Journal articles: 'Non-coding RNA detection'

1

Kazimierczyk, Marek, and Jan Wrzesinski. "Long Non-Coding RNA Epigenetics." International Journal of Molecular Sciences 22, no. 11 (June 7, 2021): 6166. http://dx.doi.org/10.3390/ijms22116166.

Full text

Abstract:

Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine–inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes.

APA, Harvard, Vancouver, ISO, and other styles

2

Romano, Giulia, Michela Saviana, Patricia Le, Howard Li, Lavender Micalo, Giovanni Nigita, Mario Acunzo, and Patrick Nana-Sinkam. "Non-Coding RNA Editing in Cancer Pathogenesis." Cancers 12, no. 7 (July 8, 2020): 1845. http://dx.doi.org/10.3390/cancers12071845.

Full text

Abstract:

In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.

APA, Harvard, Vancouver, ISO, and other styles

3

Falahi, Sedigheh, Hossain-Ali Rafiee-Pour, Mashaalah Zarejousheghani, Parvaneh Rahimi, and Yvonne Joseph. "Non-Coding RNA-Based Biosensors for Early Detection of Liver Cancer." Biomedicines 9, no. 8 (August 5, 2021): 964. http://dx.doi.org/10.3390/biomedicines9080964.

Full text

Abstract:

Primary liver cancer is an aggressive, lethal malignancy that ranks as the fourth leading cause of cancer-related death worldwide. Its 5-year mortality rate is estimated to be more than 95%. This significant low survival rate is due to poor diagnosis, which can be referred to as the lack of sufficient and early-stage detection methods. Many liver cancer-associated non-coding RNAs (ncRNAs) have been extensively examined to serve as promising biomarkers for precise diagnostics, prognostics, and the evaluation of the therapeutic progress. For the simple, rapid, and selective ncRNA detection, various nanomaterial-enhanced biosensors have been developed based on electrochemical, optical, and electromechanical detection methods. This review presents ncRNAs as the potential biomarkers for the early-stage diagnosis of liver cancer. Moreover, a comprehensive overview of recent developments in nanobiosensors for liver cancer-related ncRNA detection is provided.

APA, Harvard, Vancouver, ISO, and other styles

4

Nacher, Jose C. "Community structure of non-coding RNA interaction network." Journal of Integrative Bioinformatics 10, no. 2 (June 1, 2013): 24–34. http://dx.doi.org/10.1515/jib-2013-217.

Full text

Abstract:

Summary Rapid technological advances have shown that the ratio of non-protein coding genes rises to 98.5% in humans, suggesting that current knowledge on genetic information processing might be largely incomplete. It implies that protein-coding sequences only represent a small fraction of cellular transcriptional information. Here, we examine the community structure of the network defined by functional interactions between noncoding RNAs (ncRNAs) and proteins related bio-macrolecules (PRMs) using a two-fold approach: modularity in bipartite network and k-clique community detection. First, the high modularity scores as well as the distribution of community sizes showing a scaling-law revealed manifestly non-random features. Second, the k-clique sub-graphs and overlaps show that the identified communities of the ncRNA molecules of H. sapiens can potentially be associated with certain functions. These findings highlight the complex modular structure of ncRNA interactions and its possible regulatory roles in the cell.

APA, Harvard, Vancouver, ISO, and other styles

5

Boivin, Vincent, Gaspard Reulet, Olivier Boisvert, Sonia Couture, Sherif Abou Elela, and Michelle S. Scott. "Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA." Nucleic Acids Research 48, no. 5 (January 25, 2020): 2271–86. http://dx.doi.org/10.1093/nar/gkaa028.

Full text

Abstract:

Abstract The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. Transcripts between 20 and 500 nucleotides were filtered and crosschecked with non-coding RNA annotations revealing 111 non-annotated non-coding RNAs expressed in different cell lines and tissues. Inspecting the sequence and structural features of these transcripts indicated that 60% of these transcripts correspond to new snoRNA and tRNA-like genes. The identified genes exhibited features of their respective families in terms of structure, expression, conservation and response to depletion of interacting proteins. Together, our data reveal a new group of RNA that are difficult to detect using standard gene prediction and RNA sequencing techniques, suggesting that reliance on actual gene annotation and sequencing techniques distorts the perceived architecture of the human transcriptome.

APA, Harvard, Vancouver, ISO, and other styles

6

Islam, Md Nazmul, Sofia Moriam, Muhammad Umer, Hoang-Phuong Phan, Carlos Salomon, Richard Kline, Nam-Trung Nguyen, and Muhammad J. A. Shiddiky. "Naked-eye and electrochemical detection of isothermally amplified HOTAIR long non-coding RNA." Analyst 143, no. 13 (2018): 3021–28. http://dx.doi.org/10.1039/c7an02109g.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

Tabei, Yasuo, and Kiyoshi Asai. "A local multiple alignment method for detection of non-coding RNA sequences." Bioinformatics 25, no. 12 (April 17, 2009): 1498–505. http://dx.doi.org/10.1093/bioinformatics/btp261.

Full text

APA, Harvard, Vancouver, ISO, and other styles

8

Raasch, Peter, Ulf Schmitz, Nadja Patenge, Julio Vera, Bernd Kreikemeyer, and Olaf Wolkenhauer. "Non-coding RNA detection methods combined to improve usability, reproducibility and precision." BMC Bioinformatics 11, no. 1 (2010): 491. http://dx.doi.org/10.1186/1471-2105-11-491.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Chaabane, Mohamed, Robert M. Williams, Austin T. Stephens, and Juw Won Park. "circDeep: deep learning approach for circular RNA classification from other long non-coding RNA." Bioinformatics 36, no. 1 (July 3, 2019): 73–80. http://dx.doi.org/10.1093/bioinformatics/btz537.

Full text

Abstract:

Abstract Motivation Over the past two decades, a circular form of RNA (circular RNA), produced through alternative splicing, has become the focus of scientific studies due to its major role as a microRNA (miRNA) activity modulator and its association with various diseases including cancer. Therefore, the detection of circular RNAs is vital to understanding their biogenesis and purpose. Prediction of circular RNA can be achieved in three steps: distinguishing non-coding RNAs from protein coding gene transcripts, separating short and long non-coding RNAs and predicting circular RNAs from other long non-coding RNAs (lncRNAs). However, the available tools are less than 80 percent accurate for distinguishing circular RNAs from other lncRNAs due to difficulty of classification. Therefore, the availability of a more accurate and fast machine learning method for the identification of circular RNAs, which considers the specific features of circular RNA, is essential to the development of systematic annotation. Results Here we present an End-to-End deep learning framework, circDeep, to classify circular RNA from other lncRNA. circDeep fuses an RCM descriptor, ACNN-BLSTM sequence descriptor and a conservation descriptor into high level abstraction descriptors, where the shared representations across different modalities are integrated. The experiments show that circDeep is not only faster than existing tools but also performs at an unprecedented level of accuracy by achieving a 12 percent increase in accuracy over the other tools. Availability and implementation https://github.com/UofLBioinformatics/circDeep. Supplementary information Supplementary data are available at Bioinformatics online.

