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ncRNA
Volume 8
Issue 2
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Non-Coding RNA, Volume 8, Issue 2 (April 2022) – 8 articles

Cover Story (view full-size image): Circular RNAs (circRNAs) are involved in multiple biological processes that function through interactions with microRNAs and proteins. The dysregulation of these molecules has been shown to be key in the development of T-cell acute lymphoblastic leukemia (T-ALL). The use of circRNAs to discriminate between three different stages of thymocyte differentiation provided new circRNA-miRNA networks that play a central role in the control of the expression of genes involved in T-cell thymic differentiation. This helps us to understand the physiological and pathological processes to which they are subjected and paves the way for circRNA-based therapeutic intervention and diagnosis of human hematological diseases. View this paper.
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17 pages, 19192 KiB  
Review
New Insights into the Roles of lncRNAs as Modulators of Cytoskeleton Architecture and Their Implications in Cellular Homeostasis and in Tumorigenesis
by Carlos García-Padilla, María del Mar Muñoz-Gallardo, Estefanía Lozano-Velasco, Juan Manuel Castillo-Casas, Sheila Caño-Carrillo, Virginio García-López, Amelia Aránega, Diego Franco, Virginio García-Martínez and Carmen López-Sánchez
Non-Coding RNA 2022, 8(2), 28; https://doi.org/10.3390/ncrna8020028 - 13 Apr 2022
Cited by 9 | Viewed by 2967
Abstract
The importance of the cytoskeleton not only in cell architecture but also as a pivotal element in the transduction of signals that mediate multiple biological processes has recently been highlighted. Broadly, the cytoskeleton consists of three types of structural proteins: (1) actin filaments, [...] Read more.
The importance of the cytoskeleton not only in cell architecture but also as a pivotal element in the transduction of signals that mediate multiple biological processes has recently been highlighted. Broadly, the cytoskeleton consists of three types of structural proteins: (1) actin filaments, involved in establishing and maintaining cell shape and movement; (2) microtubules, necessary to support the different organelles and distribution of chromosomes during cell cycle; and (3) intermediate filaments, which have a mainly structural function showing specificity for the cell type where they are expressed. Interaction between these protein structures is essential for the cytoskeletal mesh to be functional. Furthermore, the cytoskeleton is subject to intense spatio-temporal regulation mediated by the assembly and disassembly of its components. Loss of cytoskeleton homeostasis and integrity of cell focal adhesion are hallmarks of several cancer types. Recently, many reports have pointed out that lncRNAs could be critical mediators in cellular homeostasis controlling dynamic structure and stability of the network formed by cytoskeletal structures, specifically in different types of carcinomas. In this review, we summarize current information available about the roles of lncRNAs as modulators of actin dependent cytoskeleton and their impact on cancer pathogenesis. Finally, we explore other examples of cytoskeletal lncRNAs currently unrelated to tumorigenesis, to illustrate knowledge about them. Full article
(This article belongs to the Section Long Non-Coding RNA)
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18 pages, 2700 KiB  
Article
Blood miRNAs Are Linked to Frequent Asthma Exacerbations in Childhood Asthma and Adult COPD
by Anshul Tiwari, Brian D. Hobbs, Jiang Li, Alvin T. Kho, Samir Amr, Juan C. Celedón, Scott T. Weiss, Craig P. Hersh, Kelan G. Tantisira and Michael J. McGeachie
Non-Coding RNA 2022, 8(2), 27; https://doi.org/10.3390/ncrna8020027 - 3 Apr 2022
Cited by 6 | Viewed by 3626
Abstract
MicroRNAs have been independently associated with asthma and COPD; however, it is unclear if microRNA associations will overlap when evaluating retrospective acute exacerbations. Objective: We hypothesized that peripheral blood microRNAs would be associated with retrospective acute asthma exacerbations in a pediatric asthma cohort [...] Read more.
