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https://www.readbyqxmd.com/read/29224155/targeted-bisulfite-sequencing-using-the-seqcap-epi-enrichment-system
#1
Jennifer Wendt, Heidi Rosenbaum, Todd A Richmond, Jeffrey A Jeddeloh, Daniel L Burgess
Cytosine methylation has been shown to have a role in a host of biological processes. In mammalian biology these include stem cell differentiation, embryonic development, genomic imprinting, inflammation, and silencing of transposable elements. Given the central importance of these processes, it is not surprising to find aberrant cytosine methylation patterns associated with many disorders in humans, including cancer, cardiovascular disease, and neurological disease. While whole genome shotgun bisulfite sequencing (WGBS) has recently become feasible, generating high sequence coverage data for the entire genome is expensive, both in terms of money and analysis time, when generally only a small subset of the genome is of interest to most researchers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223757/recent-advances-in-carbon-nanotube-based-electrochemical-biosensors
#2
REVIEW
S Gupta, C N Murthy, C Ratna Prabha
There is an increasing need for rapid, low cost, reusable, reliable and sensitive detection systems for diagnosing infectious diseases, metabolic disorders, rapidly advancing cancers and detecting the presence of environmental pollutants. Most traditional methods are invasive, slow, expensive and laborious, requiring highly specialized instruments. Introduction of biosensors with nanomaterials as transducers of signals have helped in removing the disadvantages associated with traditional detectors. The properties of high mechanical strength, better electrical conductivity and ability to serve as efficient signal transducers make carbon nanotubes (CNTs) ideal material for biosensor applications among the gamut of nanomaterials...
December 6, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29222540/validation-study-of-the-american-joint-committee-on-cancer-eighth-edition-prognostic-stage-compared-with-the-anatomic-stage-in-breast-cancer
#3
Anna Weiss, Mariana Chavez-MacGregor, Daphne Y Lichtensztajn, Min Yi, Audree Tadros, Gabriel N Hortobagyi, Sharon H Giordano, Kelly K Hunt, Elizabeth A Mittendorf
Importance: The American Joint Committee on Cancer (AJCC) eighth edition staging manual introduced a new prognostic stage for breast cancer incorporating biologic factors in addition to traditional anatomic factors. Objective: To perform a validation study of the AJCC eighth edition prognostic stage in a single-institution cohort and a large population database. Design, Setting, and Participants: Patients with breast cancer treated with surgery as an initial intervention were identified in a prospective institutional database from The University of Texas MD Anderson Cancer Center and the California Cancer Registry...
December 7, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/29222346/adiposity-inflammation-and-breast-cancer-pathogenesis-in-asian-women
#4
Neil M Iyengar, I-Chun Chen, Xi K Zhou, Dilip D Giri, Domenick J Falcone, Lisle A Winston, Hanhan Wang, Samantha Williams, Yen-Shen Lu, Tsu-Hsin Hsueh, Ann-Lii Cheng, Clifford A Hudis, Ching-Hung Lin, Andrew J Dannenberg
Obesity is associated with white adipose tissue (WAT) inflammation in the breast, elevated levels of the estrogen biosynthetic enzyme, aromatase, and systemic changes that predispose to breast cancer development. We examined whether WAT inflammation and its associated systemic effects correlate with body fat levels in an Asian population where body mass index (BMI) is not an accurate assessment of obesity and cancer risk. We also investigated whether biologic differences could account for the greater proportion of premenopausal estrogen receptor (ER)-positive breast cancer in Asian versus western countries...
