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https://www.readbyqxmd.com/read/28794025/retrovirus-based-virus-like-particle-immunogenicity-and-its-modulation-by-toll-like-receptor-activation
#1
Fabien Pitoiset, Thomas Vazquez, Beatrice Levacher, Djamel Nehar-Belaid, Nicolas Dérian, James Vigneron, David Klatzmann, Bertrand Bellier
Retrovirus-derived virus-like particles (VLPs) are particularly interesting vaccine platforms as they trigger efficient humoral and cellular immune responses and can be used to display heterologous antigens. In this study, we characterized the intrinsic immunogenicity of VLPs and investigated their possible adjuvantization by incorporation of toll-like receptor (TLR) ligands. We designed a non-coding single-stranded RNA (ncRNA) that could be encapsidated by VLPs and induce TLR7/8-signaling. We found that VLPs efficiently induce in vitro dendritic cell activation, which can be improved by ncRNA encapsidation (ncRNAVLPs)...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28777303/novel-biomarkers-in-the-diagnosis-of-chronic-kidney-disease-and-the-prediction-of-its-outcome
#2
REVIEW
Jacek Rysz, Anna Gluba-Brzózka, Beata Franczyk, Zbigniew Jabłonowski, Aleksandra Ciałkowska-Rysz
In its early stages, symptoms of chronic kidney disease (CKD) are usually not apparent. Significant reduction of the kidney function is the first obvious sign of disease. If diagnosed early (stages 1 to 3), the progression of CKD can be altered and complications reduced. In stages 4 and 5 extensive kidney damage is observed, which usually results in end-stage renal failure. Currently, the diagnosis of CKD is made usually on the levels of blood urea and serum creatinine (sCr), however, sCr has been shown to be lacking high predictive value...
August 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28765094/non-coding-rnas-as-a-new-dawn-in-tumor-diagnosis
#3
REVIEW
Anna Grimaldi, Mayra Rachele Zarone, Carlo Irace, Silvia Zappavigna, Angela Lombardi, Hiromichi Kawasaki, Michele Caraglia, Gabriella Misso
The current knowledge about non-coding RNAs (ncRNAs) as important regulators of gene expression in both physiological and pathological conditions, has been the main engine for the design of innovative platforms to finalize the pharmacological application of ncRNAs as either therapeutic tools or as molecular biomarkers in cancer. Biochemical alterations of cancer cells are, in fact, largely supported by ncRNA disregulation in the tumor site, which, in turn, reflects the cancer-associated specific modification of circulating ncRNA expression pattern...
July 29, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28762653/single-cell-transcriptomics-of-noncoding-rnas-and-their-cell-specificity
#4
REVIEW
Katerina A B Gawronski, Junhyong Kim
Recent developments of single cell transcriptome profiling methods have led to the realization that many seemingly homogeneous cells have surprising levels of expression variability. The biological implications of the high degree of variability is unclear but one possibility is that many genes are restricted in expression to small lineages of cells, suggesting the existence of many more cell types than previously estimated. Noncoding RNA (ncRNA) are thought to be key parts of gene regulatory processes and their single cell expression patterns may help to dissect the biological function of single cell variability...
August 1, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28760736/targeting-long-non-coding-rna-dancr-inhibits-triple-negative-breast-cancer-progression
#5
Sha Sha, Dongya Yuan, Yuejun Liu, Baosan Han, Nanbert Zhong, Zhiqiang Liu
Triple negative breast cancer (TNBC) is non-responsive to conventional anti-hormonal and Her2 targeted therapies, making it necessary to identify new molecular targets for therapy. Long non-coding RNA anti-differentiation ncRNA (lncRNA DANCR) was identified in participating carcinogenesis of hepatocellular carcinoma, but its expression and potential role in TNBC progression is still unclear. In the present study, our results showed that DANCR expression was increased in TNBC tissues compared with the adjacent normal tissues using quantitative real-time PCR (qRT-PCR) in 63 TNBC specimens...
