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Dna decoy

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https://www.readbyqxmd.com/read/29440232/noncoding-rnas-long-non-coding-rnas-and-micrornas-in-endocrine-related-cancers
#1
Carolyn M Klinge
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~ 22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation...
February 12, 2018: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29433938/b-cell-lymphoma-immunotherapy-using-tlr9-targeted-oligonucleotide-stat3-inhibitors
#2
Xingli Zhao, Zhuoran Zhang, Dayson Moreira, Yu-Lin Su, Haejung Won, Tomasz Adamus, Zhenyuan Dong, Yong Liang, Hongwei H Yin, Piotr Swiderski, Raju K Pillai, Larry Kwak, Stephen Forman, Marcin Kortylewski
Growing evidence links the aggressiveness of non-Hodgkin's lymphoma, especially the activated B cell-like type diffuse large B cell lymphomas (ABC-DLBCLs) to Toll-like receptor 9 (TLR9)/MyD88 and STAT3 transcription factor signaling. Here, we describe a dual-function molecule consisting of a clinically relevant TLR9 agonist (CpG7909) and a STAT3 inhibitor in the form of a high-affinity decoy oligodeoxynucleotide (dODN). The CpG-STAT3dODN blocked STAT3 DNA binding and activity, thus reducing expression of downstream target genes, such as MYC and BCL2L1, in human and mouse lymphoma cells...
January 17, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29409936/epigenetic-regulation-by-cpg-methylation-splits-strong-from-retarded-ifn%C3%AE-induced-il-18bp-in-epithelial-versus-monocytic-cells
#3
Malte Bachmann, Josef Pfeilschifter, Heiko Mühl
Interferon (IFN)-γ-inducing interleukin (IL)-18 is a crucial inflammatory cytokine systemically provided by monocytes. It is counteracted by IL-18 binding protein (IL-18BP), a decoy receptor that displays IFNγ-inducibility thus curbing inflammation by negative feedback. Since IL18BP inducibility is pronounced in human epithelial cells but diminished in monocytes, differential IL18BP regulation was investigated herein in both types of cells. Interestingly, DNA-demethylating 5-aza-2'-deoxycytidine enhanced IFNγ-induced IL-18BP only in monocytic but not in epithelial cells...
January 30, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29291159/dual-radiosensitization-and-anti-stat3-anti-proliferative-strategy-based-on-delivery-of-gold-nanoparticle-oligonucleotide-nanoconstructs-to-head-and-neck-cancer-cells
#4
Surong Zhang, Suresh Gupta, Thomas J Fitzgerald, Alexei A Bogdanov
Constitutively activated signal transducer and activator of transcription 3 (STAT3) factor is an important therapeutic target in head and neck cancer (HNC). Despite early promising results, a reliable systemic delivery system for STAT3- targeted oligonucleotide (ODN) drugs is still needed for future clinical translation of anti-STAT3 therapies. We engineered and tested a novel ODN duplex/gold nanoparticle (AuNP)-based system carrying a therapeutic STAT3 decoy (STAT3d) payload. This strategy is two-pronged because of the additive STAT3 antagonism and radiosensitizing properties of AuNP...
