Topical Collection "Feature Papers in Non-coding RNA"

Editor

Prof. Dr. George A Calin
grade Website
Guest Editor

Topical Collection Information

Dear Colleagues,

This Topical Collection “Feature Papers in Non-coding RNA” aims to collect high-quality research articles, review articles, and communications in all the fields of non-coding RNA research and their regulatory roles. Since the aim of this Topical Collection is to illustrate, through selected works, frontier research in noncoding RNA, we encourage Editorial Board Members of Non-coding RNA to contribute papers reflecting the latest progress in their research field, or relevant experts and colleagues to do so. Please kindly note that only invited papers can be published online once accepted in this collection.

Topics include, without being limited to, the following:

  • Functional studies dealing with the identification, structure–function relationships, or biological activity of miRNAs, siRNAs, piRNAs, tRNAs, long noncoding RNAs, and other classes of RNAs;
  • Analysis of RNA processing, RNA binding proteins, RNA signaling, and RNA interaction pathways;
  • RNA analyses, informatics, tools, and technologies;
  • Translational studies involving long and short noncoding RNAs.

Prof. Dr. Georges A Calin
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Non-Coding RNA is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (18 papers)

2021

Jump to: 2020

Open AccessReview
MicroRNAs as Candidate Biomarkers for Alzheimer’s Disease
Non-Coding RNA 2021, 7(1), 8; https://doi.org/10.3390/ncrna7010008 - 01 Feb 2021
Abstract
The neurological damage of Alzheimer’s disease (AD) is thought to be irreversible upon onset of dementia-like symptoms, as it takes years to decades for occult pathologic changes to become symptomatic. It is thus necessary to identify individuals at risk for the development of [...] Read more.
The neurological damage of Alzheimer’s disease (AD) is thought to be irreversible upon onset of dementia-like symptoms, as it takes years to decades for occult pathologic changes to become symptomatic. It is thus necessary to identify individuals at risk for the development of the disease before symptoms manifest in order to provide early intervention. Surrogate markers are critical for early disease detection, stratification of patients in clinical trials, prediction of disease progression, evaluation of response to treatment, and also insight into pathomechanisms. Here, we review the evidence for a number of microRNAs that may serve as biomarkers with possible mechanistic insights into the AD pathophysiologic processes, years before the clinical manifestation of the disease. Full article
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Open AccessFeature PaperReview
Exosomes in Immune Regulation
Non-Coding RNA 2021, 7(1), 4; https://doi.org/10.3390/ncrna7010004 - 08 Jan 2021
Abstract
Exosomes, small extracellular vesicles mediate intercellular communication by transferring their cargo including DNA, RNA, proteins and lipids from cell to cell. Notably, in the immune system, they have protective functions. However in cancer, exosomes acquire new, immunosuppressive properties that cause the dysregulation of [...] Read more.
Exosomes, small extracellular vesicles mediate intercellular communication by transferring their cargo including DNA, RNA, proteins and lipids from cell to cell. Notably, in the immune system, they have protective functions. However in cancer, exosomes acquire new, immunosuppressive properties that cause the dysregulation of immune cells and immune escape of tumor cells supporting cancer progression and metastasis. Therefore, current investigations focus on the regulation of exosome levels for immunotherapeutic interventions. In this review, we discuss the role of exosomes in immunomodulation of lymphoid and myeloid cells, and their use as immune stimulatory agents to elicit specific cytotoxic responses against the tumor. Full article
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2020