APA, Harvard, Vancouver, ISO, and other styles

10

Soda, Narshone, Muhammad Umer, Surasak Kasetsirikul, Carlos Salomon, Richard Kline, Nam-Trung Nguyen, Bernd H. A. Rehm, and Muhammad J. A. Shiddiky. "An amplification-free method for the detection of HOTAIR long non-coding RNA." Analytica Chimica Acta 1132 (October 2020): 66–73. http://dx.doi.org/10.1016/j.aca.2020.07.038.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

Vogel, Jörg, and Cynthia Mira Sharma. "How to find small non-coding RNAs in bacteria." Biological Chemistry 386, no. 12 (December 1, 2005): 1219–38. http://dx.doi.org/10.1515/bc.2005.140.

Full text

Abstract:

AbstractSmall non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacteriumEscherichia coli. Orthologs of theseE. colisRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.

APA, Harvard, Vancouver, ISO, and other styles

12

Kazimierczyk, Kasprowicz, Kasprzyk, and Wrzesinski. "Human Long Noncoding RNA Interactome: Detection, Characterization and Function." International Journal of Molecular Sciences 21, no. 3 (February 4, 2020): 1027. http://dx.doi.org/10.3390/ijms21031027.

Full text

Abstract:

The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter” belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.

APA, Harvard, Vancouver, ISO, and other styles

13

Zhang, Xuanping, Yidan Wang, Zhongmeng Zhao, and Jiayin Wang. "An Efficient Algorithm for Sensitively Detecting Circular RNA from RNA-seq Data." International Journal of Molecular Sciences 19, no. 10 (September 24, 2018): 2897. http://dx.doi.org/10.3390/ijms19102897.

Full text

Abstract:

Circular RNA (circRNA) is an important member of non-coding RNA family. Numerous computational methods for detecting circRNAs from RNA-seq data have been developed in the past few years, but there are dramatic differences among the algorithms regarding the balancing of the sensitivity and precision of the detection and filtering strategies. To further improve the sensitivity, while maintaining an acceptable precision of circRNA detection, a novel and efficient de novo detection algorithm, CIRCPlus, is proposed in this paper. CIRCPlus accurately locates circRNA candidates by identifying a set of back-spliced junction reads by comparing the local similar sequence of each pair of spanning junction reads. This strategy, thus, utilizes the important information provided by unbalanced spanning reads, which facilitates the detection especially when the expression levels of circRNA are unapparent. The performance of CIRCPlus was tested and compared to the existing de novo methods on the real datasets as well as a series of simulation datasets with different configurations. The experiment results demonstrated that the sensitivities of CIRCPlus were able to reach 90% in common simulation settings, while CIRCPlus held balanced sensitivity and reliability on the real datasets according to an objective assessment criteria based on RNase R-treated samples. The software tool is available for academic uses only.

APA, Harvard, Vancouver, ISO, and other styles

14

Marceca, Gioacchino P., Luisa Tomasello, Rosario Distefano, Mario Acunzo, Carlo M. Croce, and Giovanni Nigita. "Detecting and Characterizing A-To-I microRNA Editing in Cancer." Cancers 13, no. 7 (April 3, 2021): 1699. http://dx.doi.org/10.3390/cancers13071699.

Full text

Abstract:

Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. The employment of powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.

APA, Harvard, Vancouver, ISO, and other styles

15

Zhao, Youshan, Chunkang Chang, and Xiao Li. "Protein-Coding and Non-Coding RNA Expression Profiles Of Mesenchymal Stem Cells In Patients With Myelodysplastic Syndromes." Blood 122, no. 21 (November 15, 2013): 1572. http://dx.doi.org/10.1182/blood.v122.21.1572.1572.

Full text

Abstract:

Abstract Background A few reports have suggested chromosomal and gene expression abnormalities in mesenchymal stem cells in patients with MDS. Recently years, there is growing evidence for a role of the non-coding RNA in the transcriptional control of gene expression. Characterization of protein-coding and non-coding RNA expression in mesenchymal stem cells of MDS patients could be strategic for understanding gene expression regulation and role of marrow microenvironment in the pathophysiology of MDS. Methods In this study, gene expression profiles of MSC in 10 patients with MDS were compared with 5 healthy individuals using human transcriptome array. This array allows comprehensive examination of gene expression and noncoding transcripts, as well as detection of coding SNPs and genome-wide identification of alternative splicing. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts. Results In MSC of MDS patients, 2628 genes were significantly differentially expressed (p≤0.01) in comparison to healthy individuals, of which 945(36%) were protein-coding transcripts. Gene ontology and pathway analysis were performed on those protein-coding genes. The significant significant ontology themes for up-regulated gene in MDS include cell division, mitosis, DNA repair and regulation of transcription, and for down-regulated genes include cytokine-mediated signaling pathway, inflammatory response and positive regulation of mitosis. Pathway analysis identified the deregulated gene pathway were main associated with purine metabolism, cytokine-cytokine receptor interaction, toll-like receptor signaling pathway, and so on. In non-coding RNA, 79 were long noncoding RNA (LncRNA), which were reported in database. We used gene coexpression networks to cluster thousands of transcripts into phenotypically relevant coexpression modules. The coexpression patterns of lncRNAs and protein-coding RNAs in MDS and controls were different. In the MDS coexpression network, differentially expressed lncRNAs were mainly focused on gene function related to ribosome biogenesis, tRNA processing, and so on. Conclusions These results demonstrated the differential RNA expression profile between MDS and healthy individuals, suggesting that lncRNAs may play an important role in dysfunctional microenvironment in MDS. Disclosures: No relevant conflicts of interest to declare.

APA, Harvard, Vancouver, ISO, and other styles

16

Beylerli, O. A., A. T. Beylerli, and I. F. Gareev. "Long Non-Coding RNA as the Newest Perspective Biomarkers in Cancer." Innovative medicine of Kuban 14, no. 2 (June 22, 2019): 76–83. http://dx.doi.org/10.35401/2500-0268-2019-14-2-76-83.

Full text

Abstract:

Long non-coding RNAs (lncRNAs) are a large group of non-coding RNAs (ncRNAs) which are more than 200 nucleotides in length. LncRNAs, as regulation factors, show an important role in complex cellular processes, such as apoptosis, growth, differentiation, proliferation, etc. Recently, the results of many studies have also shown their significant role in carcinogenesis. Endogenous lncRNAs are known to be secreted by tumor cells in human biological fluids in the form of microvesicles, exosomes, or protein complexes, thereby forming circulating lncRNAs that do not degrade under the influence of RNases and are in a stable state. Compared with traditional biomarkers, as proteins circulating lncRNA have several advantages that will allow to consider circulating lncRNA as a new potential biomarker for various diseases. Aberrant expression of lncRNAs was observed in cancer patients. In this context, endogenous lncRNAs can regulate the main characteristics of cancer cells, controlling the expression of oncogenes associated with their suppressive and oncogenic functions. Consequently, circulating lncRNAs can be excellent biomarkers for cancer. Knowledge of the molecular mechanisms by which lncRNAs contribute to the development of cancer will improve our understanding of etiology, and open up horizons for the development of new biomarkers. In this paper, we will analyze current knowledge about the change in the expression profile of circulating lncRNAs in cancer, as well as methods for their detection.