2018: Nanotheranostics
https://www.readbyqxmd.com/read/29228714/unique-expression-signatures-of-circular-rnas-in-response-to-dna-tumor-virus-sv40-infection
#5
Jiandong Shi, Ningzhu Hu, Jianfang Li, Zhaoping Zeng, Ling Mo, Jing Sun, Meini Wu, Yunzhang Hu
Circular RNAs (circRNAs), identified as a class of widely expressed endogenous regulatory RNAs, are involved in diverse physiological and pathological processes. However, their role in viral pathogenesis and cellular antiviral response remains unexplored. In this study, a potent DNA tumor virus, simian virus 40 (SV40), was used as a model to investigate the viral influences on cellular circRNA transcriptome. Using RNA-seq, 15,241 putative circRNAs were identified de novo from 5,057 parental genes in monkey kidney-derived Vero cells...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29215015/malaria-parasite-dna-harbouring-vesicles-activate-cytosolic-immune-sensors
#6
Xavier Sisquella, Yifat Ofir-Birin, Matthew A Pimentel, Lesley Cheng, Paula Abou Karam, Natália G Sampaio, Jocelyn Sietsma Penington, Dympna Connolly, Tal Giladi, Benjamin J Scicluna, Robyn A Sharples, Andreea Waltmann, Dror Avni, Eli Schwartz, Louis Schofield, Ziv Porat, Diana S Hansen, Anthony T Papenfuss, Emily M Eriksson, Motti Gerlic, Andrew F Hill, Andrew G Bowie, Neta Regev-Rudzki
STING is an innate immune cytosolic adaptor for DNA sensors that engage malaria parasite (Plasmodium falciparum) or other pathogen DNA. As P. falciparum infects red blood cells and not leukocytes, how parasite DNA reaches such host cytosolic DNA sensors in immune cells is unclear. Here we show that malaria parasites inside red blood cells can engage host cytosolic innate immune cell receptors from a distance by secreting extracellular vesicles (EV) containing parasitic small RNA and genomic DNA. Upon internalization of DNA-harboring EVs by human monocytes, P...
December 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/29064575/dna-detection-of-jc-and-bk-virus-in-archival-urine-cytospin-slides
#7
Patricia Gioia de Assis, Carlos Eduardo de Souza Carvalho, Marcelo Soares da Mota E Silva, Maria da Gloria da Costa Carvalho
INTRODUCTION: To identify decoy cells, cytological examination was performed in urine cytospin slides. Decoy cells are related to Polyomaviruses (JC virus [JCV] and BK virus [BKV]), which are recognized worldwide due to potential infection and morbidity in kidney transplantrecipients. Cytologically, it is difficult to evaluate the cytopathic effect of JC and BK virus in urine of patients with urothelial neoplasia. For this reason, there is a need for molecular approaches. OBJECTIVE: To evaluate the incidence of BKV and JCV DNA in archival slides of urine cytospin material with benign and malignant characteristics...
October 24, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28968978/decoy-receptor-1-dcr1-promoter-hypermethylation-and-response-to-irinotecan-in-metastatic-colorectal-cancer
#8
Linda J W Bosch, Geert Trooskens, Petur Snaebjornsson, Veerle M H Coupé, Sandra Mongera, Josien C Haan, Susan D Richman, Miriam Koopman, Jolien Tol, Tim de Meyer, Joost Louwagie, Luc Dehaspe, Nicole C T van Grieken, Bauke Ylstra, Henk M W Verheul, Manon van Engeland, Iris D Nagtegaal, James G Herman, Philip Quirke, Matthew T Seymour, Cornelis J A Punt, Wim van Criekinge, Beatriz Carvalho, Gerrit A Meijer
Diversity in colorectal cancer biology is associated with variable responses to standard chemotherapy. We aimed to identify and validate DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of metastatic CRC patients. Candidate genes were selected from 389 genes involved in DNA Damage Repair by correlation analyses between gene methylation status and drug response in 32 cell lines. A large series of samples (n=818) from two phase III clinical trials was used to evaluate these candidate genes by correlating methylation status to progression-free survival after treatment with first-line single-agent fluorouracil (Capecitabine or 5-fluorouracil) or combination chemotherapy (Capecitabine or 5-fluorouracil plus irinotecan (CAPIRI/FOLFIRI))...
September 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28928124/emerging-mechanisms-of-long-noncoding-rna-function-during-normal-and-malignant-hematopoiesis
#9
REVIEW
Juan R Alvarez-Dominguez, Harvey F Lodish
Long noncoding RNAs (lncRNAs) are increasingly recognized as vital components of gene programs controlling cell differentiation and function. Central to their functions is an ability to act as scaffolds or as decoys that recruit or sequester effector proteins from their DNA, RNA, or protein targets. lncRNA-modulated effectors include regulators of transcription, chromatin organization, RNA processing, and translation, such that lncRNAs can influence gene expression at multiple levels. Here we review the current understanding of how lncRNAs help coordinate gene expression to modulate cell fate in the hematopoietic system...