MicroRNAs have been independently associated with asthma and COPD; however, it is unclear if microRNA associations will overlap when evaluating retrospective acute exacerbations. Objective: We hypothesized that peripheral blood microRNAs would be associated with retrospective acute asthma exacerbations in a pediatric asthma cohort and that such associations may also be relevant to acute COPD exacerbations. Methods: We conducted small-RNA sequencing on 374 whole-blood samples from children with asthma ages 6–14 years who participated in the Genetics of Asthma in Costa Rica Study (GACRS) and 450 current and former adult smokers with and without COPD who participated in the COPDGene study. Measurements and Main Results: After QC, we had 351 samples and 649 microRNAs for Differential Expression (DE) analysis between the frequent (n = 183) and no or infrequent exacerbation (n = 168) groups in GACRS. Fifteen upregulated miRs had odds ratios (OR) between 1.22 and 1.59 for a doubling of miR counts, while five downregulated miRs had ORs between 0.57 and 0.8. These were assessed for generalization in COPDGene, where three of the upregulated miRs (miR-532-3p, miR-296-5p, and miR-766-3p) and two of the downregulated miRs (miR-7-5p and miR-451b) replicated. Pathway enrichment analysis showed MAPK and PI3K-Akt signaling pathways were strongly enriched for target genes of DE miRNAs and miRNAs generalizing to COPD exacerbations, as well as infection response pathways to various pathogens. Conclusion: miRs (451b; 7-5p; 532-3p; 296-5p and 766-3p) associated with both childhood asthma and adult COPD exacerbations may play a vital role in airflow obstruction and exacerbations and point to shared genomic regulatory machinery underlying exacerbations in both diseases. Full article
(This article belongs to the Section Small Non-Coding RNA)
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16 pages, 4162 KiB  
Article
Patterns of Differentially Expressed circRNAs in Human Thymocytes
by Pilar López-Nieva, Pablo Fernández-Navarro, María Ángeles Cobos-Fernández, Iria González-Vasconcellos, Raúl Sánchez Pérez, Ángel Aroca, José Fernández-Piqueras and Javier Santos
Non-Coding RNA 2022, 8(2), 26; https://doi.org/10.3390/ncrna8020026 - 30 Mar 2022
Cited by 1 | Viewed by 2586
Abstract
Circular RNAs (circRNAs) are suggested to play a discriminative role between some stages of thymocyte differentiation. However, differential aspects of the stage of mature single-positive thymocytes remain to be explored. The purpose of this study is to investigate the differential expression pattern of [...] Read more.
Circular RNAs (circRNAs) are suggested to play a discriminative role between some stages of thymocyte differentiation. However, differential aspects of the stage of mature single-positive thymocytes remain to be explored. The purpose of this study is to investigate the differential expression pattern of circRNAs in three different development stages of human thymocytes, including mature single-positive cells, and perform predictions in silico regarding the ability of specific circRNAs when controlling the expression of genes involved in thymocyte differentiation. We isolate human thymocytes at three different stages of intrathymic differentiation and determine the expression of circRNAs and mRNA by RNASeq. We show that the differential expression pattern of 50 specific circRNAs serves to discriminate between the three human thymocyte populations. Interestingly, the downregulation of RAG2, a gene involved in T-cell differentiation in the thymus, could be simultaneously controlled by the downregulation of two circRNASs (hsa_circ_0031584 and hsa_circ_0019079) through the hypothetical liberation of hsa-miR-609. Our study provides, for the first time, significant insights into the usefulness of circRNAs in discriminating between different stages of thymocyte differentiation and provides new potential circRNA–miRNA–mRNA networks capable of controlling the expression of genes involved in T-cell differentiation in the thymus. Full article
(This article belongs to the Special Issue circRNAs in Cell and Organ Development)
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16 pages, 807 KiB  
Review
Role of MicroRNAs in Neuroendocrine Prostate Cancer
by Amritha Sreekumar and Sharanjot Saini
Non-Coding RNA 2022, 8(2), 25; https://doi.org/10.3390/ncrna8020025 - 30 Mar 2022
Cited by 6 | Viewed by 4696
Abstract
Therapy-induced neuroendocrine prostate cancer (t-NEPC/NEPC) is an aggressive variant of prostate cancer (PCa) that frequently emerges in castration-resistant prostate cancer (CRPC) under the selective pressure of androgen receptor (AR)-targeted therapies. This variant is extremely aggressive, metastasizes to visceral organs, tissues, and bones despite [...] Read more.
