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Cancer system biology

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https://www.readbyqxmd.com/read/28817636/uncovering-robust-patterns-of-microrna-co-expression-across-cancers-using-bayesian-relevance-networks
#1
Parameswaran Ramachandran, Daniel Sánchez-Taltavull, Theodore J Perkins
Co-expression networks have long been used as a tool for investigating the molecular circuitry governing biological systems. However, most algorithms for constructing co-expression networks were developed in the microarray era, before high-throughput sequencing-with its unique statistical properties-became the norm for expression measurement. Here we develop Bayesian Relevance Networks, an algorithm that uses Bayesian reasoning about expression levels to account for the differing levels of uncertainty in expression measurements between highly- and lowly-expressed entities, and between samples with different sequencing depths...
2017: PloS One
https://www.readbyqxmd.com/read/28817310/semaphorins-and-their-roles-in-airway-biology-potential-as-therapeutic-targets
#2
Hesam Movassagh, Forough Khadem, Abdelilah S Gounni
Semaphorins are a large family of proteins originally identified as axon guidance cues which play a crucial role in neural development. They are also ubiquitously expressed beyond the nervous system and contribute to regulation of essential cell functions such as cell migration, proliferation, and adhesion. Binding of semaphorins to their receptors, including plexins and neuropilins, triggers diverse signaling pathways which are involved in the pathogenesis of various diseases from cancer to autoimmune and allergic disorders...
August 17, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28816713/radiation-therapy-to-the-primary-in-metastatic-prostate-cancer-palliation-only-or-altering-tumor-biology
#3
Pierre Blanchard, Alberto Bossi, Karim Fizazi
PURPOSE OF REVIEW: Despite improvement in systemic treatment, the prognosis of men with de novo metastatic prostate cancer remains poor. Treating the local disease may not only reduce the occurrence of local urologic symptoms, but also slow the metastatic process, either by reducing the seeding from the primary tumor or by altering the microenvironment and thus minimizing the formation of new metastatic sites. RECENT FINDINGS: Retrospective and population-based studies have suggested that the addition of local treatment to systemic therapy may improve survival in this patient group...
August 14, 2017: Current Opinion in Urology
https://www.readbyqxmd.com/read/28815904/comparative-in-vitro-study-on-cytotoxicity-of-recombinant-%C3%AE-hairpin-peptides
#4
Denis V Kuzmin, Anna A Emelianova, Mariana B Kalashnikova, Pavel V Panteleev, Sergey V Balandin, Ekaterina O Serebrovskaya, Oksana Yu Belogurova-Ovchinnikova, Tatiana V Ovchinnikova
Natural antimicrobial peptides (AMPs) are important components of the innate immune system with a wide spectrum of biological activity. In this study, we investigated the cytotoxic effect of three recombinant β-hairpin cationic AMPs: arenicin-1 from the polychaeta Arenicola marina, tachyplesin I from the horseshoe crab Tachypleus tridentatus, and gomesin from the spider Acanthoscurria gomesiana. All the three β-hairpin AMPs were overexpressed in E. coli. Different cell lines were incubated with various concentrations of the investigated AMPs in order to evaluate their cytotoxic activity...
August 16, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28815347/the-tumor-stromal-ratio-as-a-strong-prognosticator-for-advanced-gastric-cancer-patients-proposal-of-a-new-tsnm-staging-system
#5
Chunwei Peng, Jiuyang Liu, Guifang Yang, Yan Li
BACKGROUND: Insufficient attention is paid to the underlying tumor microenvironment (TME) evolution, that resulting in tumor heterogeneity and driving differences in cancer aggressiveness and treatment outcomes. The morphological evaluation of the proportion of the stroma at the most invasive part of primary tumor (tumor-stromal ratio, TSR) in cancer is gaining momentum as evidence strengthens for the clinical relevance. METHODS: Tissue samples from the most invasive part of the primary gastric cancer (GC) of 494 patients were analyzed for their TSR, and a new TSNM (tumor-stromal node metastasis) staging system based on patho-biological behaviors was established and assessed...
