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https://www.readbyqxmd.com/read/28918050/the-function-and-therapeutic-potential-of-long-non-coding-rnas-in-cardiovascular-development-and-disease
#1
REVIEW
Clarissa P C Gomes, Helen Spencer, Kerrie L Ford, Lauriane Y M Michel, Andrew H Baker, Costanza Emanueli, Jean-Luc Balligand, Yvan Devaux
The popularization of genome-wide analyses and RNA sequencing led to the discovery that a large part of the human genome, while effectively transcribed, does not encode proteins. Long non-coding RNAs have emerged as critical regulators of gene expression in both normal and disease states. Studies of long non-coding RNAs expressed in the heart, in combination with gene association studies, revealed that these molecules are regulated during cardiovascular development and disease. Some long non-coding RNAs have been functionally implicated in cardiac pathophysiology and constitute potential therapeutic targets...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28916722/phosphoproteomics-reveals-that-glycogen-synthase-kinase-3-phosphorylates-multiple-splicing-factors-and-is-associated-with-alternative-splicing
#2
Mansi Y Shinde, Simone Sidoli, Katarzyna Kulej, Michael J Mallory, Caleb M Radens, Amanda Reicherter, Rebecca L Myers, Yoseph Barash, Kristen W Lynch, Benjamin A Garcia, Peter S Klein
Glycogen Synthase Kinase-3 (GSK-3) is a constitutively active, ubiquitously expressed protein kinase that regulates multiple signaling pathways. In vitro kinase assays and genetic and pharmacological manipulations of GSK-3 have identified more than 100 putative GSK-3 substrates in diverse cell types. Many more have been predicted on the basis of a recurrent GSK-3 consensus motif (pS/pTXXXS/T), but this prediction has not been tested by analyzing the GSK-3 phosphoproteome. Using stable isotope labeling of amino acids in culture (SILAC) and mass spectrometry (MS) techniques to analyze the repertoire of GSK-3-dependent phosphorylation in mouse embryonic stem cells (ESCs), we found that ~2...
September 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28916639/small-rna-seq-during-acute-maximal-exercise-reveal-rnas-involved-in-vascular-inflammation-and-cardiometabolic-health
#3
Ravi Shah, Ashish S Yeri, Avash Das, Amanda Courtright-Lim, Olivia Ziegler, Ernest Gervino, Jeffrey Ocel, Pablo Quintero Pinzon, Luke Wooster, Cole Shields Bailey, Kahraman Tanriverdi, Lea Beaulieu, Jane E Freedman, Ionita Ghiran, Gregory D Lewis, Kendall Van Keuren-Jensen, Saumya Das
OBJECTIVE: Exercise improves cardiometabolic and vascular function, though mechanisms remain unclear. Our objective was to demonstrate the diversity of circulating extracellular RNA (ex-RNA) release during acute exercise in humans and its relevance to exercise-mediated benefits on vascular inflammation. Approach and Results: We performed plasma small RNA sequencing (RNA-seq) in 26 individuals undergoing symptom-limited maximal treadmill exercise, with replication of our top candidate miRNA in a separate cohort of 59 individuals undergoing bicycle ergometry...
September 15, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28916481/identification-of-2-4-dihydroxy-5-pyrimidinyl-imidothiocarbomate-as-a-novel-inhibitor-to-y-box-binding-protein-1-yb-1-and-its-therapeutic-actions-against-breast-cancer
#4
Vinoth Prasanna Gunasekaran, Kumari Nishi, Dakshinamurthy Sivakumar, Thirunavukkarasu Sivaraman, Ganeshan Mathan
In spite of advances in breast cancer treatment and early diagnosis, drug toxicity, cancer relapse, multidrug resistance and metastasis are the major impediment to the developments of efficient drugs. However, unique druggable targets of cancer cells distinct from the normal cells provide new rationale in cancer treatment. Previous reports clearly emphasize the differential expression and localization of Y box binding protein-1 (YB-1) between normal breast tissues and different stages of breast cancer. Y box binding protein-1 is DNA as well as RNA binding protein involved in transcription and translation regulation of various proteins involved in cancer progression, apoptosis, cell cycle, epithelial to mesenchymal transition (EMT) and drug resistance...