July 31, 2017: Biology Open
https://www.readbyqxmd.com/read/28757239/beyond-mrna-the-role-of-non-coding-rnas-in-normal-and-aberrant-hematopoiesis
#6
REVIEW
Mark C Wilkes, Claire E Repellin, Kathleen M Sakamoto
The role of non-coding Ribonucleic Acids (ncRNAs) in biology is currently an area of intense focus. Hematopoiesis requires rapidly changing regulatory molecules to guide appropriate differentiation and ncRNA are well suited for this. It is not surprising that virtually all aspects of hematopoiesis have roles for ncRNAs assigned to them and doubtlessly much more await characterization. Stem cell maintenance, lymphoid, myeloid and erythroid differentiation are all regulated by various ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and various transposable elements within the genome...
July 25, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28751461/novel-aberrations-uncovered-in-barrett-s-esophagus-and-esophageal-adenocarcinoma-using-whole-transcriptome-sequencing
#7
Jesper Maag, Oliver M Fisher, Angelique J Levert-Mignon, Dominik C Kaczorowski, Melissa L Thomas, Damian Hussey, David Watson, Antony Wettstein, Yuri V Bobryshev, Melanie Edwards, Marcel E Dinger, Reginald V Lord
Esophageal adenocarcinoma (EAC) has one of the fastest increases in incidence of any cancer, along with poor five-year survival rates. Barrett's esophagus (BE) is the main risk factor for EAC, however the mechanisms driving EAC development remain poorly understood. Here, transcriptomic profiling was performed using RNA-sequencing (RNA-seq) on premalignant and malignant Barrett's tissues to better understand this disease. Machine-learning and network analysis methods were applied to discover novel driver genes for EAC development...
July 27, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28736855/-lnc-ing-wnt-in-female-reproductive-cancers-therapeutic-potential-of-long-non-coding-rnas-in-wnt-signaling
#8
REVIEW
Mei S Ong, Wanpei Cai, Yi Yuan, Hin C Leong, Tuan Z Tan, Asad Mohammad, Ming L You, Frank Arfuso, Boon C Goh, Sudha Warrier, Gautam Sethi, Nicholas S Tolwinski, Peter E Lobie, Celestial T Yap, Shing C Hooi, Ruby Y Huang, Alan P Kumar
Recent discoveries in the non-coding genome have challenged the original central dogma of molecular biology; non-coding RNAs and related processes have been found to be important in regulating gene expression. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are amongst some that have gained attention recently in human diseases, including cancer, with the involvement of many more ncRNAs waiting to be discovered. Non-coding RNAs (ncRNAs) are a group of ribonucleic acids transcribed from regions of the human genome, which do not become translated into proteins, despite having essential roles in cellular physiology...
July 24, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28732356/the-circrna-interactome-innovative-hallmarks-of-the-intra-and-extracellular-radiation-response
#9
Valerie Bríd O'Leary, Jan Smida, Martina Matjanovski, Corinna Brockhaus, Klaudia Winkler, Simone Moertl, Saak Victor Ovsepian, Michael John Atkinson
Generated by Quaking (QKI), circular RNAs (circRNAs) are newly recognised non-coding RNA (ncRNA) members characterised by tissue specificity, increased stability and enrichment within exosomes. Studies have shown that ionizing radiation (IR) can influence ncRNA transcription. However, it is unknown whether circRNAs or indeed QKI are regulated by IR. Microarray circRNA profiling and next generation sequencing revealed that circRNA expression was altered by low and medium dose exposure sourced predominantly from genes influencing the p53 pathway...