August 16, 2017: Journal of Gastroenterology
https://www.readbyqxmd.com/read/28815231/fluorescence-activated-cell-sorting-via-a-focused-traveling-surface-acoustic-beam
#6
Zhichao Ma, Yinning Zhou, David J Collins, Ye Ai
Fluorescence activated cell sorting (FACS) has become an essential technique widely exploited in biological studies and clinical applications. However, current FACS systems are quite complex, expensive, bulky, and pose potential sample contamination and biosafety issues due to the generation of aerosols in an open environment. Microfluidic technology capable of precise cell manipulation has great potential to reinvent and miniaturize conventional FACS systems. In this work, we demonstrate a benchtop scale FACS system that makes use of a highly focused traveling surface acoustic wave beam to sort out micron-sized particles and biological cells upon fluorescence interrogation at ∼kHz rates...
August 17, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28813705/the-lncrna-tug1-ezh2-axis-promotes-pancreatic-cancer-cell-proliferation-migration-and-emt-phenotype-formation-through-sponging-mir-382
#7
Liang Zhao, Hongwei Sun, Hongru Kong, Zongjing Chen, Bicheng Chen, Mengtao Zhou
BACKGROUND/AIMS: Pancreatic carcinoma (PC) is the one of the most common and malignant cancers worldwide. LncRNA taurine upregulated gene 1 (TUG1) was initially identified as a transcript upregulated by taurine, and the abnormal expression of TUG1 has been reported in many cancers. However, the biological role and molecular mechanism of TUG1 in PC still needs further investigation. METHODS: Quantitative real-time PCR (qRT-PCR) was performed to measure the expression of TUG1 in PC cell lines and tissues...
August 15, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28813674/an-integrated-systems-biology-approach-identifies-trim25-as-a-key-determinant-of-breast-cancer-metastasis
#8
Logan A Walsh, Mariano J Alvarez, Erich Y Sabio, Marsha Reyngold, Vladimir Makarov, Suranjit Mukherjee, Ken-Wing Lee, Alexis Desrichard, Şevin Turcan, Martin G Dalin, Vinagolu K Rajasekhar, Shuibing Chen, Linda T Vahdat, Andrea Califano, Timothy A Chan
At the root of most fatal malignancies are aberrantly activated transcriptional networks that drive metastatic dissemination. Although individual metastasis-associated genes have been described, the complex regulatory networks presiding over the initiation and maintenance of metastatic tumors are still poorly understood. There is untapped value in identifying therapeutic targets that broadly govern coordinated transcriptional modules dictating metastatic progression. Here, we reverse engineered and interrogated a breast cancer-specific transcriptional interaction network (interactome) to define transcriptional control structures causally responsible for regulating genetic programs underlying breast cancer metastasis in individual patients...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28813442/a-parallel-metaheuristic-for-large-mixed-integer-dynamic-optimization-problems-with-applications-in-computational-biology
#9
David R Penas, David Henriques, Patricia González, Ramón Doallo, Julio Saez-Rodriguez, Julio R Banga
BACKGROUND: We consider a general class of global optimization problems dealing with nonlinear dynamic models. Although this class is relevant to many areas of science and engineering, here we are interested in applying this framework to the reverse engineering problem in computational systems biology, which yields very large mixed-integer dynamic optimization (MIDO) problems. In particular, we consider the framework of logic-based ordinary differential equations (ODEs). METHODS: We present saCeSS2, a parallel method for the solution of this class of problems...
2017: PloS One
https://www.readbyqxmd.com/read/28812721/predicting-evolution
#10
Michael Lässig, Ville Mustonen, Aleksandra M Walczak
The face of evolutionary biology is changing: from reconstructing and analysing the past to predicting future evolutionary processes. Recent developments include prediction of reproducible patterns in parallel evolution experiments, forecasting the future of individual populations using data from their past, and controlled manipulation of evolutionary dynamics. Here we undertake a synthesis of central concepts for evolutionary predictions, based on examples of microbial and viral systems, cancer cell populations, and immune receptor repertoires...
February 21, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28807210/personalized-treatment-in-patients-with-colorectal-liver-metastases
#11
Dimitrios Moris, Timothy M Pawlik
BACKGROUND: Precision Medicine Initiative is a new research effort aiming to offer personalized treatment in many diseases, including cancer. The aim of the present article is to offer novel insights about the role of personalized treatment in patients with colorectal liver metastases (CRLM). METHODS: A review of the literature regarding personalized medicine and colorectal liver metastases was performed mainly in the MEDLINE/PubMed database. RESULTS: Surgical resection remains the only hope for cure of CRLM...