Jump to: 2021

Open AccessArticle
Non-Coding RNAs as Prognostic Biomarkers: A miRNA Signature Specific for Aggressive Early-Stage Lung Adenocarcinomas
Non-Coding RNA 2020, 6(4), 48; https://doi.org/10.3390/ncrna6040048 - 15 Dec 2020
Cited by 1
Abstract
Lung cancer burden can be reduced by adopting primary and secondary prevention strategies such as anti-smoking campaigns and low-dose CT screening for high risk subjects (aged >50 and smokers >30 packs/year). Recent CT screening trials demonstrated a stage-shift towards earlier stage lung cancer [...] Read more.
Lung cancer burden can be reduced by adopting primary and secondary prevention strategies such as anti-smoking campaigns and low-dose CT screening for high risk subjects (aged >50 and smokers >30 packs/year). Recent CT screening trials demonstrated a stage-shift towards earlier stage lung cancer and reduction of mortality (~20%). However, a sizable fraction of patients (30–50%) with early stage disease still experience relapse and an adverse prognosis. Thus, the identification of effective prognostic biomarkers in stage I lung cancer is nowadays paramount. Here, we applied a multi-tiered approach relying on coupled RNA-seq and miRNA-seq data analysis of a large cohort of lung cancer patients (TCGA-LUAD, n = 510), which enabled us to identify prognostic miRNA signatures in stage I lung adenocarcinoma. Such signatures showed high accuracy (AUC ranging between 0.79 and 0.85) in scoring aggressive disease. Importantly, using a network-based approach we rewired miRNA-mRNA regulatory networks, identifying a minimal signature of 7 miRNAs, which was validated in a cohort of FFPE lung adenocarcinoma samples (CSS, n = 44) and controls a variety of genes overlapping with cancer relevant pathways. Our results further demonstrate the reliability of miRNA-based biomarkers for lung cancer prognostication and make a step forward to the application of miRNA biomarkers in the clinical routine. Full article
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Open AccessReview
Emerging Roles of Long Noncoding RNAs in the Cytoplasmic Milieu
Non-Coding RNA 2020, 6(4), 44; https://doi.org/10.3390/ncrna6040044 - 09 Nov 2020
Cited by 1
Abstract
While the important functions of long noncoding RNAs (lncRNAs) in nuclear organization are well documented, their orchestrating and architectural roles in the cytoplasmic environment have long been underestimated. However, recently developed fractionation and proximity labelling approaches have shown that a considerable proportion of [...] Read more.
While the important functions of long noncoding RNAs (lncRNAs) in nuclear organization are well documented, their orchestrating and architectural roles in the cytoplasmic environment have long been underestimated. However, recently developed fractionation and proximity labelling approaches have shown that a considerable proportion of cellular lncRNAs is exported into the cytoplasm and associates nonrandomly with proteins in the cytosol and organelles. The functions of these lncRNAs range from the control of translation and mitochondrial metabolism to the anchoring of cellular components on the cytoskeleton and regulation of protein degradation at the proteasome. In the present review, we provide an overview of the functions of lncRNAs in cytoplasmic structures and machineries und discuss their emerging roles in the coordination of the dense intracellular milieu. It is becoming apparent that further research into the functions of these lncRNAs will lead to an improved understanding of the spatiotemporal organization of cytoplasmic processes during homeostasis and disease. Full article
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Open AccessReview
Involvement of Long Non-Coding RNAs (lncRNAs) in Tumor Angiogenesis
Non-Coding RNA 2020, 6(4), 42; https://doi.org/10.3390/ncrna6040042 - 25 Sep 2020
Cited by 2
Abstract
Long non-coding RNAs (lncRNAs) are defined as non-protein coding transcripts with a minimal length of 200 nucleotides. They are involved in various biological processes such as cell differentiation, apoptosis, as well as in pathophysiological processes. Numerous studies considered that frequently deregulated lncRNAs contribute [...] Read more.
