scholarly journals Noncoding RNAs in Cancer Medicine

2006 ◽  
Vol 2006 ◽  
pp. 1-8 ◽  
Author(s):  
Laura Cerchia ◽  
Vittorio De Franciscis
Keyword(s):  
Noncoding Rna ◽  
High Specificity ◽  
Affinity Ligands ◽  
Small Noncoding Rna ◽  
Innovative Methods ◽  
Attractive Candidate ◽  
Associated Proteins ◽  
Cell Growth And Differentiation ◽  
Cancer Medicine ◽  
Regulatory Rnas

Several signalling proteins involved in cell growth and differentiation represent attractive candidate targets for cancer diagnosis and/or therapy since they can act as oncogenes. Because of their high specificity and low immunogeneicity, using artificial small noncoding RNA (ncRNAs) as therapeutics has recently become a highly promising and rapidly expanding field of interest. Indeed, ncRNAs may either interfere with RNA transcription, stability, translation or directly hamper the function of the targets by binding to their surface. The recent finding that the expression of several genes is under the control of small single-stranded regulatory RNAs, including miRNAs, makes these genes as appropriate targets for ncRNA gene silencing. Furthermore, another class of small ncRNA, aptamers, act as high-affinity ligands and potential antagonists of disease-associated proteins. We will review here the recent and innovative methods that have been developed and the possible applications of ncRNAs as inhibitors or tracers in cancer medicine.

scholarly journals Extracellular Vesicles and Host–Pathogen Interactions: A Review of Inter-Kingdom Signaling by Small Noncoding RNA

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1010
Author(s):  
Bruce A. Stanton
Keyword(s):  
Extracellular Vesicles ◽  
Mammalian Cells ◽  
Noncoding Rna ◽  
Host Cells ◽  
Small Noncoding Rna ◽  
Human Host ◽  
Short Rnas ◽  
Bidirectional Communication ◽  
Regulatory Rnas

The focus of this brief review is to describe the role of noncoding regulatory RNAs, including short RNAs (sRNA), transfer RNA (tRNA) fragments and microRNAs (miRNA) secreted in extracellular vesicles (EVs), in inter-kingdom communication between bacteria and mammalian (human) host cells. Bacteria secrete vesicles that contain noncoding regulatory RNAs, and recent studies have shown that the bacterial vesicles fuse with and deliver regulatory RNAs to host cells, and similar to eukaryotic miRNAs, regulatory RNAs modulate the host immune response to infection. Recent studies have also demonstrated that mammalian cells secrete EVs containing miRNAs that regulate the gut microbiome, biofilm formation and the bacterial response to antibiotics. Thus, as evidence accumulates it is becoming clear that the secretion of noncoding regulatory RNAs and miRNAs in extracellular vesicles is an important mechanism of bidirectional communication between bacteria and mammalian (human) host cells. However, additional research is necessary to elucidate how noncoding regulatory RNAs and miRNA secreted in extracellular vesicles mediate inter-kingdom communication.

scholarly journals Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodelling by Hfq master regulator

2021 ◽  
Author(s):  
Antoine Cossa ◽  
Sylvain Trépout ◽  
Frank Wien ◽  
Etienne Le Brun ◽  
Florian Turbant ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Phase ◽  
Noncoding Rna ◽  
Stationary Growth Phase ◽  
Transcriptional Level ◽  
X Ray ◽  
Small Noncoding Rna ◽  
Associated Proteins ◽  
Post Transcriptional Regulation

Bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, thanks to proteins called Nucleoid Associated Proteins (NAPs). The NAP composition of the nucleoid varies during the bacterial life cycle and is growth phase-dependent. Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq belongs to the bridging family of NAPs. Its bridging mechanism relies on the formation of the amyloid-like structure of Hfq C-terminal region. Here, using cryo soft X-ray tomography imaging of native unlabelled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid, especially during the stationary growth phase. Hfq influences both nucleoid volume and absorbance. Hfq cumulates direct effects and indirect effects due to sRNA-based regulation of other NAPs. Taken together, our findings reveal a new role for this protein in nucleoid remodelling that may serve in response to stress conditions and in adapting to changing environments. This implies that Hfq regulates nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNA.