APA, Harvard, Vancouver, ISO, and other styles

17

Nakamura, Kazuaki, Takeshi Akama, Pham Dang Bang, Shin Sekimura, Kazunari Tanigawa, Huhehasi Wu, Akira Kawashima, Moyuru Hayashi, Koichi Suzuki, and Norihisa Ishii. "Detection of RNA expression from pseudogenes and non-coding genomic regions of Mycobacterium leprae." Microbial Pathogenesis 47, no. 3 (September 2009): 183–87. http://dx.doi.org/10.1016/j.micpath.2009.06.006.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Toffano-Nioche, Claire, Yufei Luo, Claire Kuchly, Claire Wallon, Delphine Steinbach, Matthias Zytnicki, Annick Jacq, and Daniel Gautheret. "Detection of non-coding RNA in bacteria and archaea using the DETR’PROK Galaxy pipeline." Methods 63, no. 1 (September 2013): 60–65. http://dx.doi.org/10.1016/j.ymeth.2013.06.003.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

Peng, Hua, Jia Wang, Jia Li, Mei Zhao, Sheng-kai Huang, Yu-yu Gu, Yan Li, et al. "A circulating non-coding RNA panel as an early detection predictor of non-small cell lung cancer." Life Sciences 151 (April 2016): 235–42. http://dx.doi.org/10.1016/j.lfs.2016.03.002.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

Soda, Narshone, Muhammad Umer, Navid Kashaninejad, Surasak Kasetsirikul, Richard Kline, Carlos Salomon, Nam-Trung Nguyen, and Muhammad J. A. Shiddiky. "PCR-Free Detection of Long Non-Coding HOTAIR RNA in Ovarian Cancer Cell Lines and Plasma Samples." Cancers 12, no. 8 (August 10, 2020): 2233. http://dx.doi.org/10.3390/cancers12082233.

Full text

Abstract:

Long non-coding RNA HOX transcript antisense intergenic RNA (HOTAIR) is one of the promising biomarkers that has widely been used in determining the stages of many cancers, including ovarian cancer. In cancer diagnostics, the two key analytical challenges for detecting long non-coding RNA biomarkers are i) the low concentration levels (nM to fM range) in which they are found and ii) the analytical method where broad dynamic range is required (four to six orders of magnitude) due to the large variation in expression levels for different HOTAIR RNAs. To meet these challenges, we report on a biosensing platform for the visual (colorimetric) estimation and subsequent electrochemical quantification of ovarian-cancer-specific HOTAIR using a screen-printed gold electrode (SPE-Au). Our assay utilizes a two-step strategy that involves (i) magnetic isolation and purification of target HOTAIR sequences and (ii) subsequent detection of isolated sequences using a sandwich hybridization coupled with horseradish peroxidase (HRP)-catalyzed reaction of 3,3′,5,5′-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide. The assay achieved a detection limit of 1.0 fM HOTAIR in spiked buffer samples with excellent reproducibility (% RSD ≤ 5%, for n = 3). It was successfully applied to detect HOTAIR in cancer cell lines and a panel of plasma samples derived from patients with ovarian cancer. The analytical performance of the method was validated with standard RT-qPCR. We believe that the proof of concept assay reported here may find potential use in routine clinical settings for the screening of cancer-related lncRNAs.

APA, Harvard, Vancouver, ISO, and other styles

21

Liu, Hanshao, Deji Ye, Aijun Chen, Dan Tan, Wenpeng Zhang, Wenxia Jiang, Mingliang Wang, and Xiaoren Zhang. "A pilot study of new promising non-coding RNA diagnostic biomarkers for early-stage colorectal cancers." Clinical Chemistry and Laboratory Medicine (CCLM) 57, no. 7 (June 26, 2019): 1073–83. http://dx.doi.org/10.1515/cclm-2019-0052.

Full text

Abstract:

AbstractBackgroundDiagnostic biomarkers for the detection of colorectal cancers (CRCs) are lacking. Recent studies have demonstrated that circulating long non-coding RNAs have the potential to serve as biomarkers for the detection of cancers. We analyzed the significance of lncRNAs 91H, PVT-1 and MEG3 in the detection of CRC.MethodsWe examined the expression levels of 13 candidate lncRNAs in the plasma of 18 CRC patients and 20 non-cancerous controls. Then, we validated our findings by determining the expression levels of six promising lncRNAs in CRC tissues and normal colorectal tissues. Finally, we evaluated the clinical relevance of lncRNAs 91H, PVT-1 and MEG3 in the plasma of 58 CRC patients and 56 non-cancerous controls.ResultsOur data revealed that the expression levels of lncRNAs 91H, PVT-1 and MEG3 were significantly higher in plasma samples from CRC patients than in those from non-cancerous controls. The combination of 91H, PVT-1 and MEG3 could discriminate CRC patients from non-cancerous controls with an area under the receiver-operating curve (AUC) of 0.877 at a cut-off value of 0.3816, with a sensitivity of 82.76% and 78.57% specificity. More importantly, the combination of lncRNAs shows more sensitivity in the detection of early-stage CRC than the combination of CEA and CA19-9, biomarkers currently used for CRC detection (p < 0.0001).ConclusionslncRNAs 91H, PVT-1 and MEG3 are promising diagnostic biomarkers for early-stage CRC.

APA, Harvard, Vancouver, ISO, and other styles

22

Marchio, Agnès, Christophe Batejat, Jessica Vanhomwegen, Maxence Feher, Quentin Grassin, Maxime Chazal, Olivia Raulin, et al. "ddPCR increases detection of SARS-CoV-2 RNA in patients with low viral loads." Archives of Virology 166, no. 9 (July 12, 2021): 2529–40. http://dx.doi.org/10.1007/s00705-021-05149-0.

Full text

Abstract:

AbstractRT-qPCR detection of SARS-CoV-2 RNA still represents the method of reference to diagnose and monitor COVID-19. From the onset of the pandemic, however, doubts have been expressed concerning the sensitivity of this molecular diagnosis method. Droplet digital PCR (ddPCR) is a third-generation PCR technique that is particularly adapted to detecting low-abundance targets. We developed two-color ddPCR assays for the detection of four different regions of SARS-CoV-2 RNA, including non-structural (IP4-RdRP, helicase) and structural (E, N) protein-encoding sequences. We observed that N or E subgenomic RNAs are generally more abundant than IP4 and helicase RNA sequences in cells infected in vitro, suggesting that detection of the N gene, coding for the most abundant subgenomic RNA of SARS-CoV-2, increases the sensitivity of detection during the highly replicative phase of infection. We investigated 208 nasopharyngeal swabs sampled in March-April 2020 in different hospitals of Greater Paris. We found that 8.6% of informative samples (n = 16/185, P < 0.0001) initially scored as “non-positive” (undetermined or negative) by RT-qPCR were positive for SARS-CoV-2 RNA by ddPCR. Our work confirms that the use of ddPCR modestly, but significantly, increases the proportion of upper airway samples testing positive in the framework of first-line diagnosis of a French population.

