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https://www.readbyqxmd.com/read/27926828/harnessing-cancer-cell-metabolism-for-theranostic-applications-using-metabolic-glycoengineering-of-sialic-acid-in-breast-cancer-as-a-pioneering-example
#1
REVIEW
Haitham A Badr, Dina M M AlSadek, Motawa E El-Houseini, Christopher T Saeui, Mohit P Mathew, Kevin J Yarema, Hafiz Ahmed
Abnormal cell surface display of sialic acids - a family of unusual 9-carbon sugars - is widely recognized as distinguishing feature of many types of cancer. Sialoglycans, however, typically cannot be identified with sufficiently high reproducibility and sensitivity to serve as clinically accepted biomarkers and similarly, almost all efforts to exploit cancer-specific differences in sialylation signatures for therapy remain in early stage development. In this report we provide an overview of important facets of glycosylation that contribute to cancer in general with a focus on breast cancer as an example of malignant disease characterized by aberrant sialylation...
November 25, 2016: Biomaterials
https://www.readbyqxmd.com/read/27925796/a-severe-asthma-disease-signature-from-gene-expression-profiling-of-peripheral-blood-from-u-biopred-cohorts
#2
Jeannette Bigler, Michael Boedigheimer, James P R Schofield, Paul J Skipp, Julie Corfield, Anthony Rowe, Ana R Sousa, Martin Timour, Lori Twehues, Xuguang Hu, Graham Roberts, Andrew A Welcher, Wen Yu, Kian F Chung, Ian M Adcock, Peter J Sterk, Ratko Djukanović
RATIONALE: Stratification of asthma at the molecular level, especially using accessible biospecimens, could greatly enable patient selection for targeted therapy. OBJECTIVES: To determine the value of blood to identify transcriptional differences between clinically defined asthmatic and non-asthmatic groups, identify potential patient subgroups based on gene expression, and explore biological pathways associated with identified differences. METHODS: Transcriptomics profiles were generated by microarray analysis of blood from 610 asthmatic and control participants in U-BIOPRED...
December 7, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27925615/positive-selection-in-cathelicidin-host-defense-peptides-adaptation-to-exogenous-pathogens-or-endogenous-receptors
#3
S Zhu, B Gao
The cause of adaptive protein evolution includes internal (for example, co-evolution of ligand-receptor pairs) and external (for example, adaptation to different ecological niches) mechanisms. Host defense peptides (HDPs) are a class of vertebrate-specific cationic antimicrobial peptides evolving under positive selection. Besides their antibiotic activity, HDPs also exert an effect on multiple host immune cells, thus providing an ideal model to study selective agents driving their evolution. On the basis of a combination of computational and experimental approaches, we studied the evolution of LL-37-type HDPs in mammals, the mature peptide of cathelicidin CAP18 (herein termed CAP18-MP) and investigated the driving force behind the evolution...
December 7, 2016: Heredity
https://www.readbyqxmd.com/read/27925180/a-16-yin-yang-gene-expression-ratio-signature-for-er-node-breast-cancer
#4
Wayne Xu, Gaofeng Jia, Nianguang Cai, Shujun Huang, James R Davie, Marshall Pitz, Shantanu Banerji, Leigh Murphy
Breast cancer is one of the leading causes of cancer death in women. It is a complex and heterogeneous disease with different clinical outcomes. Stratifying patients into subgroups with different outcomes could help guide clinical decision making. In this study, we used two opposing groups of genes, Yin and Yang, to develop a prognostic expression ratio signature. Using the METABRIC cohort we identified a16-gene signature capable of stratifying breast cancer patients into four risk levels with intention that low-risk patients would not undergo adjuvant systemic therapy, intermediate-low-risk patients will be treated with hormonal therapy only, and intermediate-high- and high-risk groups will be treated by chemotherapy in addition to the hormonal therapy...
December 7, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27925177/t-cell-diversification-reflects-antigen-selection-in-the-blood-of-patients-on-immune-checkpoint-inhibition-and-may-be-exploited-as-liquid-biopsy-biomarker
#5
Nuray Akyüz, Anna Brandt, Alexander Stein, Simon Schliffke, Thorben Mährle, Julia Quidde, Eray Goekkurt, Sonja Loges, Thomas Haalck, Christopher Ford, Anne Marie Asemissen, Benjamin Thiele, Janina Radloff, Toni Thenhausen, Artus Krohn-Grimberghe, Carsten Bokemeyer, Mascha Binder
Cancer immunotherapy with antibodies targeting immune checkpoints, such as programmed cell death protein 1 (PD-1), shows encouraging results, but reliable biomarkers predicting response to this costly and potentially toxic treatment approach are still lacking. To explore an immune signature predictive for response, we performed liquid biopsy immunoprofiling in 18 cancer patients undergoing PD-1 inhibition before and shortly after initiation of treatment by multicolor flow cytometry and next-generation T- and B-cell immunosequencing (TCRß/IGH)...
