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https://www.readbyqxmd.com/read/28446531/mining-exosomal-genes-for-pancreatic-cancer-targets
#1
Amy Makler, Ramaswamy Narayanan
BACKGROUND: Exosomes, cell-derived vesicles encompassing lipids, DNA, proteins coding genes and noncoding RNAs (ncRNAs) are present in diverse body fluids. They offer novel biomarker and drug therapy potential for diverse diseases, including cancer. MATERIALS AND METHODS: Using gene ontology, exosomal genes database and GeneCards metadata analysis tools, a database of cancer-associated protein coding genes and ncRNAs (n=2,777) was established. Variant analysis, expression profiling and pathway mapping were used to identify putative pancreatic cancer exosomal gene candidates...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446032/the-effect-of-intravesical-liposome-based-ngf-antisense-therapy-on-bladder-overactivity-and-nociception-in-a-rat-model-of-cystitis-induced-by-hydrogen-peroxide
#2
Tsuyoshi Majima, Pradeep Tyagi, Koji Dogishi, Mahendra Kashyap, Yasuhito Funahashi, Momokazu Gotoh, Michael Chancellor, Naoki Yoshimura
Objective We investigated the effect of intravesical liposome-based NGF antisense therapy on bladder overactivity and nociception in a rat model of cystitis induced by hydrogen peroxide (HP). Study design, materials and methods 1) HP (1.5%) was administered into the bladder on day 0. Liposomes conjugated with NGF antisense oligonucleotide (OND) tagged with TYE563 fluorescent protein was given into the bladder on day 2. The expression of TYE563 was observed under a fluorescent microscope on day 3. 2) In another set of experiments, rats were divided into 4 groups: (a) sham- liposome group, (b) sham-OND group, (c) cystitis- liposome group and (d) cystitis-OND group...
April 27, 2017: Human Gene Therapy
https://www.readbyqxmd.com/read/28443119/parsing-the-regulatory-network-between-small-rnas-and-target-genes-in-ethylene-pathway-in-tomato
#3
Yunxiang Wang, Qing Wang, Lipu Gao, Benzhong Zhu, Zheng Ju, Yunbo Luo, Jinhua Zuo
Small RNAs are a class of short non-coding endogenous RNAs that play essential roles in many biological processes. Recent studies have reported that microRNAs (miRNAs) are also involved in ethylene signaling in plants. LeERF1 is one of the ethylene response factors (ERFs) in tomato that locates in the downstream of ethylene signal transduction pathway. To elucidate the intricate regulatory roles of small RNAs in ethylene signaling pathway in tomato, the deep sequencing and bioinformatics methods were combined to decipher the small RNAs landscape in wild and sense-/antisense-LeERF1 transgenic tomato fruits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442344/mir-221-regulates-cd44-in-hepatocellular-carcinoma-through-the-pi3k-akt-mtor-pathway
#4
Jihye Kim, Jinmai Jiang, Mohamed Badawi, Thomas D Schmittgen
CD44 and miR-221 are upregulated in hepatocellular carcinoma (HCC) cell lines and tumors, however a connection between the two has not been identified. As the expression of miR-221 directly correlated with CD44 in HCC cells, we hypothesized that miR-221 may directly or indirectly regulate CD44 expression. Inhibition of miR-221 with antisense in Sk-Hep-1 or SNU-449 cell lines reduced CD44 protein expression while miR-221 mimic increased CD44 protein levels. miR-221 antisense did not alter the CD44 mRNA levels in Sk-Hep-1 or SNU-449 cells suggesting that regulation of CD44 protein occurs post transcriptionally...
April 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28440409/microrna-145-regulates-the-differentiation-of-human-adipose-derived-stem-cells-to-smooth-muscle-cells-via-targeting-kr%C3%A3-ppel-like-factor-4
#5
Kaisaier Aji, Yun Zhang, Abudusaimi Aimaiti, Yujie Wang, Mulati Rexiati, Baihetiya Azhati, Hamulati Tusong, Lei Cui, Chen Wang
Understanding the molecular mechanisms underlying human adipose-derived stem cell (hASC) differentiation to smooth muscle may contribute to the development of effective therapies for relevant muscle defects, such as bladder wall and urethral defects. A previous study described the differentiation of hASCs to smooth muscle cells (SMCs) by transforming growth factor-β1 (TGF-β1) and bone morphogenetic protein‑4 (BMP4) treatment. The present study investigated whether microRNA-145 (miR‑145) may be involved in the process of hASC differentiation...