APA, Harvard, Vancouver, ISO, and other styles

23

Ancarola, María Eugenia, Gabriel Lichtenstein, Johannes Herbig, Nancy Holroyd, Mara Mariconti, Enrico Brunetti, Matthew Berriman, et al. "Extracellular non-coding RNA signatures of the metacestode stage of Echinococcus multilocularis." PLOS Neglected Tropical Diseases 14, no. 11 (November 30, 2020): e0008890. http://dx.doi.org/10.1371/journal.pntd.0008890.

Full text

Abstract:

Extracellular RNAs (ex-RNAs) are secreted by cells through different means that may involve association with proteins, lipoproteins or extracellular vesicles (EV). In the context of parasitism, ex-RNAs represent new and exciting communication intermediaries with promising potential as novel biomarkers. In the last years, it was shown that helminth parasites secrete ex-RNAs, however, most work mainly focused on RNA secretion mediated by EV. Ex-RNA study is of special interest in those helminth infections that still lack biomarkers for early and/or follow-up diagnosis, such as echinococcosis, a neglected zoonotic disease caused by cestodes of the genus Echinococcus. In this work, we have characterised the ex-RNA profile secreted by in vitro grown metacestodes of Echinococcus multilocularis, the casuative agent of alveolar echinococcosis. We have used high throughput RNA-sequencing together with RT-qPCR to characterise the ex-RNA profile secreted towards the extra- and intra-parasite milieus in EV-enriched and EV-depleted fractions. We show that a polarized secretion of small RNAs takes place, with microRNAs mainly secreted to the extra-parasite milieu and rRNA- and tRNA-derived sequences mostly secreted to the intra-parasite milieu. In addition, we show by nanoparticle tracking analyses that viable metacestodes secrete EV mainly into the metacestode inner vesicular fluid (MVF); however, the number of nanoparticles in culture medium and MVF increases > 10-fold when metacestodes show signs of tegument impairment. Interestingly, we confirm the presence of host miRNAs in the intra-parasite milieu, implying their internalization and transport through the tegument towards the MVF. Finally, our assessment of the detection of Echinococcus miRNAs in patient samples by RT-qPCR yielded negative results suggesting the tested miRNAs may not be good biomarkers for this disease. A comprehensive study of the secretion mechanisms throughout the life cycle of these parasites will help to understand parasite interaction with the host and also, improve current diagnostic tools.

APA, Harvard, Vancouver, ISO, and other styles

24

Yalon, Michal, Amos Toren, Shany Freedman, Marc Remke, and Ruty Meharian-Shai. "MBRS-04. MEDULLOBLASTOMA DETECTION BY BLOOD TEST." Neuro-Oncology 22, Supplement_3 (December 1, 2020): iii399. http://dx.doi.org/10.1093/neuonc/noaa222.525.

Full text

Abstract:

Abstract INTRODUCTION Long non coding RNAs (lincRNAs) are functionally defined as transcripts longer than 200 nucleotides in length with no protein coding potential. lincRNA involvement in human cancers etiology is being increasingly proved. Cancer-secreted long non-coding RNAs (lncRNAs) in exosomes are emerging mediators of cancer-host cross talk communication in tumor microenvironments. The ability to monitor and detect tumor markers in real time enables access to tumor biology and may allow highly personalized treatment for each patient. METHODS AND RESULTS We analyzed RNA sequencing of 64 Medulloblastoma samples and quantified the genome wide long non coding RNAs (lincRNA) expression levels. We identified a lincRNA that is distinctively highly expressed in group 4 (MB4). MB4 expression was further examined in microarray analysis on a larger cohort of medulloblastoma patient samples and a large cohort (n=1405) of patient samples that include normal brain and different brain tumor samples. MB4 proved to be specific and highly expressed in group 4 Medulloblastoma. MB4 was detected in the plasma of medulloblastoma patients with active disease, or subtotal resection. MB4 was not detected in patients that their tumors were resected. MB4 expression is not detected in the serum of medulloblastoma type SHH, penioblastoma, ewing sarcoma and neuroblastoma patients. CONCLUSIONS We have found that MB4 lncRNA is a highly specific medulloblastoma tumor biomarker and is sensitive and noninvasive biomarker that can be quantified from a blood test. MB4 can be a good diagnostic marker, and in future both may also be a good target for therapy.

APA, Harvard, Vancouver, ISO, and other styles

25

Morozov, Igor Y., and Mark X. Caddick. "Cytoplasmic mRNA 3′ tagging in eukaryotes: does it spell the end?" Biochemical Society Transactions 40, no. 4 (July 20, 2012): 810–14. http://dx.doi.org/10.1042/bst20120068.

Full text

Abstract:

Although functional RNA is generally protected against degradation, defects or irregularity during RNA biogenesis lead to rapid degradation. Cellular surveillance mechanisms therefore need to distinguish aberrant, erroneous, damaged or aging transcripts from normal RNAs in order to maintain fidelity and control of gene expression. The detection of defects seems to be primarily based on functionality or aberrant rates of a given step in RNA biogenesis, allowing efficient detection of many different errors without recognition of their specific nature. We propose that the addition of non-templated nucleotides to the 3′ end of mRNAs and small non-coding RNAs, 3′ tagging, is the primary means by which malfunctioning RNAs are labelled, promoting their functional repression and degradation. However, the addition of non-templated nucleotides to transcripts can have diverse effects which vary with location, length, substrate and sequence.

APA, Harvard, Vancouver, ISO, and other styles

26

Schmieder, Stefan, Janek Weißpflog, Norbert Danz, Udo Klotzbach, and Frank Sonntag. "Detection of miRNA using a surface plasmon resonance biosensor and antibody amplification." Current Directions in Biomedical Engineering 2, no. 1 (September 1, 2016): 135–38. http://dx.doi.org/10.1515/cdbme-2016-0032.

Full text

Abstract:

AbstractMiRNAs are non-coding RNA molecules that control biological functions by reducing the translation of target proteins when binding to the mRNA. Alterations of the miRNA expression profile affect the cell metabolism, which can lead to distinctive disease patterns thus suggesting miRNA as an interesting biomarker. Here we present a SPR biosensor that utilizes disposable, injection-molded sensor chip/microfluidic hybrids combined with a lateral imaging optical system for parallel analysis of three one-dimensional spot arrays to detect miRNA-93. Using a RNA-DNA-hybrid antibody for signal enhancement we could reach a limit of detection of 10 pmol/l.