December 7, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27924752/predictive-biomarkers-for-checkpoint-inhibitor-based-immunotherapy
#6
REVIEW
Geoffrey T Gibney, Louis M Weiner, Michael B Atkins
The clinical development of checkpoint inhibitor-based immunotherapy has ushered in an exciting era of anticancer therapy. Durable responses can be seen in patients with melanoma and other malignancies. Although monotherapy with PD-1 or PD-L1 agents are typically well tolerated, the risk of immune-related adverse events increases with combination regimens. The development of predictive biomarkers is needed to optimise patient benefit, minimise risk of toxicities, and guide combination approaches. The greatest focus has been on tumour-cell PD-L1 expression...
December 2016: Lancet Oncology
https://www.readbyqxmd.com/read/27923842/predicting-mek-inhibitor-response-in-lung-cancer-a-proper-signature-is-required
#7
Yaohua Xue, Piro Lito
The ERK signaling pathway is one of the most commonly deregulated pathways in cancer. Assays that accurately measure ERK signaling output in clinical specimens would be extremely helpful not only in determining the parmacodynamic effects of drug treatment but also in selecting those patients most likely to respond to therapy.
December 6, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27923830/a-myc-activity-signature-predicts-poor-clinical-outcomes-in-myc-associated-cancers
#8
MoonSun Jung, Amanda J Russell, Bing Liu, Joshy George, Pei Yan Liu, Tao Liu, Anna DeFazio, David D L Bowtell, Andre Oberthuer, Wendy B London, Jamie I Fletcher, Michelle Haber, Murray D Norris, Michelle J Henderson
Myc transcriptional activity is frequently deregulated in human cancers, but a Myc-driven gene signature with prognostic ability across multiple tumor types remains lacking. Here we selected 18 Myc-regulated genes from published studies of Myc family targets in epithelial ovarian cancer (EOC) and neuroblastoma. A Myc family activity score derived from the 18 genes was correlated to MYC/MYCN/MYCL1 expression in a panel of 35 cancer cell lines. The prognostic ability of this signature was evaluated in neuroblastoma, medulloblastoma, diffuse large B-cell lymphoma (DLBCL), and EOC microarray gene expression datasets using Kaplan-Meier and multivariate Cox-regression analyses, and was further validated in 42 primary neuroblastomas using qPCR...
December 6, 2016: Cancer Research
https://www.readbyqxmd.com/read/27922113/non-small-cell-lung-cancer-quantitative-phenotypic-analysis-of-ct-images-as-a-potential-marker-of-prognosis
#9
Jiangdian Song, Zaiyi Liu, Wenzhao Zhong, Yanqi Huang, Zelan Ma, Di Dong, Changhong Liang, Jie Tian
This was a retrospective study to investigate the predictive and prognostic ability of quantitative computed tomography phenotypic features in patients with non-small cell lung cancer (NSCLC). 661 patients with pathological confirmed as NSCLC were enrolled between 2007 and 2014. 592 phenotypic descriptors was automatically extracted on the pre-therapy CT images. Firstly, support vector machine (SVM) was used to evaluate the predictive value of each feature for pathology and TNM clinical stage. Secondly, Cox proportional hazards model was used to evaluate the prognostic value of these imaging signatures selected by SVM which subjected to a primary cohort of 138 patients, and an external independent validation of 61 patients...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922085/diversity-of-major-urinary-proteins-mups-in-wild-house-mice
#10
Michaela Thoß, Viktoria Enk, Hans Yu, Ingrid Miller, Kenneth C Luzynski, Boglarka Balint, Steve Smith, Ebrahim Razzazi-Fazeli, Dustin J Penn
Major urinary proteins (MUPs) are often suggested to be highly polymorphic, and thereby provide unique chemical signatures used for individual and genetic kin recognition; however, studies on MUP variability have been lacking. We surveyed populations of wild house mice (Mus musculus musculus), and examined variation of MUP genes and proteins. We sequenced several Mup genes (9 to 11 loci) and unexpectedly found no inter-individual variation. We also found that microsatellite markers inside the MUP cluster show remarkably low levels of allelic diversity, and significantly lower than the diversity of markers flanking the cluster or other markers in the genome...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920228/exploring-novel-paths-towards-protein-signatures-of-chronic-pain
#11
David Gomez-Varela, Manuela Schmidt
Pain is a major symptom of many medical conditions and the worldwide number one reason for people to seek medical assistance. It affects the quality of life of patients and poses a heavy financial burden on society with high costs of treatment and lost productivity. Furthermore, the treatment of chronic pain presents a big challenge as pain therapeutics often lack efficacy and exhibit minimal safety profiles. The latter can be largely attributed to the fact that current therapies target molecules with key physiological functions throughout the body...