Long non-coding RNAs (lncRNAs) are defined as non-protein coding transcripts with a minimal length of 200 nucleotides. They are involved in various biological processes such as cell differentiation, apoptosis, as well as in pathophysiological processes. Numerous studies considered that frequently deregulated lncRNAs contribute to all hallmarks of cancer including metastasis, drug resistance, and angiogenesis. Angiogenesis, the formation of new blood vessels, is crucial for a tumor to receive sufficient amounts of nutrients and oxygen and therefore, to grow and exceed in its size over the diameter of 2 mm. In this review, the regulatory mechanisms of lncRNAs are described, which influence tumor angiogenesis by directly or indirectly regulating oncogenic pathways, interacting with other transcripts such as microRNAs (miRNAs) or modulating the tumor microenvironment. Further, angiogenic lncRNAs occurring in several cancer types such as liver, gastrointestinal cancer, or brain tumors are summarized. Growing evidence on the influence of lncRNAs on tumor angiogenesis verified these transcripts as potential predictive or diagnostic biomarkers or therapeutic targets of anti-angiogenesis treatment. However, there are many unsolved questions left which are pointed out in this review, hence driving comprehensive research in this area is necessary to enable an effective use of lncRNAs as either therapeutic molecules or diagnostic targets in cancer. Full article
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Open AccessReview
Non-Coding RNAs in Multiple Myeloma Bone Disease Pathophysiology
Non-Coding RNA 2020, 6(3), 37; https://doi.org/10.3390/ncrna6030037 - 09 Sep 2020
Cited by 1
Abstract
Bone remodeling is uncoupled in the multiple myeloma (MM) bone marrow niche, resulting in enhanced osteoclastogenesis responsible of MM-related bone disease (MMBD). Several studies have disclosed the mechanisms underlying increased osteoclast formation and activity triggered by the various cellular components of the MM [...] Read more.
Bone remodeling is uncoupled in the multiple myeloma (MM) bone marrow niche, resulting in enhanced osteoclastogenesis responsible of MM-related bone disease (MMBD). Several studies have disclosed the mechanisms underlying increased osteoclast formation and activity triggered by the various cellular components of the MM bone marrow microenvironment, leading to the identification of novel targets for therapeutic intervention. In this regard, recent attention has been given to non-coding RNA (ncRNA) molecules, that finely tune gene expression programs involved in bone homeostasis both in physiological and pathological settings. In this review, we will analyze major signaling pathways involved in MMBD pathophysiology, and report emerging evidence of their regulation by different classes of ncRNAs. Full article
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Open AccessPerspective
Genesis of Non-Coding RNA Genes in Human Chromosome 22—A Sequence Connection with Protein Genes Separated by Evolutionary Time
Non-Coding RNA 2020, 6(3), 36; https://doi.org/10.3390/ncrna6030036 - 03 Sep 2020
Cited by 1
Abstract
A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or [...] Read more.
A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, and the long noncoding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionarily conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin-specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it is presented. Full article
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Open AccessFeature PaperReview
Non-Coding RNA Databases in Cardiovascular Research
Non-Coding RNA 2020, 6(3), 35; https://doi.org/10.3390/ncrna6030035 - 02 Sep 2020
Abstract
Cardiovascular diseases (CVDs) are of multifactorial origin and can be attributed to several genetic and environmental components. CVDs are the leading cause of mortality worldwide and they primarily damage the heart and the vascular system. Non-coding RNA (ncRNA) refers to functional RNA molecules, [...] Read more.
Cardiovascular diseases (CVDs) are of multifactorial origin and can be attributed to several genetic and environmental components. CVDs are the leading cause of mortality worldwide and they primarily damage the heart and the vascular system. Non-coding RNA (ncRNA) refers to functional RNA molecules, which have been transcribed into DNA but do not further get translated into proteins. Recent transcriptomic studies have identified the presence of thousands of ncRNA molecules across species. In humans, less than 2% of the total genome represents the protein-coding genes. While the role of many ncRNAs is yet to be ascertained, some long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been associated with disease progression, serving as useful diagnostic and prognostic biomarkers. A plethora of data repositories specialized in ncRNAs have been developed over the years using publicly available high-throughput data from next-generation sequencing and other approaches, that cover various facets of ncRNA research like basic and functional annotation, expressional profile, structural and molecular changes, and interaction with other biomolecules. Here, we provide a compendium of the current ncRNA databases relevant to cardiovascular research. Full article
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Open AccessFeature PaperReview
Long Non-Coding RNAs in Liver Cancer and Nonalcoholic Steatohepatitis
Non-Coding RNA 2020, 6(3), 34; https://doi.org/10.3390/ncrna6030034 - 29 Aug 2020
Cited by 1
Abstract
This review aims to highlight the recent findings of long non-coding RNAs (lncRNAs) in liver disease. In particular, we focus on the functions of lncRNAs in hepatocellular carcinoma (HCC) and non-alcoholic steatohepatitis (NASH). We summarize the current research trend in lncRNAs and their [...] Read more.
This review aims to highlight the recent findings of long non-coding RNAs (lncRNAs) in liver disease. In particular, we focus on the functions of lncRNAs in hepatocellular carcinoma (HCC) and non-alcoholic steatohepatitis (NASH). We summarize the current research trend in lncRNAs and their potential as biomarkers and therapeutic targets for the treatment of HCC and NASH. Full article
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Open AccessFeature PaperReview
Changes in Non-Coding RNA in Depression and Bipolar Disorder: Can They Be Used as Diagnostic or Theranostic Biomarkers?
Non-Coding RNA 2020, 6(3), 33; https://doi.org/10.3390/ncrna6030033 - 24 Aug 2020
Abstract
The similarities between the depressive symptoms of Major Depressive Disorders (MDD) and Bipolar Disorders (BD) suggest these disorders have some commonality in their molecular pathophysiologies, which is not apparent from the risk genes shared between MDD and BD. This is significant, given the [...] Read more.
The similarities between the depressive symptoms of Major Depressive Disorders (MDD) and Bipolar Disorders (BD) suggest these disorders have some commonality in their molecular pathophysiologies, which is not apparent from the risk genes shared between MDD and BD. This is significant, given the growing literature suggesting that changes in non-coding RNA may be important in both MDD and BD, because they are causing dysfunctions in the control of biochemical pathways that are affected in both disorders. Therefore, understanding the changes in non-coding RNA in MDD and BD will lead to a better understanding of how and why these disorders develop. Furthermore, as a significant number of individuals suffering with MDD and BD do not respond to medication, identifying non-coding RNA that are altered by the drugs used to treat these disorders offer the potential to identify biomarkers that could predict medication response. Such biomarkers offer the potential to quickly identify patients who are unlikely to respond to traditional medications so clinicians can refocus treatment strategies to ensure more effective outcomes for the patient. This review will focus on the evidence supporting the involvement of non-coding RNA in MDD and BD and their potential use as biomarkers for treatment response. Full article
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Open AccessArticle
Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq
Non-Coding RNA 2020, 6(3), 32; https://doi.org/10.3390/ncrna6030032 - 21 Aug 2020
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, [...] Read more.
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. Full article
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Open AccessFeature PaperReview
Emerging Insights on the Biological Impact of Extracellular Vesicle-Associated ncRNAs in Multiple Myeloma
Non-Coding RNA 2020, 6(3), 30; https://doi.org/10.3390/ncrna6030030 - 05 Aug 2020
Cited by 2
Abstract
Increasing evidence indicates that extracellular vesicles (EVs) released from both tumor cells and the cells of the bone marrow microenvironment contribute to the pathobiology of multiple myeloma (MM). Recent studies on the mechanisms by which EVs exert their biological activity have indicated that [...] Read more.
Increasing evidence indicates that extracellular vesicles (EVs) released from both tumor cells and the cells of the bone marrow microenvironment contribute to the pathobiology of multiple myeloma (MM). Recent studies on the mechanisms by which EVs exert their biological activity have indicated that the non-coding RNA (ncRNA) cargo is key in mediating their effect on MM development and progression. In this review, we will first discuss the role of EV-associated ncRNAs in different aspects of MM pathobiology, including proliferation, angiogenesis, bone disease development, and drug resistance. Finally, since ncRNAs carried by MM vesicles have also emerged as a promising tool for early diagnosis and therapy response prediction, we will report evidence of their potential use as clinical biomarkers. Full article
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Open AccessReview
Macrophage Long Non-Coding RNAs in Pathogenesis of Cardiovascular Disease
Non-Coding RNA 2020, 6(3), 28; https://doi.org/10.3390/ncrna6030028 - 11 Jul 2020
Abstract
Chronic inflammation is inextricably linked to cardiovascular disease (CVD). Macrophages themselves play important roles in atherosclerosis, as well as acute and chronic heart failure. Although the role of macrophages in CVD pathophysiology is well-recognized, little is known regarding the precise mechanisms influencing their [...] Read more.
Chronic inflammation is inextricably linked to cardiovascular disease (CVD). Macrophages themselves play important roles in atherosclerosis, as well as acute and chronic heart failure. Although the role of macrophages in CVD pathophysiology is well-recognized, little is known regarding the precise mechanisms influencing their function in these contexts. Long non-coding RNAs (lncRNAs) have emerged as significant regulators of macrophage function; as such, there is rising interest in understanding how these nucleic acids influence macrophage signaling, cell fate decisions, and activity in health and disease. In this review, we summarize current knowledge regarding lncRNAs in directing various aspects of macrophage function in CVD. These include foam cell formation, Toll-like receptor (TLR) and NF-kβ signaling, and macrophage phenotype switching. This review will provide a comprehensive understanding concerning previous, ongoing, and future studies of lncRNAs in macrophage functions and their importance in CVD. Full article
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Open AccessReview
Long-Noncoding RNA (lncRNA) in the Regulation of Hypoxia-Inducible Factor (HIF) in Cancer
Non-Coding RNA 2020, 6(3), 27; https://doi.org/10.3390/ncrna6030027 - 06 Jul 2020
Cited by 3
Abstract
Hypoxia is dangerous for oxygen-dependent cells, therefore, physiological adaption to cellular hypoxic conditions is essential. The transcription factor hypoxia-inducible factor (HIF) is the main regulator of hypoxic metabolic adaption reducing oxygen consumption and is regulated by gradual von Hippel-Lindau (VHL)-dependent proteasomal degradation. Beyond [...] Read more.
Hypoxia is dangerous for oxygen-dependent cells, therefore, physiological adaption to cellular hypoxic conditions is essential. The transcription factor hypoxia-inducible factor (HIF) is the main regulator of hypoxic metabolic adaption reducing oxygen consumption and is regulated by gradual von Hippel-Lindau (VHL)-dependent proteasomal degradation. Beyond physiology, hypoxia is frequently encountered within solid tumors and first drugs are in clinical trials to tackle this pathway in cancer. Besides hypoxia, cancer cells may promote HIF expression under normoxic conditions by altering various upstream regulators, cumulating in HIF upregulation and enhanced glycolysis and angiogenesis, altogether promoting tumor proliferation and progression. Therefore, understanding the underlying molecular mechanisms is crucial to discover potential future therapeutic targets to evolve cancer therapy. Long non-coding RNAs (lncRNA) are a class of non-protein coding RNA molecules with a length of over 200 nucleotides. They participate in cancer development and progression and might act as either oncogenic or tumor suppressive factors. Additionally, a growing body of evidence supports the role of lncRNAs in the hypoxic and normoxic regulation of HIF and its subunits HIF-1α and HIF-2α in cancer. This review provides a comprehensive update and overview of lncRNAs as regulators of HIFs expression and activation and discusses and highlights potential involved pathways. Full article
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Open AccessFeature PaperReview
LncRNA NEAT1 in Paraspeckles: A Structural Scaffold for Cellular DNA Damage Response Systems?
Non-Coding RNA 2020, 6(3), 26; https://doi.org/10.3390/ncrna6030026 - 01 Jul 2020
Cited by 2
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect [...] Read more.
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect different cellular functions, including stress response. Furthermore, increasing evidence supports the crucial role of NEAT1 and essential structural proteins of PSs (PSPs) in the regulation of the DNA damage repair (DDR) system. This review aims to provide an overview of the current knowledge on the involvement of NEAT1 and PSPs in DDR, which might strengthen the rationale underlying future NEAT1-based therapeutic options in tumor and neurodegenerative diseases. Full article
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Open AccessFeature PaperReview
LncRNAs in Non-Small-Cell Lung Cancer
Non-Coding RNA 2020, 6(3), 25; https://doi.org/10.3390/ncrna6030025 - 30 Jun 2020
Cited by 3
Abstract
Lung cancer is associated with a high mortality, with around 1.8 million deaths worldwide in 2018. Non-small-cell lung cancer (NSCLC) accounts for around 85% of cases and, despite improvement in the management of NSCLC, most patients are diagnosed at advanced stage and the [...] Read more.
Lung cancer is associated with a high mortality, with around 1.8 million deaths worldwide in 2018. Non-small-cell lung cancer (NSCLC) accounts for around 85% of cases and, despite improvement in the management of NSCLC, most patients are diagnosed at advanced stage and the five-year survival remains around 15%. This highlights a need to identify novel ways to treat the disease to reduce the burden of NSCLC. Long non-coding RNAs (lncRNAs) are non-coding RNA molecules longer than 200 nucleotides in length which play important roles in gene expression and signaling pathways. Recently, lncRNAs were implicated in cancer, where their expression is dysregulated resulting in aberrant functions. LncRNAs were shown to function as both tumor suppressors and oncogenes in a variety of cancer types. Although there are a few well characterized lncRNAs in NSCLC, many lncRNAs remain un-characterized and their mechanisms of action largely unknown. LncRNAs have success as therapies in neurodegenerative diseases, and having a detailed understanding of their function in NSCLC may guide novel therapeutic approaches and strategies. This review discusses the role of lncRNAs in NSCLC tumorigenesis, highlighting their mechanisms of action and their clinical potential. Full article
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Open AccessReview
The Roles of Long Noncoding RNAs HNF1α-AS1 and HNF4α-AS1 in Drug Metabolism and Human Diseases
Non-Coding RNA 2020, 6(2), 24; https://doi.org/10.3390/ncrna6020024 - 24 Jun 2020
Cited by 1
Abstract
Long noncoding RNAs (lncRNAs) are RNAs with a length of over 200 nucleotides that do not have protein-coding abilities. Recent studies suggest that lncRNAs are highly involved in physiological functions and diseases. lncRNAs HNF1α-AS1 and HNF4α-AS1 are transcripts of lncRNA genes HNF1α-AS1 and [...] Read more.
Long noncoding RNAs (lncRNAs) are RNAs with a length of over 200 nucleotides that do not have protein-coding abilities. Recent studies suggest that lncRNAs are highly involved in physiological functions and diseases. lncRNAs HNF1α-AS1 and HNF4α-AS1 are transcripts of lncRNA genes HNF1α-AS1 and HNF4α-AS1, which are antisense lncRNA genes located in the neighborhood regions of the transcription factor (TF) genes HNF1α and HNF4α, respectively. HNF1α-AS1 and HNF4α-AS1 have been reported to be involved in several important functions in human physiological activities and diseases. In the liver, HNF1α-AS1 and HNF4α-AS1 regulate the expression and function of several drug-metabolizing cytochrome P450 (P450) enzymes, which also further impact P450-mediated drug metabolism and drug toxicity. In addition, HNF1α-AS1 and HNF4α-AS1 also play important roles in the tumorigenesis, progression, invasion, and treatment outcome of several cancers. Through interacting with different molecules, including miRNAs and proteins, HNF1α-AS1 and HNF4α-AS1 can regulate their target genes in several different mechanisms including miRNA sponge, decoy, or scaffold. The purpose of the current review is to summarize the identified functions and mechanisms of HNF1α-AS1 and HNF4α-AS1 and to discuss the future directions of research of these two lncRNAs. Full article
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Open AccessArticle
Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum
Non-Coding RNA 2020, 6(2), 15; https://doi.org/10.3390/ncrna6020015 - 01 Apr 2020
Cited by 2
Abstract
Schistosoma japonicum is a flatworm that causes schistosomiasis, a neglected tropical disease. S. japonicum RNA-Seq analyses has been previously reported in the literature on females and males obtained during sexual maturation from 14 to 28 days post-infection in mouse, resulting in the identification [...] Read more.
Schistosoma japonicum is a flatworm that causes schistosomiasis, a neglected tropical disease. S. japonicum RNA-Seq analyses has been previously reported in the literature on females and males obtained during sexual maturation from 14 to 28 days post-infection in mouse, resulting in the identification of protein-coding genes and pathways, whose expression levels were related to sexual development. However, this work did not include an analysis of long non-coding RNAs (lncRNAs). Here, we applied a pipeline to identify and annotate lncRNAs in 66 S. japonicum RNA-Seq publicly available libraries, from different life-cycle stages. We also performed co-expression analyses to find stage-specific lncRNAs possibly related to sexual maturation. We identified 12,291 S. japonicum expressed lncRNAs. Sequence similarity search and synteny conservation indicated that some 14% of S. japonicum intergenic lncRNAs have synteny conservation with S. mansoni intergenic lncRNAs. Co-expression analyses showed that lncRNAs and protein-coding genes in S. japonicum males and females have a dynamic co-expression throughout sexual maturation, showing differential expression between the sexes; the protein-coding genes were related to the nervous system development, lipid and drug metabolism, and overall parasite survival. Co-expression pattern suggests that lncRNAs possibly regulate these processes or are regulated by the same activation program as that of protein-coding genes. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Pre-therapeutic efficacy of miR-124 in medulloblastoma
Authors: Buzzetti Marta, Morlando Sonia, Di Leva Gianpiero.
Affiliation: School of Pharmacy and Bioengineering, Guy Hilton Research Facility, Keele University, Keele, Staffordshire ST5 5BG, UK