Therapy-induced neuroendocrine prostate cancer (t-NEPC/NEPC) is an aggressive variant of prostate cancer (PCa) that frequently emerges in castration-resistant prostate cancer (CRPC) under the selective pressure of androgen receptor (AR)-targeted therapies. This variant is extremely aggressive, metastasizes to visceral organs, tissues, and bones despite low serum PSA, and is associated with poor survival rates. It arises via a reversible trans-differentiation process, referred to as ‘neuroendocrine differentiation’ (NED), wherein PCa cells undergo a lineage switch and exhibit neuroendocrine features, characterized by the expression of neuronal markers such as enolase 2 (ENO2), chromogranin A (CHGA), and synaptophysin (SYP). The molecular and cellular mechanisms underlying NED in PCa are complex and not clearly understood, which contributes to a lack of effective molecular biomarkers for diagnosis and therapy of this variant. NEPC is thought to derive from prostate adenocarcinomas by clonal evolution. A characteristic set of genetic alterations, such as dual loss of retinoblastoma (RB1) and tumor protein (TP53) tumor suppressor genes and amplifications of Aurora kinase A (AURKA), NMYC, and EZH2, has been reported to drive NEPC. Recent evidence suggests that microRNAs (miRNAs) are important epigenetic players in driving NED in advanced PCa. In this review, we highlight the role of miRNAs in NEPC. These studies emphasize the diverse role that miRNAs play as oncogenes and tumor suppressors in driving NEPC. These studies have unveiled the important role of cellular processes such as the EMT and cancer stemness in determining NED in PCa. Furthermore, miRNAs are involved in intercellular communication between tumor cells and stromal cells via extracellular vesicles/exosomes that contribute to lineage switching. Recent studies support the promising potential of miRNAs as novel diagnostic biomarkers and therapeutic targets for NEPC. Full article
(This article belongs to the Collection Role of microRNA in Neuroendocrine Neoplasms)
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15 pages, 2526 KiB  
Article
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene
by Åse Emblem, Erik Knutsen, Tor Erik Jørgensen, Hilde Fure, Steinar Daae Johansen, Ole-Lars Brekke, Tom Eirik Mollnes and Bård Ove Karlsen
Non-Coding RNA 2022, 8(2), 24; https://doi.org/10.3390/ncrna8020024 - 29 Mar 2022
Cited by 1 | Viewed by 3211
Abstract
Many severe inflammation conditions are complement-dependent with the complement component C5a-C5aR1 axis as an important driver. At the RNA level, the blood transcriptome undergoes programmed expression of coding and long non-coding RNAs to combat invading microorganisms. Understanding the expression of long non-coding RNAs [...] Read more.
Many severe inflammation conditions are complement-dependent with the complement component C5a-C5aR1 axis as an important driver. At the RNA level, the blood transcriptome undergoes programmed expression of coding and long non-coding RNAs to combat invading microorganisms. Understanding the expression of long non-coding RNAs containing Alu elements in inflammation is important for reconstructing cell fate trajectories leading to severe disease. We have assembled a pipeline for computation mining of new Alu-containing long non-coding RNAs by intersecting immune genes with known Alu coordinates in the human genome. By applying the pipeline to patient bulk RNA-seq data with sepsis, we found immune genes containing 48 Alu insertion as robust candidates for further study. Interestingly, 1 of the 48 candidates was located within the complement system receptor gene C5aR1 and holds promise as a target for RNA therapeutics. Full article
(This article belongs to the Section Detection and Biomarkers of Non-Coding RNA)
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14 pages, 1946 KiB  
Review
Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions
by Henry E. Miller, Mirolyuba Ilieva, Alexander J. R. Bishop and Shizuka Uchida
Non-Coding RNA 2022, 8(2), 23; https://doi.org/10.3390/ncrna8020023 - 28 Mar 2022
Cited by 10 | Viewed by 4394
Abstract
Long non-coding RNAs (lncRNAs) belong to a class of non-protein-coding RNAs with their lengths longer than 200 nucleotides. Most of the mammalian genome is transcribed as RNA, yet only a small percent of the transcribed RNA corresponds to exons of protein-coding genes. Thus, [...] Read more.