November 2, 2017: Blood
https://www.readbyqxmd.com/read/28903493/editor-s-highlight-formulation-and-toxicology-evaluation-of-the-intrathecal-ayx1-dna-decoy-in-sprague-dawley-rats
#10
Julien Mamet, David C Yeomans, Tony L Yaksh, Donald C Manning, Scott Harris
The longevity of pain after surgery is debilitating and limits the recovery of patients. AYX1 is a double-stranded, unprotected, 23 base-pair oligonucleotide designed to reduce acute post-surgical pain and prevent its chronification with a single intrathecal perioperative dose. AYX1 mimics the DNA sequence normally bound by EGR1 on chromosomes, a transcription factor transiently induced in the dorsal root ganglia-spinal cord network following a noxious input. AYX1 binds to EGR1 and prevents it from launching waves of gene regulation that are necessary to maintain pain over time...
September 1, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28878400/thiamine-antagonists-trigger-p53-dependent-apoptosis-in-differentiated-sh-sy5y-cells
#11
Sergiy Chornyy, Yulia Parkhomenko, Nataliya Chorna
Accumulating evidences suggest that p53 is a key coordinator of cellular events triggered by oxidative stress often associated with the impairment in thiamine metabolism and its functions. However, there are limited data regarding the pursuant feedback between p53 transactivation and thiamine homeostasis. Impairment in thiamine metabolism can be induced experimentally via interference with the thiamine uptake and/or inhibition of the thiamin pyrophosphate-dependent enzymes using thiamine antagonists - amprolium (AM), oxythiamine (OT) or pyrithiamine (PT)...
September 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28865342/inclusion-of-oligonucleotide-antimicrobials-in-biocompatible-cationic-liposomes-a-structural-study
#12
Marianna Mamusa, Francesco Barbero, Costanza Montis, Laura Cutillo, Ana Gonzalez-Paredes, Debora Berti
HYPOTHESIS: Transcription factor decoys (TFD) are short oligonucleotides designed to block essential genetic pathways in bacteria and defeat resistant infections. TFD protection in biological fluids and their delivery to the site of infection require formulation in appropriate delivery systems. In this work, we build on a classical phosphatidylcholine/phosphatidylethanolamine (POPC/DOPE) scaffold to design TFD-loaded cationic liposomes by combining the DNA-complexing abilities of a bolaamphiphile, (1,1'-(dodecane-1,12-diyl)-bis-(9-amino-1,2,3,4-tetrahydroacridinium) chloride (12-bis-THA), with the biocompatible cationic lipid ethyl-phosphatidylcholine (DPePC)...
August 24, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28833847/simultaneous-targeted-inhibition-of-sox2-oct4-transcription-factors-using-decoy-oligodeoxynucleotides-to-repress-stemness-properties-in-mouse-embryonic-stem-cells
#13
Behrooz Johari, Jamil Zargan
Transcriptional master regulators like Sox2 and Oct4, which are expressed in various human tumors, have been shown to cause tumor growth promotion as well as epithelial dysplasia by means of interfering with progenitor cell differentiation. In order to investigate the potential of Sox2-Oct4 transcription factor decoy (TFD) strategy for differentiation therapy, mouse embryonic stem cells (mESCs) were used in this study as a model of cancer stem cells (CSCs). Sox2-Oct4 complex decoy ODNs (cd-ODNs) were designed according to their elements in the promoter region of Sox2 gene...
August 18, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28815539/long-noncoding-rnas-in-plants
#14
Hsiao-Lin V Wang, Julia A Chekanova
The eukaryotic genomes are pervasively transcribed. In addition to protein-coding RNAs, thousands of long noncoding RNAs (lncRNAs) modulate key molecular and biological processes. Most lncRNAs are found in the nucleus and associate with chromatin, but lncRNAs can function in both nuclear and cytoplasmic compartments. Emerging work has found that many lncRNAs regulate gene expression and can affect genome stability and nuclear domain organization both in plant and in the animal kingdom. Here, we describe the major plant lncRNAs and how they act, with a focus on research in Arabidopsis thaliana and our emerging understanding of lncRNA functions in serving as molecular sponges and decoys, functioning in regulation of transcription and silencing, particularly in RNA-directed DNA methylation, and in epigenetic regulation of flowering time...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#15
Subhash C Lakhotia
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28814144/-express-intrathecal-administration-of-ayx2-dna-decoy-produces-a-long-term-pain-treatment-in-rat-models-of-chronic-pain-by-inhibiting-the-klf6-klf9-and-klf15-transcription-factors
#16
Julien Mamet, Michael Klukinov, Scott Harris, Donald C Manning, Simon Xie, Conrado Pascual, Bradley K Taylor, Renee R Donahue, David C Yeomans
No abstract text is available yet for this article.