APA, Harvard, Vancouver, ISO, and other styles

27

Diez-Fraile, Araceli, Joke De Ceulaer, Charlotte Derpoorter, Christophe Spaas, Tom De Backer, Philippe Lamoral, Johan Abeloos, and Tim Lammens. "Circulating Non-Coding RNAs in Head and Neck Cancer: Roles in Diagnosis, Prognosis, and Therapy Monitoring." Cells 10, no. 1 (December 31, 2020): 48. http://dx.doi.org/10.3390/cells10010048.

Full text

Abstract:

Head and neck cancer (HNC), the seventh most common form of cancer worldwide, is a group of epithelial malignancies affecting sites in the upper aerodigestive tract. The 5-year overall survival for patients with HNC has stayed around 40–50% for decades, with mortality being attributable mainly to late diagnosis and recurrence. Recently, non-coding RNAs, including tRNA halves, YRNA fragments, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs), have been identified in the blood and saliva of patients diagnosed with HNC. These observations have recently fueled the study of their potential use in early detection, diagnosis, and risk assessment. The present review focuses on recent insights and the potential impact that circulating non-coding RNA evaluation may have on clinical decision-making in the management of HNC.

APA, Harvard, Vancouver, ISO, and other styles

28

Del Puerto, Helen L., Anilton C. Vasconcelos, Luciana Moro, Fabiana Alves, Gissandra F. Braz, and Almir S. Martins. "Canine distemper virus detection in asymptomatic and non vaccinated dogs." Pesquisa Veterinária Brasileira 30, no. 2 (February 2010): 139–44. http://dx.doi.org/10.1590/s0100-736x2010000200007.

Full text

Abstract:

A quantitative real time polymerase chain reaction (PCR) revealed canine distemper virus presence in peripheral blood samples from asymptomatic and non vaccinated dogs. Samples from eleven domestic dogs with no signs of canine distemper and not vaccinated at the month of collection were used. Canine distemper virus vaccine samples in VERO cells were used as positive controls. RNA was isolated with Trizol®, and treated with a TURBO DNA-free kit. Primers were designed for canine distemper virus nucleocapsid protein coding region fragment amplification (84 bp). Canine b-actin (93 bp) was utilized as the endogenous control for normalization. Quantitative results of real time PCR generated by ABI Prism 7000 SDS Software showed that 54.5% of dogs with asymptomatic canine distemper were positive for canine distemper virus. Dissociation curves confirmed the specificity of the real time PCR fragments. This technique could detect even a few copies of viral RNA and identificate subclinically infected dogs providing accurate diagnosis of this disease at an early stage.

APA, Harvard, Vancouver, ISO, and other styles

29

Hennig, Ewa E., Anna Kluska, Magdalena Piątkowska, Maria Kulecka, Aneta Bałabas, Natalia Zeber-Lubecka, Krzysztof Goryca, et al. "GWAS Links New Variant in Long Non-Coding RNA LINC02006 with Colorectal Cancer Susceptibility." Biology 10, no. 6 (May 25, 2021): 465. http://dx.doi.org/10.3390/biology10060465.

Full text

Abstract:

Despite great efforts, most of the genetic factors contributing to the risk of colorectal cancer (CRC) remain undetermined. Including small but homogenous populations in genome-wide association studies (GWAS) can help us discover new common risk variants specific to the studied population. In this study, including 465 CRC patients and 1548 controls, a pooled DNA samples-based GWAS was conducted in search of genetic variants associated with CRC in a Polish population. Combined with a new method of selecting single-nucleotide polymorphisms (SNPs) for verification in individual DNA samples, this approach allowed the detection of five new susceptibility loci not previously reported for CRC. The discovered loci were found to explain 10% of the overall risk of developing CRC. The strongest association was observed for rs10935945 in long non-coding RNA LINC02006 (3q25.2). Three other SNPs were also located within genes (rs17575184 in NEGR1, rs11060839 in PIWIL1, rs12935896 in BCAS3), while one was intergenic (rs9927668 at 16p13.2). An expression quantitative trait locus (eQTL) bioinformatic analysis suggested that these polymorphisms may affect transcription factor binding sites. In conclusion, four of the identified variants were located within genes likely involved in tumor invasiveness and metastasis. Therefore, they could possibly be markers of poor prognosis in CRC patients.

APA, Harvard, Vancouver, ISO, and other styles

30

Soo Yean, Cheryl Yeap, Kishanraj Selva Raju, Rathinam Xavier, Sreeramanan Subramaniam, Subash C. B. Gopinath, and Suresh V. Chinni. "Molecular Detection of Methicillin-Resistant Staphylococcus aureus by Non-Protein Coding RNA-Mediated Monoplex Polymerase Chain Reaction." PLOS ONE 11, no. 7 (July 1, 2016): e0158736. http://dx.doi.org/10.1371/journal.pone.0158736.

Full text

APA, Harvard, Vancouver, ISO, and other styles

31

Cardenosa-Rubio, Maria C., Richard M. Graybill, and Ryan C. Bailey. "Combining asymmetric PCR-based enzymatic amplification with silicon photonic microring resonators for the detection of lncRNAs from low input human RNA samples." Analyst 143, no. 5 (2018): 1210–16. http://dx.doi.org/10.1039/c7an02045g.

Full text

APA, Harvard, Vancouver, ISO, and other styles

32

Barbagallo, Cristina, Rosario Caltabiano, Giuseppe Broggi, Andrea Russo, Lidia Puzzo, Teresio Avitabile, Antonio Longo, et al. "LncRNA LINC00518 Acts as an Oncogene in Uveal Melanoma by Regulating an RNA-Based Network." Cancers 12, no. 12 (December 21, 2020): 3867. http://dx.doi.org/10.3390/cancers12123867.

Full text

Abstract:

Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults; little is known about the contribution of non-coding RNAs (ncRNAs) to UM pathogenesis. Competitive endogenous RNA (ceRNA) networks based on RNA–RNA interactions regulate physiological and pathological processes. Through a combined approach of in silico and experimental biology, we investigated the expression of a set of long non-coding RNAs (lncRNAs) in patient biopsies, identifying LINC00518 as a potential oncogene in UM. The detection of LINC00518 dysregulation associated with several in vitro functional assays allowed us to investigate its ceRNA regulatory network and shed light on its potential involvement in cancer-related processes, such as epithelial to mesenchymal transition (EMT) and CoCl2-induced hypoxia-like response. In vitro transient silencing of LINC00518 impaired cell proliferation and migration, and affected mRNA expression of LINGO2, NFIA, OTUD7B, SEC22C, and VAMP3. A “miRNA sponge” and “miRNA protector” model have been hypothesized for LINC00518-induced regulation of mRNAs. In vitro inhibition of MITF suggested its role as a potential activator of LINC00518 expression. Comprehensively, LINC00518 may be considered a new oncogene in UM and a potential target for RNA-based therapeutic approaches.