Long non-coding RNAs (lncRNAs) belong to a class of non-protein-coding RNAs with their lengths longer than 200 nucleotides. Most of the mammalian genome is transcribed as RNA, yet only a small percent of the transcribed RNA corresponds to exons of protein-coding genes. Thus, the number of lncRNAs is predicted to be several times higher than that of protein-coding genes. Because of sheer number of lncRNAs, it is often difficult to elucidate the functions of all lncRNAs, especially those arising from their relationship to their binding partners, such as DNA, RNA, and proteins. Due to their binding to other macromolecules, it has become evident that the structures of lncRNAs influence their functions. In this regard, the recent development of epitranscriptomics (the field of study to investigate RNA modifications) has become important to further elucidate the structures and functions of lncRNAs. In this review, the current status of lncRNA structures and functions influenced by epitranscriptomic marks is discussed. Full article
(This article belongs to the Special Issue Systematic Analysis of lncRNA Structures and Functions)
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15 pages, 1629 KiB  
Review
Ribosome-Associated ncRNAs (rancRNAs) Adjust Translation and Shape Proteomes
by Valentina Pecoraro, Alessia Rosina and Norbert Polacek
Non-Coding RNA 2022, 8(2), 22; https://doi.org/10.3390/ncrna8020022 - 10 Mar 2022
Cited by 6 | Viewed by 4231
Abstract
The regulation of protein synthesis is of extreme importance for cell survival in challenging environmental conditions. Modulating gene expression at the level of translation allows a swift and low-energy-cost response to external stimuli. In the last decade, an emerging class of regulatory ncRNAs, [...] Read more.
The regulation of protein synthesis is of extreme importance for cell survival in challenging environmental conditions. Modulating gene expression at the level of translation allows a swift and low-energy-cost response to external stimuli. In the last decade, an emerging class of regulatory ncRNAs, namely ribosome-associated non-coding RNAs (rancRNAs), has been discovered. These rancRNAs have proven to be efficient players in the regulation of translation as a first wave of stress adaptation by directly targeting the ribosome, the central enzyme of protein production. This underlying principle appears to be highly conserved, since rancRNAs are present in all three domains of life. Here, we review the major findings and mechanistic peculiarities of rancRNAs, a class of transcripts that is providing new and broader perspectives on the complexity of the ribosome and translation regulation. Full article
(This article belongs to the Special Issue ncRNAs in Translational Reprogramming)
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23 pages, 3164 KiB  
Review
ABHD11-AS1: An Emerging Long Non-Coding RNA (lncRNA) with Clinical Significance in Human Malignancies
by Upendarrao Golla, Kishore Sesham, Siva Dallavalasa, Naresh Kumar Manda, Sambamoorthy Unnam, Arun Kumar Sanapala, Sharada Nalla, Susmitha Kondam and Rajesh Kumar
Non-Coding RNA 2022, 8(2), 21; https://doi.org/10.3390/ncrna8020021 - 1 Mar 2022
Cited by 11 | Viewed by 5533
Abstract
The aberrant expression of lncRNAs has been linked to the development and progression of different cancers. One such lncRNA is ABHD11 antisense RNA 1 (ABHD11-AS1), which has recently gained attention for its significant role in human malignancies. ABHD11-AS1 is highly expressed in gastric, [...] Read more.
The aberrant expression of lncRNAs has been linked to the development and progression of different cancers. One such lncRNA is ABHD11 antisense RNA 1 (ABHD11-AS1), which has recently gained attention for its significant role in human malignancies. ABHD11-AS1 is highly expressed in gastric, lung, breast, colorectal, thyroid, pancreas, ovary, endometrium, cervix, and bladder cancers. Several reports highlighted the clinical significance of ABHD11-AS1 in prognosis, diagnosis, prediction of cancer progression stage, and treatment response. Significantly, the levels of ABHD11-AS1 in gastric juice had been exhibited as a clinical biomarker for the assessment of gastric cancer, while its serum levels have prognostic potential in thyroid cancers. The ABHD11-AS1 has been reported to exert oncogenic effects by sponging different microRNAs (miRNAs), altering signaling pathways such as PI3K/Akt, epigenetic mechanisms, and N6-methyladenosine (m6A) RNA modification. In contrast, the mouse homolog of AHD11-AS1 (Abhd11os) overexpression had exhibited neuroprotective effects against mutant huntingtin-induced toxicity. Considering the emerging research reports, the authors attempted in this first review on ABHD11-AS1 to summarize and highlight its oncogenic potential and clinical significance in different human cancers. Lastly, we underlined the necessity for future mechanistic studies to unravel the role of ABHD11-AS1 in tumor development, prognosis, progression, and targeted therapeutic approaches. Full article
(This article belongs to the Special Issue Feature Papers from Non-coding RNA Reviewers)
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