July 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28716689/brg1-and-smarcal1-transcriptionally-co-regulate-drosha-dgcr8-and-dicer-in-response-to-doxorubicin-induced-dna-damage
#10
Ketki Patne, Radhakrishnan Rakesh, Vijendra Arya, Upasana Bedi Chanana, Ramesh Sethy, Pynskhem Bok Swer, Rohini Muthuswami
Recent investigations have emphasized the role of miRNA biogenesis proteins in the synthesis of non-coding RNA when double-strand DNA breaks are induced by ionizing radiations. However, the role of these non-coding RNA and their regulation in response to doxorubicin-induced DNA damage is not known. In this paper, BRG1 and SMARCAL1, members of the ATP-dependent chromatin remodelling family, are shown to co-regulate the transcription of DROSHA, DGCR8, and DICER in response to double-strand DNA breaks induced by doxorubicin...
July 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28701522/yeast-non-coding-rna-interaction-network
#11
Simona Panni, Ananth Prakash, Alex Bateman, Sandra Orchard
This article describes the creation of the first expert manually curated non-coding RNA interaction networks for S. cerevisiae. The RNA-RNA and RNA-protein interaction networks have been carefully extracted from the experimental literature and made available through the IntAct database (www.ebi.ac.uk/intact). We provide an initial network analysis and compare their properties to the much larger protein-protein interaction network. We find that the proteins that bind to ncRNAs in the network contain only a small proportion of classical RNA binding domains...
July 12, 2017: RNA
https://www.readbyqxmd.com/read/28699365/activating-the-chromatin-by-noncoding-rnas
#12
Nihay Laham-Karam, Pia Laitinen, Tiia A Turunen, Seppo Ylä-Herttuala
SIGNIFICANCE: The extent and breadth of transcription have recently been uncovered and this has revealed an extensive array of noncoding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realized and to date it appears that ncRNAs may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and posttranscriptional regulation, including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding...
August 10, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28698797/new-technologies-accelerate-the-exploration-of-non-coding-rnas-in-horticultural-plants
#13
REVIEW
Degao Liu, Ritesh Mewalal, Rongbin Hu, Gerald A Tuskan, Xiaohan Yang
Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28698299/neat1-is-a-p53-inducible-lincrna-essential-for-transformation-suppression
#14
Stephano S Mello, Carolyn Sinow, Nitin Raj, Pawel K Mazur, Kathryn Bieging-Rolett, Daniela Kenzelmann Broz, Jamie F Conklin Imam, Hannes Vogel, Laura D Wood, Julien Sage, Tetsuro Hirose, Shinichi Nakagawa, John Rinn, Laura D Attardi
The p53 gene is mutated in over half of all cancers, reflecting its critical role as a tumor suppressor. Although p53 is a transcriptional activator that induces myriad target genes, those p53-inducible genes most critical for tumor suppression remain elusive. Here, we leveraged p53 ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) and RNA-seq (RNA sequencing) data sets to identify new p53 target genes, focusing on the noncoding genome. We identify Neat1, a noncoding RNA (ncRNA) constituent of paraspeckles, as a p53 target gene broadly induced by mouse and human p53 in different cell types and by diverse stress signals...
June 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28679390/lncrna-ancr-regulates-the-cell-growth-of-osteosarcoma-by-interacting-with-ezh2-and-affecting-the-expression-of-p21-and-p27
#15
Fei Zhang, Hao Peng
BACKGROUND: Osteosarcoma (OS) is one of the most common malignant tumors developed in the bone. EZH2 has been found to play pivotal roles in the development of various cancers. LncRNA-ANCR (anti-differentiation ncRNA) has been reported to interact with EZH2 and regulated osteoblast differentiation. Our study aimed to investigate the effect of lncRNA-ANCR on the tumorigenesis of osteosarcoma and explore the underlying molecular mechanism. METHODS: RT-PCR was performed to detect the messenger RNA (mRNA) levels of lncRNA-ANCR, EZH2, p21, and p27 in OS tissues and cell lines...