Exploring the Patent Landscape of RNAi-based Innovation for Plant Breeding

2019 ◽  
Vol 13 (3) ◽  
pp. 207-216 ◽  
Author(s):  
Dario Gianfranco Frisio ◽  
Vera Ventura
Keyword(s):  
Plant Breeding ◽  
High Specificity ◽  
Ownership Type ◽  
Modern Agriculture ◽  
Innovative Methods ◽  
Patent Landscape ◽  
The Us ◽  
Innovation Sector ◽  
Innovation Capacity ◽  
Rnai Technique

Background: RNA interference (RNAi) is an innovative technique for plant improvement based on naturally occurring mechanisms which show great potential because of their high specificity and possibility to be applied through innovative methods of topical application in plants. This specific innovation sector is worth analysing from the economic perspective given the great potentiality of RNAi-based plants and products to support modern agriculture in reaching the goals for the improvement of agri-food chains global sustainability. This paper aims to evaluate the global landscape of RNAi innovation by analysing patent data as indicators of innovation output. Methods: We revised all patents relating to RNAi in plants based on a dataset of roughly seven thousand patent families. The analysis classified inventions according to a set of variables able to characterise the dynamics of innovation (i.e. public/private ownership, type of plants involved, main traits) while the use of concentration indices provided insights into the evolution of this sector. Results: Results revealed that RNAi is a technique with promising future applications, able to provide solutions to a great variety of agricultural issues and principally developed by the US and Chinese applicants, whereas European innovation capacity in this field appears to be limited. Conclusion: The innovation landscape of plant breeding is rapidly evolving and RNAi technique is probably going to play a major role in this field.

scholarly journals COT-04 Circulating biomarker for glioblastoma and primary central nervous system lymphoma -Next Generation Sequencing of small noncoding RNA-

2020 ◽  
Vol 2 (Supplement_3) ◽  
pp. ii21-ii21
Author(s):  
Shumpei Onishi ◽  
Fumiyuki Yamasaki ◽  
Motoki Takano ◽  
Ushio Yonezawa ◽  
Kazuhiko Sugiyama ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Noncoding Rna ◽  
Central Nervous System Lymphoma ◽  
Serum Samples ◽  
Small Noncoding Rna ◽  
Non Invasive ◽  
Diagnostic Models ◽  
Healthy Control ◽  
Generation Sequencing

Abstract Objective: Glioblastoma (GBM) and Primary Central Nervous System Lymphoma (PCNSL) are common intracranial malignant tumors. They sometimes present similar radiological findings and diagnoses could be difficult without surgical biopsy. For improving the current management, development of non-invasive biomarkers are desired. In this study, we explored the differently expressed circulating small noncoding RNA (sncRNA) in serum for specific diagnostic tool of GBM and PCNSL. Material & Methods: Serum samples were obtained from three groups: 1) GBM patients (N=26), 2) PCNSL patients (N=14) 3) healthy control (N=114). The total small RNAs were extracted from serum. The whole expression profiles of serum sncRNAs were measured using Next-Generation Sequencing System. We analyzed serum levels of sncRNAs (15–55 nt) in each serum samples. The difference of sncRNAs expression profile among three groups were compared. Data analysis was performed by logistic regression analysis followed by leave-one-out cross-validation (LOOCV). The accuracy of diagnostic models of sncRNAs combination were evaluated by receiver operating characteristic (ROC) analysis. Results: We created the combination models using three sncRNA in each models based on the logistic regression analysis. The model 1 (based on sncRNA-X1, X2 and X3) enabled to differentiate GBM patients form healthy control with a sensitivity of 92.3% and a specificity of 99.2% (AUC: 0.993). The model 2 (based on sncRNA-Y1, Y2 and Y3) enabled to differentiate PCNSL patients form healthy control with a sensitivity of 100% and a specificity of 93.9% (AUC: 0.984). The model 3 (based on sncRNA-Z1, Z2 and Z3) enabled to differentiate GBM patients form PCNSL patients with a sensitivity of 92.3% and a specificity of 78.6% (AUC: 0.920). Conclusion: We found three diagnostic models of serum sncRNAs as non-invasive biomarkers potentially useful for detection of GBM and PCNSL from healthy control, and for differentiation GBM from PCNSL.

scholarly journals Sequence Variations of Epstein-Barr Virus-Encoded Small Noncoding RNA and Latent Membrane Protein 1 in Hematologic Tumors in Northern China

Intervirology ◽  
2021 ◽  
Vol 64 (2) ◽  
pp. 69-80
Author(s):  
Hai-Yu Wang ◽  
Lingling Sun ◽  
Ping Li ◽  
Wen Liu ◽  
Zhong-Guang Zhang ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Nested Pcr ◽  
Noncoding Rna ◽  
Epstein Barr Virus ◽  
Northern China ◽  
Latent Membrane Protein ◽  
Latent Membrane Protein 1 ◽  
Small Noncoding Rna ◽  
Barr Virus ◽  
Epstein Barr

<b><i>Objective:</i></b> To investigate the relationship between hematologic tumors and Epstein-Barr virus (EBV)-encoded small noncoding RNA (EBER) variations as well as latent membrane protein 1 (LMP1) variations. <b><i>Methods:</i></b> Patients with leukemia and myelodysplastic syndrome (MDS) were selected as subjects. Genotypes 1/2 and genotypes F/f were analyzed using the nested PCR technology, while EBER and LMP1 subtypes were analyzed by the nested PCR and DNA sequencing. <b><i>Results:</i></b> Type 1 was more dominant than type 2, found in 59 out of 82 (72%) leukemia and in 31 out of 35 (88.6%) MDS, while type F was more prevalent than type f in leukemia (83/85, 97.6%) and MDS (29/31, 93.5%) samples. The distribution of EBV genotypes 1/2 was not significantly different among leukemia, MDS, and healthy donor groups, neither was that of EBV genotypes F/f. EB-6m prototype was the dominant subtype of EBER in leukemia and MDS (73.2% [30/41] and 83.3% [10/12], respectively). The frequency of EB-6m was lower than that of healthy people (96.7%, 89/92), and the difference was significant (<i>p</i> &#x3c; 0.05). China 1 subtype was the dominant subtype of LMP1 in leukemia and MDS (70% [28/40] and 90% [9/10], respectively), and there was no significant difference in the distribution of LMP1 subtypes among the 3 groups (<i>p</i> &#x3e; 0.05). <b><i>Conclusion:</i></b> The distribution of EBV 1/2, F/f, EBER, and LMP1 subtypes in leukemia and MDS was similar to that in the background population in Northern China, which means that these subtypes may be rather region-restricted but not associated with leukemia and MDS pathogenesis.

scholarly journals Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Ce Yuan ◽  
Michael B. Burns ◽  
Subbaya Subramanian ◽  
Ran Blekhman
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Mirna Expression ◽  
Gut Microbiome ◽  
Noncoding Rna ◽  
Microbial Community Composition ◽  
Host Cells ◽  
Microbiome Composition ◽  
Small Noncoding Rna

ABSTRACT Although variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and are associated with patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome. Here, we investigated the association between miRNA expression and microbiome composition in human CRC tumor and normal tissues. We identified 76 miRNAs as differentially expressed (DE) in tissue from CRC tumors and normal tissue, including the known oncogenic miRNAs miR-182, miR-503, and mir-17~92 cluster. These DE miRNAs were correlated with the relative abundances of several bacterial taxa, including Firmicutes , Bacteroidetes , and Proteobacteria . Bacteria correlated with DE miRNAs were enriched with distinct predicted metabolic categories. Additionally, we found that miRNAs that correlated with CRC-associated bacteria are predicted to regulate targets that are relevant for host-microbiome interactions and highlight a possible role for miRNA-driven glycan production in the recruitment of pathogenic microbial taxa. Our work characterized a global relationship between microbial community composition and miRNA expression in human CRC tissues. IMPORTANCE Recent studies have found an association between colorectal cancer (CRC) and the gut microbiota. One potential mechanism by which the microbiota can influence host physiology is through affecting gene expression in host cells. MicroRNAs (miRNAs) are small noncoding RNA molecules that can regulate gene expression and have important roles in cancer development. Here, we investigated the link between the gut microbiota and the expression of miRNA in CRC. We found that dozens of miRNAs are differentially regulated in CRC tumors and adjacent normal colon and that these miRNAs are correlated with the abundance of microbes in the tumor microenvironment. Moreover, we found that microbes that have been previously associated with CRC are correlated with miRNAs that regulate genes related to interactions with microbes. Notably, these miRNAs likely regulate glycan production, which is important for the recruitment of pathogenic microbial taxa to the tumor. This work provides a first systems-level map of the association between microbes and host miRNAs in the context of CRC and provides targets for further experimental validation and potential interventions.