September 12, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28916360/trancriptome-profiles-of-amur-sturgeon-spleen-in-response-to-yersinia-ruckeri-infection
#5
Shaowu Li, Ying Zhang, Yongsheng Cao, Di Wang, Hongbai Liu, Tongyan Lu
Yersinia ruckeri (YR) is the causative agent of yersiniosis which has caused significant economic losses in fish culture worldwide, including in Amur sturgeon (Acipenser schrenckii) culture. To better understand the mechanism of the immune responses to YR in Amur sturgeon, the transcriptomic profiles of the spleens from YR-infected and non-infected groups were obtained using RNA-seq techniques. The de novo assemblies yielded totally 145 670 unigenes from the two libraries. The total numbers of transcripts in YR-infected and non-infected groups were from 110 893 to 147 336, with the mean length varying from 560 to 631 (N50: from 882 to 1083)...
September 12, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28910938/-comparison-of-commercial-hiv-1-viral-load-tests-by-using-proficiency-test-results-in-china-2013-2015
#6
L Zhang, C Jin, Z Jiang, T Tang, Y Jiang, P L Pan
Objective: To compare the bio-equivalence among commercial HIV-1 viral load tests, including EasyQ HIV-1 v2.0 (EasyQ) from bioMerieux NucliSens of France; VERSANT HIV-1 RNA 3.0 assay (bDNA) from Siemens Healthcare Diagnostics of USA; COBAS AmpliPrep/COBAS TaqMan HIV-1 test (Taqman) from Roche Molecular Diagnosis of USA; Abbott Real Time HIV-1 Kit (M2000) from Abbott Molecular of USA and two domestic HIV-1 viral load test kits (domestic kit) from DaAn Gene Company of Sun Yat-Sen University and Liaoning Bio-Pharmaceutical company of Northeast pharmaceutical group, by using proficiency test results in China from 2013 to 2015...
September 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28910620/ctag-paperclip-reveals-alternative-polyadenylation-promotes-cell-type-specific-protein-diversity-and-shifts-araf-isoforms-with-microglia-activation
#7
Hun-Way Hwang, Yuhki Saito, Christopher Y Park, Nathalie E Blachère, Yoko Tajima, John J Fak, Ilana Zucker-Scharff, Robert B Darnell
Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell types, but obtaining APA maps from individual cell types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2...
September 13, 2017: Neuron
https://www.readbyqxmd.com/read/28905886/time-series-oligonucleotide-count-to-assign-antiviral-sirnas-with-long-utility-fit-in-the-big-data-era
#8
K Wada, Y Wada, Y Iwasaki, T Ikemura
Oligonucleotides are key elements of nucleic acid therapeutics such as small interfering RNAs (siRNAs). Influenza and Ebolaviruses are zoonotic RNA viruses mutating very rapidly, and their sequence changes must be characterized intensively to design therapeutic oligonucleotides with long utility. Focusing on a total of 182 experimentally validated siRNAs for influenza A, B and Ebolaviruses compiled by the siRNA database, we conducted time-series analyses of occurrences of siRNA targets in these viral genomes...
September 14, 2017: Gene Therapy
https://www.readbyqxmd.com/read/28904016/lncrna-ak017368-promotes-proliferation-and-suppresses-differentiation-of-myoblasts-in-skeletal-muscle-development-by-attenuating-the-function-of-mir-30c
#9
Tingting Liang, Bo Zhou, Lei Shi, Han Wang, Qingpo Chu, Feilong Xu, Yuan Li, Ruonan Chen, Chunyan Shen, Allan P Schinckel
Long noncoding RNAs (lncRNAs) have been reported to play diverse roles in biologic and pathologic processes, including myogenesis. We found that lncRNA AK017368 is highly expressed in skeletal muscle cells. Functional analyses showed that overexpression of AK017368 promoted proliferation and restrained differentiation of myoblasts; whereas inhibition of AK017368 had completely opposite effects in vitro In mice, knockdown of AK017368 promoted muscle hypertrophy in vivo RNA molecules of AK017368 acted mechanistically as competing endogenous RNAs to target micro-RNA (miR)-30c, which was supported by the results of bioinformatics analyses and dual-luciferase reporter assays...
September 13, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28900081/-mir-218-promoted-the-apoptosis-of-human-ovarian-carcinoma-cells-via-suppression-of-the-wnt-%C3%AE-catenin-signaling-pathway
#10
Y Huang, S-H Liang, L-B Xiang, X-T Han, W Zhang, J Tang, X-H Wu, M-Q Zhang
MicroRNA-218 (miR-218) is a short, noncoding RNA, with multiple biological functions. In this study, we aimed to investigate the potential effects of miR-218 on the apoptosis of human ovarian carcinoma cells and the underlying mechanisms by which miR-218 exerted its actions. After over-expressing miR-218 in human ovarian carcinoma (OVCAR3) cells, cell viability was determined by MTT method, cell apoptosis was observed by flow cytometry (FCM), mRNA expression of miR-218, Bcl2, Bax was measured by RT-PCR and protein expression levels of Wnt, tankyrase and β-catenin were quantified by Western blots...