APA, Harvard, Vancouver, ISO, and other styles

33

Nannini, Margherita, and Maria A. Pantaleo. "Next generation sequencing (NGS) in oncology: lights and shadows." Cancer Breaking News 4, no. 1 (March 15, 2016): 17–19. http://dx.doi.org/10.19156/cbn.2016.0004.

Full text

Abstract:

Advances in tumor genome sequencing using next generation sequencing (NGS) technologies have facilitated a greater understanding of the genetic abnormalities involved in cancer development and progression, dramatically changing oncology research. There are several different types of NGS technologies. Whole genome sequencing (WGS) determines the sequence of the complete genome, providing information on both coding and non-coding regions and structural variants. However, use is limited by the large volume of data generated, and associated time and resource costs. Whole exome sequencing (WES) determines the sequence of coding regions only, making it faster and cheaper than WGS, and the functional consequences of variants are easier to interpret. However, all variations in non-coding regions are missed. WGS and WES are often used together to maximize detection of variants. A less costly approach is the use of targeted sequencing, which focuses on particular regions of interest, based on their biological relevance. NGS technologies can also be used to sequence RNA, referred to as RNA-Seq. All these NGS technologies, individually or in combination, have a number of potential applications, including identification of biomarkers, and development of diagnostic and therapeutic strategies. However, although advances have been made, there are a number of limitations to be overcome before NGS technologies are routinely applied in both research and clinical practice.

APA, Harvard, Vancouver, ISO, and other styles

34

Cui, Yi, Sheng Lu, Hongbo Tan, Jun Li, Min Zhu, and Yongqing Xu. "Silencing of Long Non-Coding RNA NONHSAT009968 Ameliorates the Staphylococcal Protein A-Inhibited Osteogenic Differentiation in Human Bone Mesenchymal Stem Cells." Cellular Physiology and Biochemistry 39, no. 4 (2016): 1347–59. http://dx.doi.org/10.1159/000447839.

Full text

Abstract:

Background/Aims: Osteomyelitis is defined as an inflammation of the bones and bone marrow. The inflammatory microenvironment attenuates the osteogenic differentiation capacity of stem cells and inhibits osteoblast-mediated bone formation, leading to net bone loss. However, the whole expression profile, function and side effect of long non-coding RNAs (lncRNAs) on osteogenic differentiation of stem cells in an inflammatory microenvironment of osteomyelitis are not known. Methods: In the present study, human bone mesenchymal stem cells (hBMSCs) were treated with different concentrations of Staphylococcal protein A (SpA) to trigger an inflammatory microenvironment in vitro to partly duplicate the inflammatory microenvironment of osteomyelitis, which was confirmed using ELISA for detecting the inflammatory cytokines. The complete expression profiles of lncRNAs and mRNA during osteogenic differentiation of hBMSCs in an inflammatory microenvironment triggered by SpA were analyzed using a lncRNA microarray. LncRNA expression levels were verified by quantitative reverse transcription PCR analysis (qRT-PCR). The expression of NONHSAT009968 in hB-MSCs was silenced by infection with lentivirus expressing NONHSAT009968-shRNA. The expression of Runx2, OCN, OPN, COL1A1, and alkaline phosphatase (ALP) activity was detected by western blot. Alizarin red staining and ALP activity detection were carried out. Results: The results of ELISA showed that SpA treatment induced secretion of inflammatory cytokines IL-1A, IL-6, and TNFA. The results of alizarin red staining and ALP detection showed that SpA treatment suppressed the osteogenic differentiation of hBMSCs. A total of 2033 lncRNAs were found with aberrant expression in SpA-treated hBMSCs compared to controls. Among these lncRNAs, 641 were down-regulated and 1392 were up-regulated. Based on the results of qRT-PCR, lncRNA NONHSAT009968 was chosen for further investigation. The results of alizarin red staining, ALP activity detection, and western blot detection of Runx2, OCN, OPN, COL1A1, and ALP indicated that NONHSAT009968 silencing ameliorates SpA-inhibited osteogenic differentiation in hBMSCs. Conclusion: Our present study provides a basis for future analyses of the role of lncRNAs in osteoblastic differentiation in an inflammatory environment triggered by SpA, and lncRNA NONHSAT009968 might be a new target for promoting osteoblast formation.

APA, Harvard, Vancouver, ISO, and other styles

35

Dahlgren, Anna R., Erica Y. Scott, Tamer Mansour, Erin N. Hales, Pablo J. Ross, Theodore S. Kalbfleisch, James N. MacLeod, Jessica L. Petersen, Rebecca R. Bellone, and Carrie J. Finno. "Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq." Non-Coding RNA 6, no. 3 (August 21, 2020): 32. http://dx.doi.org/10.3390/ncrna6030032.

Full text

Abstract:

Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares, RNA-seq libraries were prepared using standard poly-A+ selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A+ selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively. More lncRNA were found to be unique to poly-A+ selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A+ selected libraries. Overall, poly-A+ selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs.

APA, Harvard, Vancouver, ISO, and other styles

36

Timmons, J. A., and L. Good. "Does everything now make (anti)sense?" Biochemical Society Transactions 34, no. 6 (October 25, 2006): 1148–50. http://dx.doi.org/10.1042/bst0341148.

Full text

Abstract:

The data generated by the FANTOM (Functional Annotation of Mouse) consortium, Compugen and Affymetrix have collectively provided evidence that most of the mammalian genomes are actively transcribed. The emergence of an antisense RNA world brings new practical complexities to the study and detection of gene expression. However, we also need to address the fundamental questions regarding the functional importance of these molecules. In this brief paper, we focus on non-coding natural antisense transcription, as it appears to be a potentially powerful mechanism for extending the complexity of the protein coding genome, which is currently unable to explain inter-species diversification.

APA, Harvard, Vancouver, ISO, and other styles

37

Huang, Heping, Shangfeng Fu, and Dewu Liu. "Detection and Analysis of the Hedgehog Signaling Pathway-Related Long Non-Coding RNA (lncRNA) Expression Profiles in Keloid." Medical Science Monitor 24 (December 13, 2018): 9032–44. http://dx.doi.org/10.12659/msm.911159.

Full text

APA, Harvard, Vancouver, ISO, and other styles

38

Zhang, Kaijiong, Zhenglian Luo, Yi Zhang, Yuzhi Wang, Meng Cui, Lian Liu, Li Zhang, and Jinbo Liu. "Detection and analysis of circulating large intergenic non-coding RNA regulator of reprogramming in plasma for breast cancer." Thoracic Cancer 9, no. 1 (November 1, 2017): 66–74. http://dx.doi.org/10.1111/1759-7714.12537.

Full text

APA, Harvard, Vancouver, ISO, and other styles

39

Vijian, Dinesh, Suresh V. Chinni, Lee Su Yin, Benchaporn Lertanantawong, and Werasak Surareungchai. "Non-protein coding RNA-based genosensor with quantum dots as electrochemical labels for attomolar detection of multiple pathogens." Biosensors and Bioelectronics 77 (March 2016): 805–11. http://dx.doi.org/10.1016/j.bios.2015.10.057.