December 8, 2017: Cancer Prevention Research
https://www.readbyqxmd.com/read/29221196/identification-of-cellular-genes-and-pathways-important-for-tumorigenicity-of-hepatocellular-carcinoma-cell-lines-by-proteomic-profiling
#5
Ali Zamani, Huahao Fan, Guangxiang Luo
Hepatocellular carcinoma (HCC) is the most commonly diagnosed malignancy of the liver. A more thorough understanding of HCC pathogenesis will provide novel targets for development of cancer drugs to effectively treat HCC. To further this goal, we carried out a proteomic profiling of HCC cell lines Huh-7.4 and Huh-7.5. These two cell lines were derived from subgenomic HCV RNA-replicating Huh-7 cells upon clearance of HCV RNA by antiviral drug treatment. Initially, the tumorigenicity of each cell line was determined and compared in parallel in the same immunedeficient mice...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220122/expression-profile-analysis-of-long-noncoding-rna-in-acute-myeloid-leukemia-by-microarray-and-bioinformatics
#6
Yuandong Feng, Ying Shen, Hongli Chen, Xiaman Wang, Ru Zhang, Yue Peng, Xiaoru Lei, Tian Liu, Jing Liu, Liufang Gu, Fangxia Wang, Yun Yang, Ju Bai, Jianli Wang, Wanhong Zhao, Aili He
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides, which are involved in tumorigenesis and play a key role in cancer progression. To determine whether lncRNAs are involved in acute myeloid leukemia (AML), we analyzed the expression profile of lncRNAs and mRNAs in AML. 5 pairs of AML patients and iron deficiency anemia (IDA) controls were screened by microarray. Through co-expression analysis, differently expressed transcripts were done into modules, and lncRNAs got the functional annotations...
December 8, 2017: Cancer Science
https://www.readbyqxmd.com/read/29218918/annotating-gene-sets-by-mining-large-literature-collections-with-protein-networks
#7
Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W Huang, Jiawei Han, Jian Peng, Trey Ideker
Analysis of patient genomes and transcriptomes routinely recognizes new gene sets associated with human disease. Here we present an integrative natural language processing system which infers common functions for a gene set through automatic mining of the scientific literature with biological networks. This system links genes with associated literature phrases and combines these links with protein interactions in a single heterogeneous network. Multiscale functional annotations are inferred based on network distances between phrases and genes and then visualized as an ontology of biological concepts...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218879/an-ultra-fast-and-scalable-quantification-pipeline-for-transposable-elements-from-next-generation-sequencing-data
#8
Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M Shulman, Zhandong Liu
Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative disease, and aging. Rapid development in RNA-sequencing technology has enabled us, for the first time, to study the activity of TE at the systems level.However, efficient TE analysis tools are not yet developed. In this work, we developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218871/extracting-a-biologically-relevant-latent-space-from-cancer-transcriptomes-with-variational-autoencoders
#9
Gregory P Way, Casey S Greene
The Cancer Genome Atlas (TCGA) has profiled over 10,000 tumors across 33 different cancer-types for many genomic features, including gene expression levels. Gene expression measurements capture substantial information about the state of each tumor. Certain classes of deep neural network models are capable of learning a meaningful latent space. Such a latent space could be used to explore and generate hypothetical gene expression profiles under various types of molecular and genetic perturbation. For example, one might wish to use such a model to predict a tumor's response to specific therapies or to characterize complex gene expression activations existing in differential proportions in different tumors...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29217849/life-time-dosimetric-assessment-for-mice-and-rats-exposed-in-reverberation-chambers-of-the-2-year-ntp-cancer-bioassay-study-on-cell-phone-radiation
#10
Yijian Gong, Myles Capstick, Sven Kuehn, Perry Wilson, John Ladbury, Galen Koepke, David L McCormick, Ronald L Melnick, Niels Kuster
In this paper, we present the detailed life-time dosimetry analysis for rodents exposed in the reverberation exposure system designed for the two-year cancer bioassay study conducted by the National Toxicology Program of the National Institute of Environmental Health Sciences. The study required the well-controlled and characterized exposure of individually housed, unrestrained mice at 1900 MHz and rats at 900 MHz, frequencies chosen to give best uniformity exposure of organs and tissues. The wbSAR, the peak spatial SAR and the organ specific SAR as well as the uncertainty and variation due to the exposure environment, differences in the growth rates, and animal posture were assessed...
December 2017: IEEE Transactions on Electromagnetic Compatibility
https://www.readbyqxmd.com/read/29216759/pharmaceutical-potential-of-quantum-dots
#11
Swati Jha, Prateek Mathur, Suman Ramteke, Narendra Kumar Jain
Quantum dots (QDs) or fluorescent nanocrystals are designed nanoparticles that are promising for several biological and bio-medical applications as well as drug delivery and simultaneous cellular imaging. QD's have exhibited promising potential primarily in receptor based targeting as a result of their distinctive physicochemical properties. Functionalized QDs (f-QDs) have been developed as effective, safe, nano-sized smart systems to deliver a wide range of bio-actives. Surface modified fluorescent carbon QDs with surface modification have attracted attention as targeting ligand to accomplish cellular targeting with enhanced specificity...