April 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28437437/use-of-short-interfering-rna-delivered-by-cationic-liposomes-to-enable-efficient-down-regulation-of-ptpn22-gene-in-human-t-lymphocytes
#6
Valentina Perri, Marsha Pellegrino, Francesca Ceccacci, Anita Scipioni, Stefania Petrini, Elena Gianchecchi, Anna Lo Russo, Serena De Santis, Giovanna Mancini, Alessandra Fierabracci
Type 1 diabetes and thyroid disease are T cell-dependent autoimmune endocrinopathies. The standard substitutive administration of the deficient hormones does not halt the autoimmune process; therefore, development of immunotherapies aiming to preserve the residual hormonal cells, is of crucial importance. PTPN22 C1858T mutation encoding for the R620W lymphoid tyrosine phosphatase variant, plays a potential pathophysiological role in autoimmunity. The PTPN22 encoded protein Lyp is a negative regulator of T cell antigen receptor signaling; R620W variant, leading to a gain of function with paradoxical reduced T cell activation, may represent a valid therapeutic target...
2017: PloS One
https://www.readbyqxmd.com/read/28435135/noninvasive-delivery-of-oligonucleotide-by-penetratin-modified-polyplexes-to-inhibit-protein-expression-of-intraocular-tumor
#7
Lingyu Tai, Chang Liu, Kuan Jiang, Xishan Chen, Gang Wei, Weiyue Lu, Weisan Pan
Our present study aimed to develop an antisense oligonucleotide (ASO) delivery system to achieve gene silencing in intraocular tumor via topical instillation. ASO specific for luciferase was chosen as model drug, polyamidoamine (PG5) was employed to condense ASO, and penetratin (Pene) was used to enhance cellular uptake. Nanoscale PG5/ASO/Pene polyplex was stabilized via noncovalent bonding. In vitro evaluations indicated that PG5/ASO/Pene exhibited improved cell-penetrating and gene silencing ability compared with naked ASO and PG5/ASO...
April 20, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/28431250/nuclear-proximity-of-mtr4-to-rna-exosome-restricts-dna-mutational-asymmetry
#8
Junghyun Lim, Pankaj Kumar Giri, David Kazadi, Brice Laffleur, Wanwei Zhang, Veronika Grinstein, Evangelos Pefanis, Lewis M Brown, Erik Ladewig, Ophélie Martin, Yuling Chen, Raul Rabadan, François Boyer, Gerson Rothschild, Michel Cogné, Eric Pinaud, Haiteng Deng, Uttiya Basu
The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28430659/lncrna-afap1-as1-promotes-growth-and-metastasis-of-cholangiocarcinoma-cells
#9
Xiuhui Shi, Hang Zhang, Min Wang, Xiaodong Xu, Yan Zhao, Ruizhi He, Min Zhang, Min Zhou, Xu Li, Feng Peng, Chengjian Shi, Ming Shen, Xin Wang, Xingjun Guo, Renyi Qin
We investigated the role of actin filament associated protein 1 antisense RNA1 (AFAP1-AS1) lncRNA in promoting cholangiocarcinoma (CCA). qRT-PCR analysis of patient samples showed that AFAP1-AS1 expression was higher in CCA tumors than matched adjacent non-tumor tissue. AFAP1-AS1 levels were also higher in CCA cell lines (HuCCT1 and TFK-1) than a normal biliary epithelium cell line (HIBEpic). AFAP1-AS1 knockdown in CCA cell lines using shAFAP1-AS1 reduced cell proliferation and colony formation in CCK-8 and colony formation assays, respectively...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28427205/mns16a-tandem-repeat-minisatellite-of-human-telomerase-gene-functional-studies-in-colorectal-lung-and-prostate-cancer
#10
Philipp Hofer, Cornelia Zöchmeister, Christian Behm, Stefanie Brezina, Andreas Baierl, Angelina Doriguzzi, Vanita Vanas, Klaus Holzmann, Hedwig Sutterlüty-Fall, Andrea Gsur
MNS16A, a functional polymorphic tandem repeat minisatellite, is located in the promoter region of an antisense transcript of the human telomerase reverse transcriptase gene. MNS16A promoter activity depends on the variable number of tandem repeats (VNTR) presenting varying numbers of transcription factor binding sites for GATA binding protein 1. Although MNS16A has been investigated in multiple cancer epidemiology studies with incongruent findings, functional data of only two VNTRs (VNTR-243 and VNTR-302) were available thus far, linking the shorter VNTR to higher promoter activity...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420437/bidirectional-nucleolar-dysfunction-in-c9orf72-frontotemporal-lobar-degeneration
#11
Sarah Mizielinska, Charlotte E Ridler, Rubika Balendra, Annora Thoeng, Nathan S Woodling, Friedrich A Grässer, Vincent Plagnol, Tammaryn Lashley, Linda Partridge, Adrian M Isaacs