Full text

APA, Harvard, Vancouver, ISO, and other styles

40

Chen, Jing, Yaya Yu, Kui Kang, and Daowei Zhang. "SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera." PeerJ 8 (June 9, 2020): e9320. http://dx.doi.org/10.7717/peerj.9320.

Full text

Abstract:

The white-backed planthopper Sogatella furcifera is an economically important rice pest distributed throughout Asia. It damages rice crops by sucking phloem sap, resulting in stunted growth and plant virus transmission. We aimed to obtain the full-length transcriptome data of S. furcifera using PacBio single-molecule real-time (SMRT) sequencing. Total RNA extracted from S. furcifera at various developmental stages (egg, larval, and adult stages) was mixed and used to generate a full-length transcriptome for SMRT sequencing. Long non-coding RNA (lncRNA) identification, full-length coding sequence prediction, full-length non-chimeric (FLNC) read detection, simple sequence repeat (SSR) analysis, transcription factor detection, and transcript functional annotation were performed. A total of 12,514,449 subreads (15.64 Gbp, clean reads) were generated, including 630,447 circular consensus sequences and 388,348 FLNC reads. Transcript cluster analysis of the FLNC reads revealed 251,109 consensus reads including 29,700 high-quality reads. Additionally, 100,360 SSRs and 121,395 coding sequences were identified using SSR analysis and ANGEL software, respectively. Furthermore, 44,324 lncRNAs were annotated using four tools and 1,288 transcription factors were identified. In total, 95,495 transcripts were functionally annotated based on searches of seven different databases. To the best of our knowledge, this is the first study of the full-length transcriptome of the white-backed planthopper obtained using SMRT sequencing. The acquired transcriptome data can facilitate further studies on the ecological and viral-host interactions of this agricultural pest.

APA, Harvard, Vancouver, ISO, and other styles

41

Markou, Athina N., Stavroula Smilkou, Emilia Tsaroucha, and Evi Lianidou. "The Effect of Genomic DNA Contamination on the Detection of Circulating Long Non-Coding RNAs: The Paradigm of MALAT1." Diagnostics 11, no. 7 (June 25, 2021): 1160. http://dx.doi.org/10.3390/diagnostics11071160.

Full text

Abstract:

The presence of contaminating gDNA in RNA preparations is a frequent cause of false positives in RT-PCR-based analysis. However, in some cases, this cannot be avoided, especially when there are no exons–intron junctions in the lncRNA sequences. Due to the lack of exons in few of long noncoding RNAs (lncRNAs) and the lack of DNAse treatment step in most studies reported so far, serious questions are raised about the specificity of lncRNA detection and the potential of reporting false-positive results. We hypothesized that minute amounts of gDNA usually co-extracted with RNA could give false-positive signals since primers would specifically bind to gDNA due to the lack of junction. In the current study, we evaluated the effect of gDNA and other forms of DNA like extrachromosomal circular DNAs (eccDNAs) contamination and the importance of including a DNAse treatment step on lncRNAsexpression.As a model, we have chosen as one of the most widely studied lncRNAs in cancer namely MALAT1, which lacks exons. When we tested this hypothesis in plasma and primary tissue samples from NSCLC patients, our findings clearly indicated that results on MALAT1 expression are highly affected by the presence of DNA contamination and that the DNAse treatment step is absolutely necessary to avoid false positive results.

APA, Harvard, Vancouver, ISO, and other styles

42

Rivas, Elena, Jody Clements, and Sean R. Eddy. "Estimating the power of sequence covariation for detecting conserved RNA structure." Bioinformatics 36, no. 10 (February 7, 2020): 3072–76. http://dx.doi.org/10.1093/bioinformatics/btaa080.

Full text

Abstract:

Abstract Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long non-coding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures. Availability and implementation The R-scape web server is at eddylab.org/R-scape, with a link to download the source code. Supplementary information Supplementary data are available at Bioinformatics online.

APA, Harvard, Vancouver, ISO, and other styles

43

Dai, Shui-Ping, Jing Jin, and Wei-Min Li. "Diagnostic efficacy of long non-coding RNA in lung cancer: a systematic review and meta-analysis." Postgraduate Medical Journal 94, no. 1116 (October 2018): 578–87. http://dx.doi.org/10.1136/postgradmedj-2018-135862.

Full text

Abstract:

The detection of long non-coding RNA (lncRNA) is a novel method for lung cancer diagnosis. However, the diagnostic efficacy of lncRNA in different studies is inconsistent. Therefore, we conducted this meta-analysis to elucidate the diagnostic efficacy of lncRNA in identification of lung cancer including small cell lung cancer. The online PubMed, Medline, EMBASE, CNKI and Wanfang literature databases were searched to identify all related articles about the diagnostic efficacy of lncRNA for lung cancer. 28 articles including 3044 patients with lung cancer and 2598 controls were enrolled in our meta-analysis. lncRNA sustained a high diagnostic efficacy, pooled sensitivity of 0.82 (95% CI 0.79 to 0.84), specificity of 0.82 (95% CI 0.78 to 0.84) and area under the curve (AUC) of 0.88 (95% CI 0.85 to 0.91) in identification of patients with lung cancer from controls. Furthermore, the diagnostic efficacy of paralleled lncRNA was better than single lncRNA (sensitivity: 0.86 vs 0.80; specificity: 0.88 vs 0.78; AUC: 0.93 vs 0.86). MALAT1 had a better diagnostic efficacy than GAS5 (AUC: 0.90 vs 0.81; sensitivity: 0.83 vs 0.70; specificity: 0.83 vs 0.78). lncRNA in tissues was observed to achieve lower diagnostic efficacy than that in plasma or serum (AUC: 0.87 vs 0.90 vs 0.90) when stratified by sample types. In summary, our meta-analysis suggests that lncRNA might be a promising biomarker(s) for identifying lung cancer and the combination of lncRNA or with other biomarkers had a better diagnostic efficacy.

APA, Harvard, Vancouver, ISO, and other styles

44

Kwok, Zhi Hao, Kareemah Ni, and Yang Jin. "Extracellular Vesicle Associated Non-Coding RNAs in Lung Infections and Injury." Cells 10, no. 5 (April 21, 2021): 965. http://dx.doi.org/10.3390/cells10050965.

Full text

Abstract:

Extracellular vesicles (EVs) refer to a heterogenous population of membrane-bound vesicles that are released by cells under physiological and pathological conditions. The detection of EVs in the majority of the bodily fluids, coupled with their diverse cargo comprising of DNA, RNA, lipids, and proteins, have led to the accumulated interests in leveraging these nanoparticles for diagnostic and therapeutic purposes. In particular, emerging studies have identified enhanced levels of a wide range of specific subclasses of non-coding RNAs (ncRNAs) in EVs, thereby suggesting the existence of highly selective and regulated molecular processes governing the sorting of these RNAs into EVs. Recent studies have also illustrated the functional relevance of these enriched ncRNAs in a variety of human diseases. This review summarizes the current state of knowledge on EV-ncRNAs, as well as their functions and significance in lung infection and injury. As a majority of the studies on EV-ncRNAs in lung diseases have focused on EV-microRNAs, we will particularly highlight the relevance of these molecules in the pathophysiology of these conditions, as well as their potential as novel biomarkers therein. We also outline the current challenges in the EV field amidst the tremendous efforts to propel the clinical utility of EVs for human diseases. The lack of published literature on the functional roles of other EV-ncRNA subtypes may in turn provide new avenues for future research to exploit their feasibility as novel diagnostic and therapeutic targets in human diseases.