Title: Global analysis of all RNA-dependent RNA Polymerase small RNAs reveals new substrates and functions for Suppressor of Gene Silencing 3 in Arabidopsis
Authors: Xia Hua1, Nathan Berkowitz1,2, Matthew Willmann3, Xiang Yu1, and Brian D. Gregory1,2
Affiliation: 1 Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA. 2 Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. 3 School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA

Title: Non coding RNAs: strategy for viruses offensive?
Authors: Alessia Gallo
Affiliation: Unit of Regenerative Medicine and Biomedical Technologies IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies) Via Tricomi, 5 Palermo 90127

Title: Non-coding RNAs in retinoic acid-driven cell differentiation and disease
Authors: Diego Franco Jaime
Affiliation: Universidad de Jaén, Departamento de Biología Experimental, B3-362

Title: Circulating RNAs associated with the metabolic syndrome
Authors: Louise Torp Dalgaard
Affiliation: Eukaryot Cellebiologi, The Department of Science, Systems and Models, Roskilde University, Universitetsvej 1, 18.2, DK-4000, Roskilde, Denmark

Title: MicroRNAs as biomarkers for neurodegenerative diseases
Authors: Ivana Delalle
Affiliation: Boston University School of Medicine, Department of Pathology and Laboratory Medicine, Boston

Title: Emerging roles of microRNA-200 family in dentistry
Authors: Pei-Ling Hsieh, Cheng-Chia Yu
Affiliation: Institute of Oral Sciences, Chung Shan Medical University, Taiwan.