2016: Molecular Pain
https://www.readbyqxmd.com/read/27917920/transcriptome-and-long-noncoding-rna-sequencing-of-three-extracellular-vesicle-subtypes-released-from-the-human-colon-cancer-lim1863-cell-line
#12
Maoshan Chen, Rong Xu, Hong Ji, David W Greening, Alin Rai, Keiichi Izumikawa, Hideaki Ishikawa, Nobuhiro Takahashi, Richard J Simpson
Previously we reported that LIM1863 colorectal cancer (CRC) cells secrete three distinct extracellular vesicle subtypes - two subpopulations of exosomes (apical EpCAM-Exos and basolateral A33-Exos) and shed microvesicles (sMVs) - with distinct protein and miRNA signatures. Here, we extend our omics approach to understand the fundamental role of LIM1863-derived EVs by performing a comprehensive analysis of their mRNAs and long non-coding RNAs (lncRNAs) using RNA-Seq. We show that 2,389 mRNAs, 317 pseudogene transcripts, 1,028 lncRNAs and 206 short non-coding RNAs selectively distributed to (i...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27913357/introducing-a-stable-bootstrap-validation-framework-for-reliable-genomic-signature-extraction
#13
Nikolaos-Kosmas Chlis, Ekaterini S Bei, Michael Zervakis
The application of machine learning methods for the identification of candidate genes responsible for phenotypes of interest, such as cancer, is a major challenge in the field of bioinformatics. These lists of genes are often called genomic signatures and their linkage to phenotype associations may form a significant step in discovering the causation between genotypes and phenotypes. Traditional methods that produce genomic signatures from DNA Microarray data tend to extract significantly different lists under relatively small variations of the training data...
November 29, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27911780/selective-sweep-suggests-transcriptional-regulation-may-underlie-plasmodium-vivax-resilience-to-malaria-control-measures-in-cambodia
#14
Christian M Parobek, Jessica T Lin, David L Saunders, Eric J Barnett, Chanthap Lon, Charlotte A Lanteri, Sujata Balasubramanian, Nicholas Brazeau, Derrick K DeConti, Deen L Garba, Steven R Meshnick, Michele D Spring, Char Meng Chuor, Jeffrey A Bailey, Jonathan J Juliano
Cambodia, in which both Plasmodium vivax and Plasmodium falciparum are endemic, has been the focus of numerous malaria-control interventions, resulting in a marked decline in overall malaria incidence. Despite this decline, the number of P vivax cases has actually increased. To understand better the factors underlying this resilience, we compared the genetic responses of the two species to recent selective pressures. We sequenced and studied the genomes of 70 P vivax and 80 P falciparum isolates collected between 2009 and 2013...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910803/the-prognostic-and-predictive-value-of-tmprss2-erg-gene-fusion-and-erg-protein-expression-in-prostate-cancer-biopsies
#15
Kasper Drimer Berg
BACKGROUND: The clinical course of prostate carcinoma (PCa) is very heterogeneous. Consequently, a personalised approach for risk stratification and treatment planning is important. Recently, it has become evident that PCa, also at the genomic level, is heterogeneous. An early and common alteration is the gene fusion between the transmembrane protease serine 2 (TMPRSS2) gene and the v-ets avian erythroblastosis virus E26 oncogene homolog (ERG) gene resulting in expression of the oncoprotein ERG...
