normal A549 cells were identified using the limma package in R. The alternative splicing genes (ASGs) in FOXD3-knockout samples were identified by Replicate Multivariate Analysis of Transcript Splicing software...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434842/comprehensive-characterization-of-cancer-genes-in-hepatocellular-carcinoma-genomes
#14
Zhihao Zhang, Liping Xu, Changyu Sun
The present study was performed to detect moderate or low-frequency mutated cancer driver genes in hepatocellular carcinoma (HCC), using OncodriveFM and Dendrix. Following this, integrated analyses were conducted on these novel cancer driver genes. A total of 112,980 somatic mutations were retrieved from TCGA and classified into 11 categories based on their function. Driver genes and pathways were predicted by OncodriveFM and Dendrix, followed by differential expression, DNA-methylation, copy number variations and survival analyses...
February 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434705/identification-of-a-progression-associated-long-non-coding-rna-signature-for-predicting-the-prognosis-of-lung-squamous-cell-carcinoma
#15
Yanyan Wang, Fang Yang, Yongzhi Zhuang
Long non-coding RNAs (lncRNAs) have been indicated to have prognostic roles in various cancer types. However, the association between lncRNAs and lung squamous cell carcinoma (LSCC) progression, and the prognostic value of lncRNAs as a marker for early detection of LSCC have not been systematically investigated. The present study performed a genome-wide comparative analysis in order to determine the expression profiles of 10,207 lncRNAs to investigate the expression patterns between patients with early stages of LSCC (stage I-II) and those with late-stage disease (stage III-IV)...
February 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29434467/genomic-analysis-using-regularized-regression-in-high-grade-serous-ovarian-cancer
#16
Yanina Natanzon, Madalene Earp, Julie M Cunningham, Kimberly R Kalli, Chen Wang, Sebastian M Armasu, Melissa C Larson, David Dl Bowtell, Dale W Garsed, Brooke L Fridley, Stacey J Winham, Ellen L Goode
High-grade serous ovarian cancer (HGSOC) is a complex disease in which initiation and progression have been associated with copy number alterations, epigenetic processes, and, to a lesser extent, germline variation. We hypothesized that, when summarized at the gene level, tumor methylation and germline genetic variation, alone or in combination, influence tumor gene expression in HGSOC. We used Elastic Net (ENET) penalized regression method to evaluate these associations and adjust for somatic copy number in 3 independent data sets comprising tumors from more than 470 patients...
2018: Cancer Informatics
https://www.readbyqxmd.com/read/29433427/methcna-a-database-for-integrating-genomic-and-epigenomic-data-in-human-cancer
#17
Gaofeng Deng, Jian Yang, Qing Zhang, Zhi-Xiong Xiao, Haoyang Cai
BACKGROUND: The integration of DNA methylation and copy number alteration data promises to provide valuable insight into the underlying molecular mechanisms responsible for cancer initiation and progression. However, the generation and processing of these datasets are costly and time-consuming if carried out separately. The Illumina Infinium HumanMethylation450 BeadChip, initially designed for the evaluation of DNA methylation levels, allows copy number variant calling using bioinformatics tools...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29431110/the-personal-genome-project-canada-findings-from-whole-genome-sequences-of-the-inaugural-56-participants
#18
Miriam S Reuter, Susan Walker, Bhooma Thiruvahindrapuram, Joe Whitney, Iris Cohn, Neal Sondheimer, Ryan K C Yuen, Brett Trost, Tara A Paton, Sergio L Pereira, Jo-Anne Herbrick, Richard F Wintle, Daniele Merico, Jennifer Howe, Jeffrey R MacDonald, Chao Lu, Thomas Nalpathamkalam, Wilson W L Sung, Zhuozhi Wang, Rohan V Patel, Giovanna Pellecchia, John Wei, Lisa J Strug, Sherilyn Bell, Barbara Kellam, Melanie M Mahtani, Anne S Bassett, Yvonne Bombard, Rosanna Weksberg, Cheryl Shuman, Ronald D Cohn, Dimitri J Stavropoulos, Sarah Bowdin, Matthew R Hildebrandt, Wei Wei, Asli Romm, Peter Pasceri, James Ellis, Peter Ray, M Stephen Meyn, Nasim Monfared, S Mohsen Hosseini, Ann M Joseph-George, Fred W Keeley, Ryan A Cook, Marc Fiume, Hin C Lee, Christian R Marshall, Jill Davies, Allison Hazell, Janet A Buchanan, Michael J Szego, Stephen W Scherer
BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant...
February 5, 2018: CMAJ: Canadian Medical Association Journal, Journal de L'Association Medicale Canadienne
https://www.readbyqxmd.com/read/29430186/identification-of-genomic-expression-differences-between-right-sided-and-left-sided-colon-cancer-based-on-bioinformatics-analysis
#19
Qiliang Peng, Kaisu Lin, Tao Chang, Li Zou, Pengfei Xing, Yuntian Shen, Yaqun Zhu
Introduction: More and more findings have demonstrated that right-sided colon cancers (RCC) and left-sided colon cancers (LCC) are distinct clinical and biological entities and suggest that they should be treated as different diseases. However, the reasons why RCC and LCC harbor different clinical and biological features remain unclear. Materials and methods: To identify the genomic expression differences between RCC and LCC and uncover the mechanisms underlying these differences, we chose the gene expression profiles of GSE14333 from the Gene Expression Omnibus (GEO) database as an object of study...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29429988/the-deubiquitylase-usp15-regulates-topoisomerase-ii-alpha-to-maintain-genome-integrity
#20
Andrew B Fielding, Matthew Concannon, Sarah Darling, Emma V Rusilowicz-Jones, Joseph J Sacco, Ian A Prior, Michael J Clague, Sylvie Urbé, Judy M Coulson
Ubiquitin-specific protease 15 (USP15) is a widely expressed deubiquitylase that has been implicated in diverse cellular processes in cancer. Here we identify topoisomerase II (TOP2A) as a novel protein that is regulated by USP15. TOP2A accumulates during G2 and functions to decatenate intertwined sister chromatids at prophase, ensuring the replicated genome can be accurately divided into daughter cells at anaphase. We show that USP15 is required for TOP2A accumulation, and that USP15 depletion leads to the formation of anaphase chromosome bridges...
February 12, 2018: Oncogene
keyword
keyword
24824
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"