July 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28895721/eukaryotic-ribosomal-expansion-segments-as-antimicrobial-targets
#11
Lizzette M Gómez Ramos, Natalya N Degtyareva, Nicholas A Kovacs, Stefany Y Holguin, Liuwei Jiang, Anton S Petrov, Marcin Biesiada, Michael Y Hu, Katarzyna J Purzycka, Dev Priya Arya, Loren Dean Williams
Diversity in eukaryotic rRNA structure and function offers possibilities of novel therapeutic targets. Unlike ribosomes of prokaryotes, eukaryotic ribosomes contain species-specific rRNA expansion segments (ESs) with idiosyncratic structures and functions that are essential and specific to some organisms. Here we investigate expansion segment 7 (ES7), one of the largest and most variable expansions of the eukaryotic ribosome. We hypothesize that ES7 of the pathogenic fungi Candida albicans (ES7CA) could be a prototypic drug target...
September 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28895414/knockdown-of-tripartite-motif-containing-28-suppresses-the-migration-invasion-and-epithelial-mesenchymal-transition-in-ovarian-carcinoma-cells-through-down-regulation-of-wnt-%C3%AE-catenin-signaling-pathway
#12
B Deng, S Zhang, Y Zhang, Y Miao, X Meng, K Guo
Tripartite motif containing 28 (TRIM28) is a transcriptional corepressor of Kruppel-associated box zinc finger protein, which has been reported to participate in carcinogenesis. Nonetheless, whether TRIM28 plays a role in the metastasis of ovarian carcinoma (OC) is unclear and requires further investigation. In this study, two OC cell lines (A2780 and OVCAR-3) with stable low expression of TRIM28 were established via RNA interference. We found that the migratory and invasive ability of TRIM28-silenced OC cells significantly decreased...
September 12, 2017: Neoplasma
https://www.readbyqxmd.com/read/28895409/long-noncoding-rna-asap1-it1-promotes-cancer-stemness-and-predicts-a-poor-prognosis-in-patients-with-bladder-cancer
#13
L Yang, Y Xue, J Liu, J Zhuang, L Shen, B Shen, J Yan, H Guo
Urinary bladder cancer (UBC) is one of the most common urogenital malignancies. Cancer stem-like cells (CSCs) play a vital role in tumor development and recurrence. Long noncoding RNAs (lncRNAs) are reported to influence cancer progression via transcriptional, posttranscriptional or epigenetic regulation. Dysregulation of several lncRNAs has been implicated in UBC. In our study, we found that an uncharacterized lncRNA, ASAP1-IT1, was overexpressed in UBC tissues compared with adjacent non-malignant tissues...
September 12, 2017: Neoplasma
https://www.readbyqxmd.com/read/28895406/identification-of-potential-key-genes-associated-with-diffuse-large-b-cell-lymphoma-based-on-microarray-gene-expression-profiling
#14
X Luo, F Shi, H Qiu, Y Tong, X Gao
The study aimed to screen potential key genes, and their targeted miRNAs and transcription factors (TFs) that were related to diffuse large B-cell lymphoma (DLBCL), and explore potential therapeutic targets for the progression of DLBCL. Dataset GSE56315 extracted from human tonsils was downloaded from Gene Expression Omnibus. Limma package was used to identify differential expression genes (DEG) between DLBCL and normal human tonsils samples, and the function and pathway enrichment analyses were performed. Then, functional interaction (FI) networks analyses of DEGs were implemented, and modules were extracted...
September 12, 2017: Neoplasma
https://www.readbyqxmd.com/read/28892262/glycan-stimulation-enables-purification-of-prostate-cancer-circulating-tumor-cells-on-pedot-nanovelcro-chips-for-rna-biomarker-detection
#15
Mo-Yuan Shen, Jie-Fu Chen, Chun-Hao Luo, Sangjun Lee, Cheng-Hsuan Li, Yung-Ling Yang, Yu-Han Tsai, Bo-Cheng Ho, Li-Rong Bao, Tien-Jung Lee, Yu Jen Jan, Ya-Zhen Zhu, Shirley Cheng, Felix Y Feng, Peilin Chen, Shuang Hou, Vatche Agopian, Yu-Sheng Hsiao, Hsian-Rong Tseng, Edwin M Posadas, Hsiao-Hua Yu
A glycan-stimulated and poly(3,4-ethylene-dioxythiophene)s (PEDOT)-based nanomaterial platform is fabricated to purify circulating tumor cells (CTCs) from blood samples of prostate cancer (PCa) patients. This new platform, phenylboronic acid (PBA)-grafted PEDOT NanoVelcro, combines the 3D PEDOT nanosubstrate, which greatly enhances CTC capturing efficiency, with a poly(EDOT-PBA-co-EDOT-EG3) interfacial layer, which not only provides high specificity for CTC capture upon antibody conjugation but also enables competitive binding of sorbitol to gently release the captured cells...