APA, Harvard, Vancouver, ISO, and other styles

45

Eissa, Sanaa, Marwa Matboli, Nada O. E. Essawy, Mahmoud Shehta, and Youssef M. Kotb. "Rapid detection of urinary long non-coding RNA urothelial carcinoma associated one using a PCR-free nanoparticle-based assay." Biomarkers 20, no. 3 (April 3, 2015): 212–17. http://dx.doi.org/10.3109/1354750x.2015.1062918.

Full text

APA, Harvard, Vancouver, ISO, and other styles

46

Martens-Uzunova, E. S., N. Dits, and G. Jenster. "A duplex quantitative real-time PCR assay for the detection of small non-coding RNA in urinary extracellular vesicles." European Urology Supplements 18, no. 8 (October 2019): e3052. http://dx.doi.org/10.1016/s1569-9056(19)33301-9.

Full text

APA, Harvard, Vancouver, ISO, and other styles

47

Panza, Anna, Stefano Castellana, Giuseppe Biscaglia, Ada Piepoli, Luca Parca, Annamaria Gentile, Anna Latiano, et al. "Transcriptome and Gene Fusion Analysis of Synchronous Lesions Reveals lncMRPS31P5 as a Novel Transcript Involved in Colorectal Cancer." International Journal of Molecular Sciences 21, no. 19 (September 27, 2020): 7120. http://dx.doi.org/10.3390/ijms21197120.

Full text

Abstract:

Fusion genes and epigenetic regulators (i.e., miRNAs and long non-coding RNAs) constitute essential pieces of the puzzle of the tumor genomic landscape, in particular in mechanisms behind the adenoma-to-carcinoma progression of colorectal cancer (CRC). In this work, we aimed to identify molecular signatures of the different steps of sporadic CRC development in eleven patients, of which synchronous samples of adenomas, tumors, and normal tissues were analyzed by RNA-Seq. At a functional level, tumors and adenomas were all characterized by increased activity of the cell cycle, cell development, cell growth, and biological proliferation functions. In contrast, organic survival and apoptosis-related functions were inhibited both in tumors and adenomas at different levels. At a molecular level, we found that three individuals shared a tumor-specific fusion named MRPS31-SUGT1, generated through an intra-chromosomal translocation on chromosome 13, whose sequence resulted in being 100% identical to the long non-coding RNA (lncRNA) MRPS31P5. Our analyses suggest that MRPS31P5 could take part to a competitive endogenous (ce)RNA network by acting as a miRNA sponge or/and as an interactor of other mRNAs, and thus it may be an important gene expression regulatory factor and could be used as a potential biomarker for the detection of early CRC events.

APA, Harvard, Vancouver, ISO, and other styles

48

Sukowati, Caecilia H. C., Loraine Kay D. Cabral, Claudio Tiribelli, and Devis Pascut. "Circulating Long and Circular Noncoding RNA as Non-Invasive Diagnostic Tools of Hepatocellular Carcinoma." Biomedicines 9, no. 1 (January 19, 2021): 90. http://dx.doi.org/10.3390/biomedicines9010090.

Full text

Abstract:

Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide, partially due to late diagnosis of the disease. Growing evidence in the field of biomarker discovery has shown the promising use of nucleic acid in the early detection of many cancers, including HCC. Here, we review data on how various long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) could be used as a diagnostic tool for HCC being differentially expressed in HCC compared to non-HCC patients. These non-coding RNAs (ncRNAs) showed high stability in the blood being present as free-circulating molecules or encapsulated into exosomes. This review reports some recent evidence on the use of lncRNAs and circRNAs as possible diagnostic biomarkers for HCC. Further, their pathophysiological mechanism in liver carcinogenesis was also described, elucidating the complex regulatory networks making these ncRNAs of particular relevance for the study of liver malignancy cancer.

APA, Harvard, Vancouver, ISO, and other styles

49

Zong, Wei, Wei Feng, Yun Jiang, Shaoqing Ju, Ming Cui, and Rongrong Jing. "Evaluating the diagnostic and prognostic value of serum long non-coding RNA CTC-497E21.4 in gastric cancer." Clinical Chemistry and Laboratory Medicine (CCLM) 57, no. 7 (June 26, 2019): 1063–72. http://dx.doi.org/10.1515/cclm-2018-0929.

Full text

Abstract:

Abstract Background Long non-coding RNAs (lncRNAs) have been reported to play a key role in gastric cancer (GC) tumorigenesis. However, the clinical application value of serum lncRNAs in GC has remained largely unknown. We investigated the role of a novel lncRNA named CTC-497E21.4 in the diagnosis and the prognosis of GC. Methods We focused on evaluation of lncRNA CTC-497E21.4 by real-time fluorescent quantitative polymerase chain reaction (RTFQ-PCR). The study involved following aspects: (1) confirmation of the higher lncRNA CTC-497E21.4 expression in different types of GC specimens than corresponding controls; (2) evaluation of monitoring tumor dynamics by the serum lncRNA CTC-497E21.4 assay; (3) evaluation of the prognostic value of lncRNA CTC-497E21.4 assay in GC. Results (1) The method of RTFQ-PCR detection of lncRNA CTC-497E21.4 was evaluated to have high sensitivity and specificity. (2) The expression levels of lncRNA CTC-497E21.4 were higher in GC patients compared with corresponding controls (p<0.001), and the combination of serum lncRNA CTC-497E21.4, CEA and CA19-9 could improve diagnostic sensitivity (96.36%). (3) The serum lncRNA CTC-497E21.4 expression levels were lower in postoperative samples than preoperative samples (p=0.0021) and survival curves downloaded from TCGA showed high lncRNA CTC-497E21.4 levels were associated with poor OS of GC (p=0.0351). Conclusions lncRNA CTC-497E21.4 may be a potential biomarker for the diagnosis and the prognosis of GC.

APA, Harvard, Vancouver, ISO, and other styles

50

Chisholm, Karen M., Yue Wan, Rui Li, Kelli D. Montgomery, Howard Y. Chang, and Robert B. West. "Detection of Long Non-Coding RNA in Archival Tissue: Correlation with Polycomb Protein Expression in Primary and Metastatic Breast Carcinoma." PLoS ONE 7, no. 10 (October 25, 2012): e47998. http://dx.doi.org/10.1371/journal.pone.0047998.

Full text

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Non-coding RNA detection'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles