Non-Coding RNA最新文献

{"title":"Extracellular microRNAs in Relation to Weight Loss-A Systematic Review and Meta-Analysis.","authors":"Camilla H B Veie,&nbsp;Isabella M T Nielsen,&nbsp;Nanna L S Frisk,&nbsp;Louise T Dalgaard","doi":"10.3390/ncrna9050053","DOIUrl":"https://doi.org/10.3390/ncrna9050053","url":null,"abstract":"<p><p>Obesity is an important risk factor for cardiovascular disease and type 2 diabetes mellitus. Even a modest weight loss of 5-15% improves metabolic health, but circulating markers to indicate weight loss efficiency are lacking. MicroRNAs, small non-coding post-transcriptional regulators of gene expression, are secreted from tissues into the circulation and may be potential biomarkers for metabolic health. However, it is not known which specific microRNA species are reproducibly changed in levels by weight loss. In this study, we performed a systematic review and meta-analysis to investigate the microRNAs associated with weight loss by comparing baseline to follow-up levels following intervention-driven weight loss. This systematic review was performed according to the PRISMA guidelines with searches in PubMed and SCOPUS. The primary search resulted in a total of 697 articles, which were screened according to the prior established inclusion and exclusion criteria. Following the screening of articles, the review was based on the inclusion of 27 full-text articles, which were evaluated for quality and the risk of bias. We performed systematic data extraction, whereafter the relative values for miRNAs were calculated. A meta-analysis was performed for the miRNA species investigated in three or more studies: miR-26a, miR-126, and miR-223 were overall significantly increased following weight loss, while miR-142 was significantly decreased after weight loss. miR-221, miR-140, miR-122, and miR-146 were not significantly changed by intervention-driven weight loss. These results indicate that few miRNAs are significantly changed during weight loss.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41168041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Potential microRNA Prognostic Signature in HNSCCs: A Systematic Review.","authors":"Mario Dioguardi,&nbsp;Francesca Spirito,&nbsp;Giovanna Iacovelli,&nbsp;Diego Sovereto,&nbsp;Enrica Laneve,&nbsp;Luigi Laino,&nbsp;Giorgia Apollonia Caloro,&nbsp;Ari Qadir Nabi,&nbsp;Andrea Ballini,&nbsp;Lorenzo Lo Muzio,&nbsp;Giuseppe Troiano","doi":"10.3390/ncrna9050054","DOIUrl":"https://doi.org/10.3390/ncrna9050054","url":null,"abstract":"<p><p>Head and neck squamous cell carcinomas (HNSCCs) are often diagnosed at advanced stages, incurring significant high mortality and morbidity. Several microRNAs (miRs) have been identified as pivotal players in the onset and advancement of HNSCCs, operating as either oncogenes or tumor suppressors. Distinctive miR patterns identified in tumor samples, as well as in serum, plasma, or saliva, from patients have significant clinical potential for use in the diagnosis and prognosis of HNSCCs and as potential therapeutic targets. The aim of this study was to identify previous systematic reviews with meta-analysis data and clinical trials that showed the most promising miRs in HNSCCs, enclosing them into a biomolecular signature to test the prognostic value on a cohort of HNSCC patients according to The Cancer Genome Atlas (TCGA). Three electronic databases (PubMed, Scopus, and Science Direct) and one registry (the Cochrane Library) were investigated, and a combination of keywords such as \"signature microRNA OR miR\" AND \"HNSCC OR LSCC OR OSCC OR oral cancer\" were searched. In total, 15 systematic literature reviews and 76 prognostic clinical reports were identified for the study design and inclusion process. All survival index data were extracted, and the three miRs (miR-21, miR-155, and miR-375) most investigated and presenting the largest number of patients included in the studies were selected in a molecular biosignature. The difference between high and low tissue expression levels of miR-21, miR-155, and miR-375 for OS had an HR = 1.28, with 95% CI: [0.95, 1.72]. In conclusion, the current evidence suggests that miRNAs have potential prognostic value to serve as screening tools for clinical practice in HNSCC follow-up and treatment. Further large-scale cohort studies focusing on these miRNAs are recommended to verify the clinical utility of these markers individually and/or in combination.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41151831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inverse-Folding Design of Yeast Telomerase RNA Increases Activity In Vitro.","authors":"Kevin J Lebo,&nbsp;David C Zappulla","doi":"10.3390/ncrna9050051","DOIUrl":"https://doi.org/10.3390/ncrna9050051","url":null,"abstract":"<p><p><i>Saccharomyces cerevisiae</i> telomerase RNA, TLC1, is an 1157 nt non-coding RNA that functions as both a template for DNA synthesis and a flexible scaffold for telomerase RNP holoenzyme protein subunits. The tractable budding yeast system has provided landmark discoveries about telomere biology in vivo, but yeast telomerase research has been hampered by the fact that the large TLC1 RNA subunit does not support robust telomerase activity in vitro. In contrast, 155-500 nt miniaturized TLC1 alleles comprising the catalytic core domain and lacking the RNA's long arms do reconstitute robust activity. We hypothesized that full-length TLC1 is prone to misfolding in vitro. To create a full-length yeast telomerase RNA, predicted to fold into its biologically relevant structure, we took an inverse RNA-folding approach, changing 59 nucleotides predicted to increase the energetic favorability of folding into the modeled native structure based on the <i>p-num</i> feature of <i>Mfold</i> software. The sequence changes lowered the predicted ∆G of this \"determined-arm\" allele, DA-TLC1, by 61 kcal/mol (-19%) compared to wild-type. We tested DA-TLC1 for reconstituted activity and found it to be ~5-fold more robust than wild-type TLC1, suggesting that the inverse-folding design indeed improved folding in vitro into a catalytically active conformation. We also tested if DA-TLC1 functions in vivo, discovering that it complements a <i>tlc1</i>∆ strain, allowing cells to avoid senescence and maintain telomeres of nearly wild-type length. However, all inverse-designed RNAs that we tested had reduced abundance in vivo. In particular, inverse-designing nearly all of the Ku arm caused a profound reduction in telomerase RNA abundance in the cell and very short telomeres. Overall, these results show that the inverse design of <i>S. cerevisiae</i> telomerase RNA increases activity in vitro, while reducing abundance in vivo. This study provides a biochemically and biologically tested approach to inverse-design RNAs using <i>Mfold</i> that could be useful for controlling RNA structure in basic research and biomedicine.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514824/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41143676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-Coding RNAs: Foes or Friends for Targeting Tumor Microenvironment.","authors":"Anna Szymanowska,&nbsp;Cristian Rodriguez-Aguayo,&nbsp;Gabriel Lopez-Berestein,&nbsp;Paola Amero","doi":"10.3390/ncrna9050052","DOIUrl":"https://doi.org/10.3390/ncrna9050052","url":null,"abstract":"<p><p>Non-coding RNAs (ncRNAs) are a group of molecules critical for cell development and growth regulation. They are key regulators of important cellular pathways in the tumor microenvironment. To analyze ncRNAs in the tumor microenvironment, the use of RNA sequencing technology has revolutionized the field. The advancement of this technique has broadened our understanding of the molecular biology of cancer, presenting abundant possibilities for the exploration of novel biomarkers for cancer treatment. In this review, we will summarize recent achievements in understanding the complex role of ncRNA in the tumor microenvironment, we will report the latest studies on the tumor microenvironment using RNA sequencing, and we will discuss the potential use of ncRNAs as therapeutics for the treatment of cancer.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41143334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages.","authors":"Na Qian,&nbsp;Rebecca Distefano,&nbsp;Mirolyuba Ilieva,&nbsp;Jens Hedelund Madsen,&nbsp;Sarah Rennie,&nbsp;Shizuka Uchida","doi":"10.3390/ncrna9050050","DOIUrl":"https://doi.org/10.3390/ncrna9050050","url":null,"abstract":"<p><p>The NLRP3 inflammasome plays a pivotal role in regulating inflammation and immune responses. Its activation can lead to an inflammatory response and pyroptotic cell death. This is beneficial in the case of infections, but excessive activation can lead to chronic inflammation and tissue damage. Moreover, while most of the mammalian genome is transcribed as RNAs, only a small fraction codes for proteins. Among non-protein-coding RNAs, long non-coding RNAs (lncRNAs) have been shown to play key roles in regulating gene expression and cellular processes. They interact with DNA, RNAs, and proteins, and their dysregulation can provide insights into disease mechanisms, including NLRP3 inflammasome activation. Here, we systematically analyzed previously published RNA sequencing (RNA-seq) data of NLRP3 inflammasome activation in monocytes/macrophages to uncover inflammasome-regulated lncRNA genes. To uncover the functional importance of inflammasome-regulated lncRNA genes, one inflammasome-regulated lncRNA, <i>ENSG00000273124</i>, was knocked down in an in vitro model of macrophage polarization. The results indicate that silencing of <i>ENSG00000273124</i> resulted in the up-regulation tumor necrosis factor (<i>TNF</i>), suggesting that this lncRNA might be involved in pro-inflammatory response in macrophages. To make our analyzed data more accessible, we developed the web database InflammasomeDB.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41136640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances and Obstacles in Using CRISPR/Cas9 Technology for Non-Coding RNA Gene Knockout in Human Mesenchymal Stromal Cells.","authors":"Nataliya Basalova,&nbsp;Maria Illarionova,&nbsp;Mariya Skryabina,&nbsp;Maksim Vigovskiy,&nbsp;Anastasia Tolstoluzhinskaya,&nbsp;Alexandra Primak,&nbsp;Elizaveta Chechekhina,&nbsp;Vadim Chechekhin,&nbsp;Maxim Karagyaur,&nbsp;Anastasia Efimenko","doi":"10.3390/ncrna9050049","DOIUrl":"https://doi.org/10.3390/ncrna9050049","url":null,"abstract":"<p><p>Non-coding RNA (ncRNAs) genes have attracted increasing attention in recent years due to their widespread involvement in physiological and pathological processes and regulatory networks. The study of the function and molecular partners of ncRNAs opens up opportunities for the early diagnosis and treatment of previously incurable diseases. However, the classical \"loss-of-function\" approach in ncRNA function analysis is challenged due to some specific issues. Here, we have studied the potency of two CRISPR/Cas9 variants, wild-type (SpCas9wt) and nickase (SpCas9D10A) programmable nucleases, for the editing of extended DNA sequences in human mesenchymal stromal cells (MSCs). Editing the genes of fibrosis-related hsa-miR-21-5p and hsa-miR-29c-3p, we have shown that a pair of SpCas9D10A molecules can effectively disrupt miRNA genes within the genomes of MSCs. This leads not only to a decrease in the level of knockout miRNA in MSCs and MSC-produced extracellular vesicles, but also to a change in cell physiology and the antifibrotic properties of the cell secretome. These changes correlate well with previously published data for the knockdown of certain miRNAs. The proposed approach can be used to knock out ncRNA genes within the genomes of MSCs or similar cell types in order to study their function in biological processes.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41143000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of lncRNAs in <i>Lupinus mutabilis</i> (Tarwi) and Their Potential Role in Drought Response.","authors":"Manuel Hidalgo,&nbsp;Cynthia Ramos,&nbsp;Gaston Zolla","doi":"10.3390/ncrna9050048","DOIUrl":"https://doi.org/10.3390/ncrna9050048","url":null,"abstract":"<p><p><i>Lupinus mutabilis</i> is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in <i>L. mutabilis</i>. To achieve this, we used a multilevel approach based on lncRNA prediction, annotation, subcellular location, thermodynamic characterization, structural conservation, and validation. Thus, 590 lncRNAs were identified by at least two algorithms of lncRNA identification. Annotation with the PLncDB database showed 571 lncRNAs unique to tarwi and 19 lncRNAs with homology in 28 botanical families including Solanaceae (19), Fabaceae (17), Brassicaceae (17), Rutaceae (17), Rosaceae (16), and Malvaceae (16), among others. In total, 12 lncRNAs had homology in more than 40 species. A total of 67% of lncRNAs were located in the cytoplasm and 33% in exosomes. Thermodynamic characterization of S03 showed a stable secondary structure with -105.67 kcal/mol. This structure included three regions, with a multibranch loop containing a hairpin with a SECIS-like element. Evaluation of the structural conservation by CROSSalign revealed partial similarities between <i>L. mutabilis</i> (S03) and <i>S. lycopersicum</i> (Solyc04r022210.1). RT-PCR validation demonstrated that S03 was upregulated in a drought-tolerant accession of <i>L. mutabilis</i>. Finally, these results highlighted the importance of lncRNAs in tarwi improvement under drought conditions.