December 2016: Danish Medical Journal
https://www.readbyqxmd.com/read/27908728/activation-of-evi1-transcription-by-the-lef1-%C3%AE-catenin-complex-with-p53-alteration-in-myeloid-blast-crisis-of-chronic-myeloid-leukemia
#16
Nawin Manachai, Yusuke Saito, Shingo Nakahata, Avinash Govind Bahirvani, Tomomi Osato, Kazuhiro Morishita
The presence of a BCR-ABL1 fusion gene is necessary for the pathogenesis of chronic myeloid leukemia (CML) through t(9;22)(q34;q11) translocation. Imatinib, an ABL tyrosine kinase inhibitor, is dramatically effective in CML patients; however, 30% of CML patients will need further treatment due to progression of CML to blastic crisis (BC). Aberrant high expression of ecotropic viral integration site 1 (EVI1) is frequently observed in CML during myeloid-BC as a potent driver with a CML stem cell signature; however, the precise molecular mechanism of EVI1 transcriptional regulation during CML progression is poorly defined...
November 28, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27907170/complementation-of-an-aglb-mutant-of-methanococcus-maripaludis-with-heterologous-oligosaccharyltransferases
#17
Yan Ding, Helen A Vrionis, James Schneider, Alison Berezuk, Cezar M Khursigara, Ken F Jarrell
The oligosaccharyltransferase is the signature enzyme for N-linked glycosylation in all domains of life. In Archaea, this enzyme termed AglB, is responsible for transferring lipid carrier-linked glycans to select asparagine residues in a variety of target proteins including archaellins, S-layer proteins and pilins. This study investigated the ability of a variety of AglBs to compensate for the oligosaccharyltransferase activity in Methanococcus maripaludis deleted for aglB, using archaellin FlaB2 as the reporter protein since all archaellins in Mc...
2016: PloS One
https://www.readbyqxmd.com/read/27905576/label-free-monitoring-of-tissue-biochemistry-following-traumatic-brain-injury-using-raman-spectroscopy
#18
Jakub Maciej Surmacki, Laura Ansel-Bollepalli, Francesca Pischiutta, Elisa R Zanier, Ari Ercole, Sarah Elizabeth Bohndiek
Traumatic brain injury (TBI) constitutes a major cause of death and long-term disability. At present, we lack methods to non-invasively track tissue biochemistry and hence select appropriate interventions for patients. We hypothesized that detailed label-free vibrational chemical analysis of focal TBI could provide such information. We assessed the early spatial and temporal changes in tissue biochemistry that are associated with brain injury in mice. Numerous differences were observed in the spectra of the contusion core and pericontusional tissue between 2 and 7 days...
December 1, 2016: Analyst
https://www.readbyqxmd.com/read/27904140/restrictions-in-the-t-cell-repertoire-of-chronic-lymphocytic-leukemia-high-throughput-immunoprofiling-supports-selection-by-shared-antigenic-elements
#19
A Vardi, E Vlachonikola, M Karypidou, E Stalika, V Bikos, K Gemenetzi, C Maramis, A Siorenta, A Anagnostopoulos, S Pospisilova, N Maglaveras, I Chouvarda, K Stamatopoulos, A Hadzidimitriou
Immunoglobulin (IG) gene repertoire restrictions strongly support antigen selection in the pathogenesis of chronic lymphocytic leukemia (CLL). Given the emerging multifarious interactions between CLL and bystander T cells, we sought to determine whether antigen(s) are also selecting T cells in CLL. We performed a large-scale, next-generation sequencing (NGS) study of the T-cell repertoire, focusing on major stereotyped subsets representing CLL subgroups with undisputed antigenic drive, but also included patients carrying non-subset IG rearrangements to seek for T-cell immunogenetic signatures ubiquitous in CLL...
December 1, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27903835/identification-of-microrna-signature-and-potential-pathway-targets-in-prostate-cancer
#20
Ahmed A Moustafa, Mohammed Ziada, Abubaker Elshaikh, Amrita Datta, Hogyoung Kim, Krzysztof Moroz, Sudesh Srivastav, Raju Thomas, Jonathan L Silberstein, Krishnarao Moparty, Fatma Elzahraa H Salem, Ola H El-Habit, Asim B Abdel-Mageed
Prostate cancer (PC) is the most common and the second leading cause of cancer-related death among American men. Early diagnosis is a prerequisite to improving therapeutic benefits. However, the current clinical biomarkers for PC do not reliably decipher indolent PC from other urogenital disorders. Thus, effective clinical intervention necessitates development of new biomarkers for early detection of PC. The present study aimed to identify the miRNA signature in organ-confined (Gleason Score 6) prostate tumors...
November 29, 2016: Experimental Biology and Medicine
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