MicroRNAs in domestic livestock

2013 ◽  
Vol 45 (16) ◽  
pp. 685-696 ◽  
Author(s):  
Attia Fatima ◽  
Dermot G. Morris
Keyword(s):  
Posttranscriptional Regulation ◽  
Noncoding Rna ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Noncoding Rna ◽  
Domestic Livestock ◽  
Temporal Expression Pattern ◽  
Mrna Binding

microRNAs (miRNAs) are a class of small noncoding RNA that bind to complementary sequences in the untranslated regions of multiple target mRNAs resulting in posttranscriptional regulation of gene expression. The recent discovery and expression-profiling studies of miRNAs in domestic livestock have revealed both their tissue-specific and temporal expression pattern. In addition, breed-dependent expression patterns as well as single nucleotide polymorphisms in either the miRNA or in the target mRNA binding site have revealed associations with traits of economic importance and highlight the potential use of miRNAs in future genomic selection programs.

scholarly journals Parvovirus Expresses a Small Noncoding RNA That Plays an Essential Role in Virus Replication

2017 ◽  
Vol 91 (8) ◽  
Author(s):  
Zekun Wang ◽  
Weiran Shen ◽  
Fang Cheng ◽  
Xuefeng Deng ◽  
John F. Engelhardt ◽  
...  
Keyword(s):  
Dna Replication ◽  
Noncoding Rna ◽  
Rna Polymerase Iii ◽  
Human Bocavirus ◽  
Nonstructural Proteins ◽  
Viral Dna ◽  
Content Type ◽  
Small Noncoding Rna ◽  
Pol Iii ◽  
Tract Infections

ABSTRACT Human bocavirus 1 (HBoV1) belongs to the species Primate bocaparvovirus of the genus Bocaparvovirus of the Parvoviridae family. HBoV1 causes acute respiratory tract infections in young children and has a selective tropism for the apical surface of well-differentiated human airway epithelia (HAE). In this study, we identified an additional HBoV1 gene, bocavirus-transcribed small noncoding RNA (BocaSR), within the 3′ noncoding region (nucleotides [nt] 5199 to 5338) of the viral genome of positive sense. BocaSR is transcribed by RNA polymerase III (Pol III) from an intragenic promoter at levels similar to that of the capsid protein-coding mRNA and is essential for replication of the viral DNA in both transfected HEK293 and infected HAE cells. Mechanistically, we showed that BocaSR regulates the expression of HBoV1-encoded nonstructural proteins NS1, NS2, NS3, and NP1 but not NS4. BocaSR is similar to the adenovirus-associated type I (VAI) RNA in terms of both nucleotide sequence and secondary structure but differs from it in that its regulation of viral protein expression is independent of RNA-activated protein kinase (PKR) regulation. Notably, BocaSR accumulates in the viral DNA replication centers within the nucleus and likely plays a direct role in replication of the viral DNA. Our findings reveal BocaSR to be a novel viral noncoding RNA that coordinates the expression of viral proteins and regulates replication of viral DNA within the nucleus. Thus, BocaSR may be a target for antiviral therapies for HBoV and may also have utility in the production of recombinant HBoV vectors. IMPORTANCE Human bocavirus 1 (HBoV1) is pathogenic to humans, causing acute respiratory tract infections in young children. In this study, we identified a novel HBoV1 gene that lies in the 3′ noncoding region of the viral positive-sense genome and is transcribed by RNA polymerase III into a noncoding RNA of 140 nt. This bocavirus-transcribed small RNA (BocaSR) diverges from both adenovirus-associated (VA) RNAs and Epstein-Barr virus-encoded small RNAs (EBERs) with respect to RNA sequence, representing a third species of this kind of Pol III-dependent viral noncoding RNA and the first noncoding RNA identified in autonomous parvoviruses. Unlike the VA RNAs, BocaSR localizes to the viral DNA replication centers of the nucleus and is essential for expression of viral nonstructural proteins independent of RNA-activated protein kinase R and replication of HBoV1 genomes. The identification of BocaSR and its role in virus DNA replication reveals potential avenues for developing antiviral therapies.

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