An intronic GGGGCC expansion in C9orf72 is the most common known cause of both frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). The repeat expansion leads to the generation of sense and antisense repeat RNA aggregates and dipeptide repeat (DPR) proteins, generated by repeat-associated non-ATG translation. The arginine-rich DPR proteins poly(glycine-arginine or GR) and poly(proline-arginine or PR) are potently neurotoxic and can localise to the nucleolus when expressed in cells, resulting in enlarged nucleoli with disrupted functionality...
April 18, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28412515/genome-wide-determination-of-transcription-start-sites-reveals-new-insights-into-promoter-structures-in-the-actinomycete-corynebacterium-glutamicum
#12
Andreas Albersmeier, Katharina Pfeifer-Sancar, Christian Rückert, Jörn Kalinowski
The genome-wide identification of transcription start sites, enabled by high-throughput sequencing of a cDNA library enriched for native 5' transcript ends, is ideally suited for the analysis of promoters. Here, the transcriptome of Corynebacterium glutamicum, a non-pathogenic soil bacterium from the actinomycetes branch that is used in industry for the production of amino acids, was analysed by transcriptome sequencing of the 5'-ends of native transcripts. Total RNA samples were harvested from the exponential phase of growth, therefore the study mainly addressed promoters recognized by the main house-keeping sigma factor σ(A)...
April 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28412171/gender-specific-amelioration-of-sma-phenotype-upon-disruption-of-a-deep-intronic-structure-by-an-oligonucleotide
#13
Matthew D Howell, Eric W Ottesen, Natalia N Singh, Rachel L Anderson, Ravindra N Singh
Spinal muscular atrophy (SMA), the leading genetic disease of children, is caused by low levels of survival motor neuron (SMN) protein. Here, we employ A15/283, an antisense oligonucleotide targeting a deep intronic sequence/structure, to examine the impact of restoration of SMN in a mild SMA mouse model. We show gender-specific amelioration of tail necrosis upon subcutaneous administrations of A15/283 into SMA mice at postnatal days 1 and 3. We also demonstrate that a modest increase in SMN due to early administrations of A15/283 dramatically improves testicular development and spermatogenesis...
April 13, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28411216/construction-of-a-dcas9-based-gene-knockdown-system-in-staphylococcus-aureus
#14
Changlong Zhao, Xueqin Shu, Baolin Sun
There has been constant absence of an efficient gene knockdown method in the important human pathogen Staphylococcus aureus like RNA interference in eukaryotes. The early developed antisense RNA technology is mainly applied for forward genetic screen, but is rather limiting in specific gene knockdown for the lack of rational antisense RNA design strategies. Here we report an efficient and specific gene knockdown system in S. aureus based on type II clustered regularly interspaced short palindromic repeats (CRISPR) system from Streptococcus pyogenes...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28410209/mir-106b-inhibitors-sensitize-trail-induced-apoptosis-in-hepatocellular-carcinoma-through-increase-of-death-receptor-4
#15
Changlong Xu, Liang Shi, Weilai Chen, Peipei Fang, Jie Li, Lingxiang Jin, Zhenzhen Pan, Chenwei Pan
TNF-related apoptosis-inducing ligand (TRAIL), which is a member of the TNF superfamily, can induce tumor cell apoptosis. However, multiple types of tumor, including hepatocellular carcinoma, show tolerance to TRAIL. Previous studies have demonstrated that tumor cells usually change their expression profile of microRNA (miRNA) to obtain the ability of tolerance to drugs. However, whether such change of miRNA on TRAIL sensitivity is seen in hepatocellular carcinoma still needs to be explored. In this study, we observed overexpression of miR-106b in both HCC patients' tumor tissues and cell lines...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28408313/preventing-cardiovascular-heart-disease-promising-nutraceutical-and-non-nutraceutical-treatments-for-cholesterol-management
#16
REVIEW
T P Johnston, T A Korolenko, M Pirro, A Sahebkar
Hypercholesterolemia is one of the major risk factors for the development of cardiovascular disease. Atherosclerosis resulting from hypercholesterolemia causes many serious cardiovascular diseases. Statins are generally accepted as a treatment of choice for lowering low-density lipoprotein (LDL) cholesterol, which reduces coronary heart disease morbidity and mortality. Since statin use can be associated with muscle problems and other adverse symptoms, non-adherence and discontinuation of statin therapy often leads to inadequate control of plasma cholesterol levels and increased cardiovascular risk...