December 7, 2017: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/29216340/incorporating-blood-based-liquid-biopsy-information-into-cancer-staging-time-for-a-tnmb-system
#12
M Yang, M E Forbes, R L Bitting, S S O'Neill, P-C Chou, U Topaloglu, L D Miller, G A Hawkins, S C Grant, B R DeYoung, W J Petty, K Chen, B C Pasche, W Zhang
Tissue biopsy is the standard diagnostic procedure for cancer. Biopsy may also provide material for genotyping, which can assist in the diagnosis and selection of targeted therapies but may fall short in cases of inadequate sampling, particularly from highly heterogeneous tumors. Traditional tissue biopsy suffers greater limitations in its prognostic capability over the course of disease, most obviously as an invasive procedure with potential complications, but also with respect to probable tumor clonal evolution and metastasis over time from initial biopsy evaluation...
December 5, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29216271/genomic-and-phenotypic-characteristics-of-swedish-c-jejuni-water-isolates
#13
Anna Nilsson, Cecilia Johansson, Astrid Skarp, René Kaden, Lars Engstrand, Hilpi Rautelin
Campylobacter jejuni is the most common cause of bacterial gastroenteritis. Major reservoirs are warm-blooded animals, poultry in particular, but Campylobacter can also be transmitted via water. In this paper, we have taken a closer look at the biology and potential virulence of C. jejuni water isolates. Seven C. jejuni isolates from incoming surface water at water plants in Sweden were characterized with whole genome sequencing and phenotypical testing. Multi locus sequence typing analysis revealed that these isolates belonged to groups known to include both common (ST48CC) and uncommon (ST1275CC, ST683, ST793 and ST8853) human pathogens...
2017: PloS One
https://www.readbyqxmd.com/read/29215700/novel-smoothened-antagonists-as-anti-neoplastic-agents-for-the-treatment-of-osteosarcoma
#14
Giulia Bernardini, Michela Geminiani, Silvia Gambassi, Maurizio Orlandini, Elena Petricci, Barbara Marzocchi, Marcella Laschi, Maurizio Taddei, Fabrizio Manetti, Annalisa Santucci
Osteosarcoma (OS) is an ultra-rare highly malignant tumor of the skeletal system affecting mainly children and young adults and it is characterized by an extremely aggressive clinical course. OS patients are currently treated with chemotherapy and complete surgical resection of cancer tissue. However, resistance to chemotherapy and the recurrence of disease, as pulmonary metastasis, remain the two greatest challenges in the management and treatment of this tumour. For these reasons, it is of primary interest to find alternative therapeutic strategies for OS...
December 7, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29215164/magnetically-guided-self-assembly-and-coding-of-3d-living-architectures
#15
Alessandro Tocchio, Naside Gozde Durmus, Kaushik Sridhar, Vigneshwaran Mani, Bukre Coskun, Rami El Assal, Utkan Demirci
In nature, cells self-assemble at the microscale into complex functional configurations. This mechanism is increasingly exploited to assemble biofidelic biological systems in vitro. However, precise coding of 3D multicellular living materials is challenging due to their architectural complexity and spatiotemporal heterogeneity. Therefore, there is an unmet need for an effective assembly method with deterministic control on the biomanufacturing of functional living systems, which can be used to model physiological and pathological behavior...
December 7, 2017: Advanced Materials
https://www.readbyqxmd.com/read/29211454/latent-warheads-for-targeted-cancer-therapy-design-and-synthesis-of-pro-pyrrolobenzodiazepines-and-conjugates
#16
Iontcho R Vlahov, Longwu Qi, Paul J Kleindl, Hari K Santhapuram, Albert Felten, Garth L Parham, Kevin Wang, Fei You, Jeremy F Vaughn, Spencer J Hahn, Hanna F Klein, Marilynn Vetzel, Joseph A Reddy, Melissa Nelson, Jeff Nicoson, Christopher P Leamon
Pyrrolobenzodiazepines (PBDs) and their dimers (bis-PBDs) have emerged as some of the most potent chemotherapeutic compounds, and are currently under development as novel payloads in antibody-drug conjugates (ADCs). However, when used as stand-alone therapeutics or as warheads for small molecule drug conjugates (SMDCs), dose-limiting toxicities are often observed. As an elegant solution to this inherent problem, we designed diazepine-ring-opened conjugated prodrugs lacking the imine moiety. Once the prodrug (pro-PBD) conjugate enters a targeted cell, cleavage of the linker system triggers the generation of a reactive intermediate possessing an aldehyde and aromatic amine...