September 11, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28892047/a-system-for-detecting-high-impact-low-frequency-mutations-in-primary-tumors-and-metastases
#16
M Anjanappa, Y Hao, E R Simpson, P Bhat-Nakshatri, J B Nelson, S A Tersey, R G Mirmira, A A Cohen-Gadol, M R Saadatzadeh, L Li, F Fang, K P Nephew, K D Miller, Y Liu, H Nakshatri
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis...
September 11, 2017: Oncogene
https://www.readbyqxmd.com/read/28891069/use-of-supplemental-anti-hbc-testing-of-donors-showing-non-discriminating-reactive-results-in-multiplex-nucleic-acid-testing
#17
J W Kang, J H Seo, K W Youn, Y I Seo, K Huh, G R Choi, H K Min, D J Oh, H J Jo, J N Kim
BACKGROUND AND OBJECTIVES: The Korean Red Cross began nucleic acid amplification testing (NAT) for HIV and HCV in February 2005, and added HBV NAT beginning in June 2012. The current NAT system utilizes a multiplex assay for simultaneous detection of HBV DNA, HCV RNA and HIV-1 RNA. For samples that are reactive in the multiplex assay, we do specific tests for each virus. However, there have been cases of non-discriminated reactive (NDR) results which appear to be the result of non-specific reactions or cross-contamination, although some cases are considered to arise from the presence of low levels of HBV DNA due to occult hepatitis B infection...
September 10, 2017: Vox Sanguinis
https://www.readbyqxmd.com/read/28888129/leveraging-blood-and-tissue-cd4-t-cell-heterogeneity-at-the-single-cell-level-to-identify-mechanisms-of-disease-in-rheumatoid-arthritis
#18
REVIEW
Chamith Y Fonseka, Deepak A Rao, Soumya Raychaudhuri
CD4+ T cells have been long known to play an important role in the pathogenesis of rheumatoid arthritis (RA), but the specific cell populations and states that drive the disease have been challenging to identify with low dimensional single cell data and bulk assays. The advent of high dimensional single cell technologies-like single cell RNA-seq or mass cytometry-has offered promise to defining key populations, but brings new methodological and statistical challenges. Recent single cell profiling studies have revealed a broad diversity of cell types among CD4+ T cells, identifying novel populations that are expanded or altered in RA...
September 6, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28886318/new-insights-into-the-expression-profile-of-microrna-34c-and-p53-in-infertile-men-spermatozoa-and-testicular-tissue
#19
S Rahbar, M G Novin, E Alizadeh, V Shahnazi, F Pashaei-Asl, Y A AsrBadr, L Farzadi, E Ebrahimie, M Pashaiasl
Spermatogenesis is proliferation and differentiation processes of stem spermatogonia into mature spermatozoa controlled by the genes responsible for transcription and post transcription levels. MicroRNAs (miRNA) are  the key factors during gene expression in RNA silencing and post-transcriptional regulation. They play main roles in regulation of early and late spermatogenesis, and reproduction. In this study, we investigate the role of miRNAs in infertile males.The patients were assigned to five groups based on semen analysis (n=55), including normozoospermic (N), moderate oligoasthenoteratozoospermic (MOAT), severe oligoasthenoteratozoospermic (SOAT), obstructive azoospermia (OA) and non-obstructive azoospermia (NOA)...
August 30, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28886064/sexcmd-development-and-validation-of-sex-marker-sequences-for-whole-exome-genome-and-rna-sequencing
#20
Seongmun Jeong, Jiwoong Kim, Won Park, Hongmin Jeon, Namshin Kim
Over the last decade, a large number of nucleotide sequences have been generated by next-generation sequencing technologies and deposited to public databases. However, most of these datasets do not specify the sex of individuals sampled because researchers typically ignore or hide this information. Male and female genomes in many species have distinctive sex chromosomes, XX/XY and ZW/ZZ, and expression levels of many sex-related genes differ between the sexes. Herein, we describe how to develop sex marker sequences from syntenic regions of sex chromosomes and use them to quickly identify the sex of individuals being analyzed...
2017: PloS One
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