July 5, 2017: Journal of Orthopaedic Surgery and Research
https://www.readbyqxmd.com/read/28669734/inhibition-of-mir-664a-interferes-with-the-migration-of-osteosarcoma-cells-via-modulation-of-meg3
#16
Yunus Sahin, Zekiye Altan, Kaifee Arman, Esra Bozgeyik, Meltem Koruk Ozer, Ahmet Arslan
Osteosarcoma is the most common primary bone tumor in children and adolescents. Understanding the basic molecular mechanisms in developing cancer can be helpful in developing alternative treatment strategies. The relationship between dysregulated non-coding RNAs' (ncRNA) expression level and osteosarcoma was detected. Among those ncRNAs, the expression levels of miR-664a were detected to be upregulated and MEG3 long non-coding RNA levels were detected to be downregulated in osteosarcoma tissue and cell lines...
August 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28652179/non-coding-rna-regulation-of-t-cell-biology-implications-for-age-associated-cardiovascular-diseases
#17
REVIEW
Jose Coelho-Lima, Ioakim Spyridopoulos
Prevalence of age-associated cardiovascular diseases (CVD) has dramatically increased as a result of improvements in life expectancy. Chronic inflammation is a shared pathophysiological feature of age-associated CVDs, indicating a role for the immune system in the onset and development of CVDs. Indeed, ageing elicits profound changes in both the cardiovascular and immune system, especially in the T cell compartment. Although such changes have been well described at the cellular level, the molecular mechanisms underlying immune-mediated cardiovascular ageing remain largely unexplored...
June 23, 2017: Experimental Gerontology
https://www.readbyqxmd.com/read/28645654/epigenome-dysregulation-in-cholangiocarcinoma
#18
REVIEW
Colm J O'Rourke, Patricia Munoz-Garrido, Esmeralda L Aguayo, Jesper B Andersen
Epigenomics is a fast-evolving field of research that has lately attracted considerable interest, mainly due to the reversibility of epigenetic marks. Clinically, among solid tumors, the field is still limited. In cholangiocarcinoma (CCA) it is well known that the epigenetic landscape is deregulated both during carcinogenesis and disease progression as a consequence of aberrant mechanisms leading to genome instability. In this article, we will briefly review the molecular alterations that have been described in the transformation of normal cholangiocytes into malignant derivatives, focusing on the role of non-coding RNA (ncRNA) interactions, DNA methylation, post-translational modifications (PTMs) of histones and chromatin remodeling complexes...
June 20, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28643459/construction-of-competitive-endogenous-rna-network-reveals-regulatory-role-of-long-non-coding-rnas-in-type-2-diabetes-mellitus
#19
Zijing Lin, Xinyu Li, Xiaorong Zhan, Lijie Sun, Jie Gao, Yan Cao, Hui Qiu
Increasing epidemic of type 2 diabetes mellitus (T2DM) and its comorbidities makes it urgent to understand the pathogenesis and regulatory mechanism. However, little is known about the regulatory role of lncRNAs in diabetes. Here, we constructed a T2DM-related competitive endogenous RNA (ceRNA) network (DMCN) to explore biological function of lncRNAs during the development of diabetes mellitus. This network contained 351 nodes including 98 mRNAs, 86 microRNAs and 167 lncRNAs. Functional analysis showed that the mRNAs in DMCN were annotated into some diabetes-related pathways...
June 23, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28641521/lncrna-hotair-polymorphisms-association-with-cancer-susceptibility-in-different-tumor-types
#20
Gerardo Botti, Francesca Collina, Giosuè Scognamiglio, Gabriella Aquino, Margherita Cerrone, Giuseppina Liguori, Vincenzo Gigantino, Maria Gabriella Malzone, Monica Cantile
Single nucleotide polymorphisms (SNPs) in non coding RNAs (ncRNA) molecules affect gene and protein expression and generate genetic variability influencing the risk of tumor diseases. HOTAIR is locates at the heart of the cell memory gene program and represents a prototype of long non coding RNA (LncRNA) due to its capacity to regulate in-trans a distant chromosome landscape. Aberrant expression of HOTAIR is frequently associated with pathogenesis and mostly with metastatic progression of several human cancers...
June 21, 2017: Current Drug Targets
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