Title: ncRNAs in liquid biopsy
Authors: Peter Gahan;; Heidi Schwarzenbach
Affiliation: Fondazione “Enrico Puccinelli” Onlus, Perugia, Italy

Title: Bioinformatic analyses of conserved microRNAs-target gene networks between the human left ventricle and peripheral plasma could reveal new functional biomarkers of ischaemic heart disease in diabetic patients
Authors: Maryam Anwar1, Junyi Liu1, Ibrahim Nasser1, Gianni Angelini1,2, Prakash Punjabi1, Kerrie Ford, Aranzazu Chamorro-Jorganes1, Costanza Emanueli1, 2
Affiliation: 1National Heart and Lung Institute, Imperial College London, London, UK 2Bristol Heart Institute, University of Bristol, Bristol, UK

Title: ncRNAs and prostate cancer from a diagnostic point of view
Authors: Barbara Pardini
Affiliation: Italian Institute for Genomic Medicine - IIGM, c/o FPO IRCCS, 10060 Candiolo (To), Italy

Title: microRNAs in the 8q24 region and risk of cancer
Authors: Barbara Pardini
Affiliation: Italian Institute for Genomic Medicine - IIGM, c/o FPO IRCCS, 10060 Candiolo (To), Italy

Title: Exosomes in immune regulation
Authors: Peter Gahan; Heidi Schwarzenbach
Affiliation: Fondazione “Enrico Puccinelli” Onlus, Perugia, Italy
Abstract: Exosomes, small extracellular vesicles mediate intercellular communication by transferring their cargo including DNA, RNA, proteins and lipids from cell to cell. Notably, in the immune system, they have protective functions. However in cancer, exosomes acquire new, immunosuppressive properties that cause the dysregulation of immune cells and immune escape of tumor cells supporting cancer progression and metastasis. Therefore, current investigations focus on the regulation of exosome levels for immunotherapeutic interventions. In this review, we discuss the role of exosomes in immunomodulation of lymphoid and myeloid cells, and their use as immune stimulatory agents to elicit specific cytotoxic responses against the tumor.

Title: MiR-294 and miR-410 negatively regulates Tnfa, arginine transporters Cat1/2, and Nos2 mRNAs in macrophages infected with Leishmania amazonensis
Authors: Stephanie Maia Acuña, Jonathan Miguel Zanatta, Camilla de Almeida Bento, Lucile Maria Floeter-Winter, Sandra Marcia Muxel.
Affiliation: Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
Abstract: MicroRNAs are small non-coding RNA that regulate post-transcriptionally several physiological processes, including immune responses. Murine macrophages infected with Leishmania amazonensis present crucial inflammatory response changes and metabolism accompanied by miRNA profile shifting. In this context, L-arginine is one of the mechanisms that modulate the inflammatory response through Nitric Oxide Synthase 2 (Nos2), producing NO, or arginase 1 (Arg1), providing fueling polyamine formation. This work aims to evaluate the expression and function of miR-294 and miR-410 during C57BL/6 bone marrow-derived macrophages early infection with L. amazonensis. We observed that after 4 and 24h of infection, miR-294 and miR-410 levels were upregulated, correlating with the decreased levels of mRNAs coding for tumor necrosis factor-alpha (Tnfa), Nos2, and cationic amino acid transporters 1 and 2 (Cat1 and Cat2). The functional inhibition of miR-294 led to increased levels of Tnfa, Nos2, and Cat2. Likewise, miR-410 inhibition increased Cat1 levels. Moreover, Nos2-/- infected macrophages showed decreased levels of Tnfa, but the miR-294 level remained the same. Also, miRNA inhibition reduced the parasite’s infectivity. Altogether, these data suggest that the microRNAs miR-294 and miR-410 play a role in the macrophage inflammatory response against L. amazonensis, contributing to the infection outcome definition.

Title: Beyond base pairing: complex interactions between structured noncoding RNAs
Authors: Jinwei Zhang
Affiliation: Laboratory of Molecular Biology NIDDK, NIH 50 South Drive, Room 4503 Bethesda, MD 20892

Title: non coding RNA impacting on mitochondrial functions
Authors: Nicola Amodio
Affiliation: Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy

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