January 2017: Molecular Pain
https://www.readbyqxmd.com/read/28700344/decoy-receptor-1-dcr1-promoter-hypermethylation-and-response-to-irinotecan-in-metastatic-colorectal-cancer
#17
Linda J W Bosch, Geert Trooskens, Petur Snaebjornsson, Veerle M H Coupé, Sandra Mongera, Josien C Haan, Susan D Richman, Miriam Koopman, Jolien Tol, Tim de Meyer, Joost Louwagie, Luc Dehaspe, Nicole C T van Grieken, Bauke Ylstra, Henk M W Verheul, Manon van Engeland, Iris D Nagtegaal, James G Herman, Philip Quirke, Matthew T Seymour, Cornelis J A Punt, Wim van Criekinge, Beatriz Carvalho, Gerrit A Meijer
Diversity in colorectal cancer biology is associated with variable responses to standard chemotherapy. We aimed to identify and validate DNA hypermethylated genes as predictive biomarkers for irinotecan treatment of metastatic CRC patients.Candidate genes were selected from 389 genes involved in DNA Damage Repair by correlation analyses between gene methylation status and drug response in 32 cell lines. A large series of samples (n=818) from two phase III clinical trials was used to evaluate these candidate genes by correlating methylation status to progression-free survival after treatment with first-line single-agent fluorouracil (Capecitabine or 5-fluorouracil) or combination chemotherapy (Capecitabine or 5-fluorouracil plus irinotecan (CAPIRI/FOLFIRI))...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28678467/a-two-photon-photocleavable-linker-for-triggering-light-induced-strand-breaks-in-oligonucleotides
#18
Xenia M M Weyel, Manuela A H Fichte, Alexander Heckel
We synthesized a two-photon-sensitive photocleavable linker based on the 7-diethylaminocoumarin structure and introduced it successfully into DNA strands. First, we demonstrated the inducibility of strand scissions upon irradiation at 365 nm. To verify and visualize the two-photon activity, we used a fluorescence assay based on a DNA strand displacement immobilized in a hydrogel. Additionally, we investigated its use in a new class of DNA decoys that are able to catch and release nuclear factor κB (NF-κB) by using light as an external trigger signal...
July 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28642036/transcription-factor-decoy-technology-a-therapeutic-update
#19
REVIEW
Markus Hecker, Andreas H Wagner
Targeting transcription factors represents one possibility to interfere with a known activated regulatory pathway that promotes disease. Double-stranded transcription factor decoy (TFD) oligodeoxynucleotides (ODN) are therapeutic drug candidates, which are able to specifically target and neutralize key transcription factors involved in the pathogenesis of a given disease. These short double-stranded TFD molecules mimic the consensus DNA binding site of a specific transcription factor in the promoter region of its target genes...
November 15, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28617169/the-frequency-and-associated-factors-for-bk-virus-infection-in-a-center-performing-mainly-living-kidney-transplantations
#20
Selma Alagoz, Mert Kuskucu, Sibel Gulcicek, Serkan Feyyaz Yalin, Meric Oruc, Kenan Midilli, Erkan Yılmaz, Mehmet Riza Altiparmak, Nurhan Seyahi
PURPOSE: BK virus (BKV) nephropathy has increasingly become an important cause of morbidity in renal transplant recipients. We evaluated the frequency and associated factors for BKV infection in a center performing mainly living donor transplantations over a long time period. METHODS: One hundred consecutive renal transplant patients were included. Quarterly visits were planned to examine urine for decoy cells and to measure the BKV DNA in the blood and urine. Renal biopsy was performed in case of deteriorated allograft function...
June 2017: Progress in Transplantation
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