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41166506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation into the Role of Long-Non-Coding RNA <i>MIAT</i> in Leukemia.","authors":"Alessia Ostini,&nbsp;Mirna Mourtada-Maarabouni","doi":"10.3390/ncrna9040047","DOIUrl":"https://doi.org/10.3390/ncrna9040047","url":null,"abstract":"<p><p>Myocardial Infarction Associated Transcript (<i>MIAT</i>) is a nuclear long non-coding RNA (LncRNA) with four different splicing variants. <i>MIAT</i> dysregulation is associated with carcinogenesis, mainly acting as an oncogene regulating cellular growth, invasion, and metastasis. The aim of the current study is to investigate the role of <i>MIAT</i> in the regulation of T and chronic myeloid leukemic cell survival. To this end, <i>MIAT</i> was silenced using <i>MIAT</i>-specific siRNAs in leukemic cell lines, and functional assays were performed thereafter. This investigation also aims to investigate the effects of <i>MIAT</i> silencing on the expression of core genes involved in cancer. Functional studies and gene expression determination confirm that <i>MIAT</i> knockdown not only affects short- and long-term survival and the apoptosis of leukemic cells but also plays a pivotal role in the alteration of key genes involved in cancer, including <i>c-MYC</i> and <i>HIF-1A</i>. Our observations suggest that <i>MIAT</i> could act as an oncogene and it has the potential to be used not only as a reliable biomarker for leukemia, but also be employed for prognostic and therapeutic purposes.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10459085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10158892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural Modifications and Novel Protein-Binding Sites in Pre-miR-675-Explaining Its Regulatory Mechanism in Carcinogenesis.","authors":"Abhishek Dey","doi":"10.3390/ncrna9040045","DOIUrl":"10.3390/ncrna9040045","url":null,"abstract":"<p><p>Pre-miR-675 is a microRNA expressed from the exon 1 of H19 long noncoding RNA, and the atypical expression of pre-miR-675 has been linked with several diseases and disorders including cancer. To execute its function inside the cell, pre-miR-675 is folded into a particular conformation, which aids in its interaction with several other biological molecules. However, the exact folding dynamics of pre-miR-675 and its protein-binding motifs are currently unknown. Moreover, how H19 lncRNA and pre-miR-675 crosstalk and modulate each other's activities is also unclear. The detailed structural analysis of pre-miR-675 in this study determines its earlier unknown conformation and identifies novel protein-binding sites on pre-miR-675, thus making it an excellent therapeutic target against cancer. Co-folding analysis between H19 lncRNA and pre-miR-675 determine structural transformations in pre-miR-675, thus describing the earlier unknown mechanism of interaction between these two molecules. Comprehensively, this study details the conformation of pre-miR-675 and its protein-binding sites and explains its relationship with H19 lncRNA, which can be interpreted to understand the role of pre-miR-675 in the development and progression of tumorigenesis and designing new therapeutics against cancers.</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10105416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Methods and Tools in RNA Biology.","authors":"Mirolyuba Ilieva,&nbsp;Shizuka Uchida","doi":"10.3390/ncrna9040046","DOIUrl":"https://doi.org/10.3390/ncrna9040046","url":null,"abstract":"<p><p>Breakthroughs in innovative techniques and instruments have driven the exploration of non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) [...].</p>","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10459291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10071699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}