August 2017: Journal of Surgical Research
https://www.readbyqxmd.com/read/28806522/development-of-a-recombinant-multifunctional-biomacromolecule-for-targeted-gene-transfer-to-prostate-cancer-cells
#12
Arash Hatefi, Zahra Karjoo, Alireza Nomani
The objective of this study was to genetically engineer a fully functional single chain fusion peptide composed of motifs from diverse biological and synthetic origins that can perform multiple tasks including DNA condensation, cell targeting, cell transfection, particle shielding from immune system and effective gene transfer to prostate tumors. To achieve the objective, a single chain biomacromolecule (vector) consisted of four repetative units of histone H2A peptide, fusogenic peptide GALA, short elastin-like peptide and PC-3 cell targeting peptide was designed...
August 14, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28805867/coumarin-containing-thermoresponsive-hyaluronic-acid-based-nanogels-as-delivery-systems-for-anticancer-chemotherapy
#13
Talitha F Stefanello, Benoit Couturaud, Anna Szarpak-Jankowska, David Fournier, Benoit Louage, Francielle P Garcia, Celso V Nakamura, Bruno G De Geest, Patrice Woisel, Boudewijn van der Sanden, Rachel Auzély-Velty
Multi-stimuli responsive nanogels based on biocompatible hydrophilic polymers have emerged as promising drug delivery systems to improve anticancer therapy with hydrophobic drugs, through increase of circulating-time in the bloodstream, tumor-targeting and reduction of systemic toxicity. This paper reports on the synthesis, characterization and biological perspectives of light- and thermoresponsive hyaluronic acid (HA)-based nanogels containing coumarin as the photocleavable group. Newly synthesized nanogels exhibited interesting features: formation by a temperature-triggered self-assembly process, successful incorporation of poorly water-soluble molecules, light-responsiveness as demonstrated by a significant shift in the critical aggregation temperature after light irradiation, efficient internalization by cancer cells overexpressing the CD44 receptor of HA, ability to circulate for a prolonged period of time in the bloodstream after intravenous injection in mice and considerable detection in tumor tissues...
August 14, 2017: Nanoscale
https://www.readbyqxmd.com/read/28805741/alcohol-and-cancer-mechanisms-and-therapies
#14
REVIEW
Anuradha Ratna, Pranoti Mandrekar
Several scientific and clinical studies have shown an association between chronic alcohol consumption and the occurrence of cancer in humans. The mechanism for alcohol-induced carcinogenesis has not been fully understood, although plausible events include genotoxic effects of acetaldehyde, cytochrome P450 2E1 (CYP2E1)-mediated generation of reactive oxygen species, aberrant metabolism of folate and retinoids, increased estrogen, and genetic polymorphisms. Here, we summarize the impact of alcohol drinking on the risk of cancer development and potential underlying molecular mechanisms...
August 14, 2017: Biomolecules
https://www.readbyqxmd.com/read/28805211/all-atom-md-indicates-ion-dependent-behavior-of-therapeutic-dna-polymer
#15
Ryan L Melvin, William H Gmeiner, Freddie R Salsbury
Understanding the efficacy of and creating delivery mechanisms for therapeutic nucleic acids requires understanding structural and kinetic properties which allow these polymers to promote the death of cancerous cells. One molecule of interest is a 10 mer of FdUMP (5-fluoro-2'-deoxyuridine-5'-O-monophosphate) - also called F10. Here we investigate the structural and kinetic behavior of F10 in intracellular and extracellular solvent conditions along with non-biological conditions that may be efficacious in in vitro preparations of F10 delivery systems...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28804700/abridged-version-of-the-awmf-guideline-for-the-medical-clinical-diagnostics-of-indoor-mould-exposure-s2k-guideline-of-the-german-society-of-hygiene-environmental-medicine-and-preventive-medicine-ghup-in-collaboration-with-the-german-association-of-allergists
#16
Gerhard A Wiesmüller, Birger Heinzow, Ute Aurbach, Karl-Christian Bergmann, Albrecht Bufe, Walter Buzina, Oliver A Cornely, Steffen Engelhart, Guido Fischer, Thomas Gabrio, Werner Heinz, Caroline E W Herr, Jörg Kleine-Tebbe, Ludger Klimek, Martin Köberle, Herbert Lichtnecker, Thomas Lob-Corzilius, Rolf Merget, Norbert Mülleneisen, Dennis Nowak, Uta Rabe, Monika Raulf, Hans Peter Seidl, Jens-Oliver Steiß, Regine Szewszyk, Peter Thomas, Kerttu Valtanen, Julia Hurraß
This article is an abridged version of the AWMF mould guideline "Medical clinical diagnostics of indoor mould exposure" presented in April 2016 by the German Society of Hygiene, Environmental Medicine and Preventive Medicine (Gesellschaft für Hygiene, Umweltmedizin und Präventivmedizin, GHUP), in collaboration with the above-mentioned scientific medical societies, German and Austrian societies, medical associations and experts. Indoor mould growth is a potential health risk, even if a quantitative and/or causal relationship between the occurrence of individual mould species and health problems has yet to be established...