April 10, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28406439/protein-coding-genes-retrocopies-and-their-functions
#17
REVIEW
Magdalena Regina Kubiak, Izabela Makałowska
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of "relaxed" selection and remain "dormant" because they are lacking regulatory regions; however, many become functional...
April 13, 2017: Viruses
https://www.readbyqxmd.com/read/28405024/antisense-oligonucleotide-therapy-for-spinocerebellar-ataxia-type-2
#18
Daniel R Scoles, Pratap Meera, Matthew D Schneider, Sharan Paul, Warunee Dansithong, Karla P Figueroa, Gene Hung, Frank Rigo, C Frank Bennett, Thomas S Otis, Stefan M Pulst
There are no disease-modifying treatments for adult human neurodegenerative diseases. Here we test RNA-targeted therapies in two mouse models of spinocerebellar ataxia type 2 (SCA2), an autosomal dominant polyglutamine disease. Both models recreate the progressive adult-onset dysfunction and degeneration of a neuronal network that are seen in patients, including decreased firing frequency of cerebellar Purkinje cells and a decline in motor function. We developed a potential therapy directed at the ATXN2 gene by screening 152 antisense oligonucleotides (ASOs)...
April 20, 2017: Nature
https://www.readbyqxmd.com/read/28405022/therapeutic-reduction-of-ataxin-2-extends-lifespan-and-reduces-pathology-in-tdp-43-mice
#19
Lindsay A Becker, Brenda Huang, Gregor Bieri, Rosanna Ma, David A Knowles, Paymaan Jafar-Nejad, James Messing, Hong Joo Kim, Armand Soriano, Georg Auburger, Stefan M Pulst, J Paul Taylor, Frank Rigo, Aaron D Gitler
Amyotrophic lateral sclerosis (ALS) is a rapidly progressing neurodegenerative disease that is characterized by motor neuron loss and that leads to paralysis and death 2-5 years after disease onset. Nearly all patients with ALS have aggregates of the RNA-binding protein TDP-43 in their brains and spinal cords, and rare mutations in the gene encoding TDP-43 can cause ALS. There are no effective TDP-43-directed therapies for ALS or related TDP-43 proteinopathies, such as frontotemporal dementia. Antisense oligonucleotides (ASOs) and RNA-interference approaches are emerging as attractive therapeutic strategies in neurological diseases...
April 20, 2017: Nature
https://www.readbyqxmd.com/read/28404970/pseudogene-phbp1-promotes-esophageal-squamous-cell-carcinoma-proliferation-by-increasing-its-cognate-gene-phb-expression
#20
Feiyue Feng, Bin Qiu, Ruochuan Zang, Peng Song, Shugeng Gao
Natural antisense transcripts (NATs) as one of the most diverse classes of long noncoding RNAs (lncRNAs), have been demonstrated involved in fundamental biological processes in human. Here, we reported that human prohibitin gene pseudogene 1 (PHBP1) was upregulated in ESCC, and increased PHBP1 expression in ESCC was associated with clinical advanced stage. Functional experiments showed that PHBP1 knockdown inhibited ESCC cells proliferation, colony formation and xenograft tumor growth in vitro and in vivo by causing cell-cycle arrest at the G1-G0 phase...
March 16, 2017: Oncotarget
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