December 6, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29210428/lectin-gated-and-glycan-functionalized-mesoporous-silica-nanocontainers-for-targeting-cancer-cells-overexpressing-lewis-x-antigen
#17
R Bhat, I García, E Aznar, B Arnaiz, M C Martínez-Bisbal, L M Liz-Marzán, S Penadés, R Martínez-Máñez
Gated mesoporous silica nanoparticles can deliver payload upon the application of a predefined stimulus, and therefore are promising drug delivery systems. Despite their important role, relatively low emphasis has been placed on the design of gating systems that actively target carbohydrate tumor cell membrane receptors. We describe herein a new Lewis X (Lex) antigen-targeted delivery system comprising mesoporous silica nanoparticles (MSNs) loaded with ATTO 430LS dye, functionalized with a Lex derivative (1) and capped with a fucose-specific carbohydrate-binding protein (Aleuria aurantia lectin (AAL))...
December 6, 2017: Nanoscale
https://www.readbyqxmd.com/read/29209560/pd-l1-and-epithelial-mesenchymal-transition-in-circulating-tumor-cells-from-non-small-cell-lung-cancer-patients-a-molecular-shield-to-evade-immune-system
#18
Cristina Raimondi, Guido Carpino, Chiara Nicolazzo, Angela Gradilone, Walter Gianni, Alain Gelibter, Eugenio Gaudio, Enrico Cortesi, Paola Gazzaniga
The programmed cell death 1 (PD-1)/PD-1 ligand 1 (PD-L1) pathway has emerged as a critical inhibitory pathway regulating T-cell response in non-small-cell lung cancer (NSCLC), and the development of PD-1/PD-L1 inhibitors has changed the landscape of NSCLC therapy. Nevertheless, the high degree of non-responders demonstrates that we are still far from completely understanding the events underlying tumor immune resistance. Although the expression of PD-L1 in tumor tissue has been correlated with clinical response to anti PD-1 inhibitors, the ability of this marker to discriminate the subgroup of patients who derive benefit from immunotherapy is suboptimal...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29209467/biological-roles-and-potential-applications-of-immune-cell-derived-extracellular-vesicles
#19
REVIEW
Chuan Wen, Robert C Seeger, Muller Fabbri, Larry Wang, Alan S Wayne, Ambrose Y Jong
Extracellular vesicles (EVs) deliver bioactive macromolecules (i.e. proteins, lipids and nucleic acids) for intercellular communication in multicellular organisms. EVs are secreted by all cell types including immune cells. Immune cell-derived EVs modulate diverse aspects of the immune system to either enhance or suppress immune activities. The extensive effects of immune cell-derived EVs have become the focus of great interest for various nano-biomedical applications, ranging from the medical use of nanoplatform-based diagnostic agents to the development of therapeutic interventions as well as vaccine applications, and thus may be ideal for 'immune-theranostic'...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/29209003/prostate-cancer-diagnosis-and-characterization-with-mass-spectrometry-imaging
#20
REVIEW
Annika Kurreck, Lindsey A Vandergrift, Taylor L Fuss, Piet Habbel, Nathalie Y R Agar, Leo L Cheng
BACKGROUND: Prostate cancer (PCa), the most common cancer and second leading cause of cancer death in American men, presents the clinical challenge of distinguishing between indolent and aggressive tumors for proper treatment. PCa presents significant alterations in metabolic pathways that can potentially be measured using techniques like mass spectrometry (MS) or MS imaging (MSI) and used to characterize PCa aggressiveness. MS quantifies metabolomic, proteomic, and lipidomic profiles of biological systems that can be further visualized for their spatial distributions through MSI...
December 5, 2017: Prostate Cancer and Prostatic Diseases
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