2017: Allergo Journal International
https://www.readbyqxmd.com/read/28804509/lifetime-stress-exposure-and-health-a-review-of-contemporary-assessment-methods-and-biological-mechanisms
#17
Grant S Shields, George M Slavich
Life stress is a central construct in health research because it is associated with increased risk for a variety of serious mental and physical health problems, including anxiety disorders, depression, cardiovascular disease, autoimmune disorders, Alzheimer's disease, certain cancers, and other diseases of aging. In this review, we examine how lifetime stress exposure contributes to elevated disease risk, and explore ongoing measurement and scientific issues related to this topic. To accomplish these goals, we first review existing instruments that have been developed for assessing perceived stress, self-reported life events, interviewer-assessed life stressors, and lifetime stress exposure...
August 2017: Social and Personality Psychology Compass
https://www.readbyqxmd.com/read/28804460/editorial-systems-biology-and-the-challenge-of-deciphering-the-metabolic-mechanisms-underlying-cancer
#18
EDITORIAL
Osbaldo Resendis-Antonio, Christian Diener
No abstract text is available yet for this article.
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28802766/a-phase-i-trial-of-intraperitoneal-gen-1-an-il-12-plasmid-formulated-with-peg-pei-cholesterol-lipopolymer-administered-with-pegylated-liposomal-doxorubicin-in-patients-with-recurrent-or-persistent-epithelial-ovarian-fallopian-tube-or-primary-peritoneal-cancers
#19
REVIEW
Premal H Thaker, William E Brady, Heather A Lankes, Kunle Odunsi, William H Bradley, Kathleen N Moore, Carolyn Y Muller, Khursheed Anwer, Russell J Schilder, Ronald D Alvarez, Paula M Fracasso
OBJECTIVE: The study's purpose was to assess safety and efficacy of escalating doses of weekly GEN-1 with pegylated liposomal doxorubicin (PLD) in patients with recurrent or persistent epithelial ovarian, fallopian tube or primary peritoneal cancers (EOC). METHODS: Patients had persistent or recurrent platinum-resistant EOC. The trial was a standard 3+3 phase I dose escalation design with patients receiving intravenous PLD 40mg/m(2) (dose level 1 and 2) or 50mg/m(2) (dose level 3) every 28days and intraperitoneal GEN-1 at 24mg/m(2) (dose level 1) or 36mg/m(2) (dose level 2 and 3) on days 1, 8, 15, and 22 of a 28day cycle...
August 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28802037/the-pi3k-pathway-in-human-disease
#20
REVIEW
David A Fruman, Honyin Chiu, Benjamin D Hopkins, Shubha Bagrodia, Lewis C Cantley, Robert T Abraham
Phosphoinositide 3-kinase (PI3K) activity is stimulated by diverse oncogenes and growth factor receptors, and elevated PI3K signaling is considered a hallmark of cancer. Many PI3K pathway-targeted therapies have been tested in oncology trials, resulting in regulatory approval of one isoform-selective inhibitor (idelalisib) for treatment of certain blood cancers and a variety of other agents at different stages of development. In parallel to PI3K research by cancer biologists, investigations in other fields have uncovered exciting and often unpredicted roles for PI3K catalytic and regulatory subunits in normal cell function and in disease...
August 10, 2017: Cell
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