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CRISPR/Cas Technology Applied to the Study of Non-coding RNAs in...
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CRISPR/Cas Technology Applied to the Study of Non-coding RNAs in Human Disease

A special issue of Non-Coding RNA (ISSN 2311-553X). This special issue belongs to the section "Clinical Applications of Non-Coding RNA".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 21070

Special Issue Editors

Prof. Dr. Pier Paolo Pandolfi

grade E-Mail Website
Guest Editor
1. Department of Molecular Biotechnologies & Health Sciences, Molecular Biotechnology Center, University of Turin, Turin, Italy
2. Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, USA
Interests: cancer genetics; tumor suppressor genes and oncogenes; non-coding RNAs; microRNAs; circ-RNAs; ceRNAs; pseudogenes
Dr. Laura Poliseno

E-Mail Website
Guest Editor
Oncogenomics Unit, Institute of Clinical Physiology (IFC), National Research Council (CNR), and Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), 56124 Pisa, Italy
Interests: melanoma; BRAFV600E isoforms; microRNAs; ceRNAs; pigmentation; melanoma modeling in zebrafish and mice; attenuated Listeria monocytogenes; pseudogenes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleague,

Originally used by bacteria to protect themselves against viruses, CRISPR/Cas system-based editing of DNA and RNA has, in recent years, been adapted to a wide variety of purposes, including the study of complex biological processes, the design of new therapeutic approaches, and the development of new biotechnological tools.

This Special Issue will collect original research articles and communications in which CRISPR/Cas technology is used in human disease:

  1. To study the biological role played by non-coding RNAs, through the modulation of their expression at the genomic, transcriptional, or post-transcriptional level; through the identification of RNA and protein species directly bound to them; or through their visualization and tracking inside human cells.
  2. To target non-coding RNAs for therapeutic purposes.

Submissions describing in vivo data obtained in animal models are strongly encouraged.

This Special Issue will also include concept articles in which, rather than giving an overview of the literature, authors provide insights and explain ideas that can contribute to stimulate discussion and move the field forward.

Prof. Dr. Pier Paolo Pandolfi
Dr. Laura Poliseno
Guest Editors

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 submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue 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 semimonthly 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 1800 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.

Keywords

  • CRISPR/Cas system
  • Cas9
  • Cas13
  • genome editing
  • CRISPRa/i
  • RNA knock-down
  • RNA editing
  • RNA immunoprecipitation/pull-down
  • RNA tracking
  • CRISPR-based therapeutics

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Published Papers (5 papers)

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Research

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17 pages, 10277 KiB  
Article
LncRNA-Based Classification of Triple Negative Breast Cancer Revealed Inherent Tumor Heterogeneity and Vulnerabilities
by Radhakrishnan Vishnubalaji, Ramesh Elango and Nehad M. Alajez
Non-Coding RNA 2022, 8(4), 44; https://doi.org/10.3390/ncrna8040044 - 21 Jun 2022
Cited by 7 | Viewed by 2952
Abstract
Triple negative breast cancer (TNBC) represents a diverse group of cancers based on their gene expression profiles. While the current mRNA-based classification of TNBC has contributed to our understanding of the heterogeneity of this disease, whether such heterogeneity can be resolved employing a [...] Read more.
Triple negative breast cancer (TNBC) represents a diverse group of cancers based on their gene expression profiles. While the current mRNA-based classification of TNBC has contributed to our understanding of the heterogeneity of this disease, whether such heterogeneity can be resolved employing a long noncoding RNA (lncRNA) transcriptome has not been established thus far. Herein, we used iterative clustering and guide-gene selection (ICGS) and uniform manifold approximation and projection (UMAP) dimensionality reduction analysis on a large cohort of TNBC transcriptomic data (TNBC = 360, normal = 88) and classified TNBC into four main clusters: LINC00511-enriched, LINC00393-enriched, FIRRE-enriched, and normal tissue-like. Delving into associated gene expression profiles revealed remarkable differences in canonical, casual, upstream, and functional categories among different lncRNA-derived TNBC clusters, suggesting functional consequences for altered lncRNA expression. Correlation and survival analysis comparing mRNA- and lncRNA-based clustering revealed similarities and differences between the two classification approaches. To provide insight into the potential role of the identified lncRNAs in TNBC biology, CRISPR-Cas9 mediated LINC00511 promoter deletion reduced colony formation and enhanced the sensitivity of TNBC cells to paclitaxel, suggesting a role for LINC00511 in conferring tumorigenicity and resistance to therapy. Our data revealed a novel lncRNA-based classification of TNBC and suggested their potential utilization as disease biomarkers and therapeutic targets. Full article
(This article belongs to the Special Issue CRISPR/Cas Technology Applied to the Study of Non-coding RNAs in Human Disease)
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20 pages, 9132 KiB  
Article
CRISPR/CasRx-Mediated RNA Knockdown Reveals That ACE2 Is Involved in the Regulation of Oligodendroglial Cell Morphological Differentiation
by Yukino Kato, Kenji Tago, Shoya Fukatsu, Miyu Okabe, Remina Shirai, Hiroaki Oizumi, Katsuya Ohbuchi, Masahiro Yamamoto, Kazushige Mizoguchi, Yuki Miyamoto and Junji Yamauchi
Non-Coding RNA 2022, 8(3), 42; https://doi.org/10.3390/ncrna8030042 - 6 Jun 2022
Cited by 4 | Viewed by 3208
Abstract
Angiotensin-converting enzyme 2 (ACE2) plays a role in catalyzing angiotensin II conversion to angiotensin (1–7), which often counteracts the renin-angiotensin system. ACE2 is expressed not only in the cells of peripheral tissues such as the heart and kidney, but also in those of [...] Read more.
Angiotensin-converting enzyme 2 (ACE2) plays a role in catalyzing angiotensin II conversion to angiotensin (1–7), which often counteracts the renin-angiotensin system. ACE2 is expressed not only in the cells of peripheral tissues such as the heart and kidney, but also in those of the central nervous system (CNS). Additionally, ACE2 acts as the receptor required for the entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), whose binding leads to endocytotic recycling and possible degradation of the ACE2 proteins themselves. One of the target cells for SARS-CoV-2 in the CNS is oligodendrocytes (oligodendroglial cells), which wrap neuronal axons with their differentiated plasma membranes called myelin membranes. Here, for the first time, we describe the role of ACE2 in FBD-102b cells, which are used as the differentiation models of oligodendroglial cells. Unexpectedly, RNA knockdown of ACE2 with CasRx-mediated gRNA or the cognate siRNA promoted oligodendroglial cell morphological differentiation with increased expression or phosphorylation levels of differentiation and/or myelin marker proteins, suggesting the negative role of ACE2 in morphological differentiation. Notably, ACE2′s intracellular region preferentially interacted with the active GTP-bound form of Ras. Thus, knockdown of ACE2 relatively increased GTP-bound Ras in an affinity-precipitation assay. Indeed, inhibition of Ras resulted in decreasing both morphological differentiation and expression or phosphorylation levels of marker proteins, confirming the positive role of Ras in differentiation. These results indicate the role of ACE2 itself as a negative regulator of oligodendroglial cell morphological differentiation, newly adding ACE2 to the list of regulators of oligodendroglial morphogenesis as well as of Ras-binding proteins. These findings might help us to understand why SARS-CoV-2 causes pathological effects in the CNS. Full article
(This article belongs to the Special Issue CRISPR/Cas Technology Applied to the Study of Non-coding RNAs in Human Disease)
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19 pages, 5430 KiB  
Article
Comprehensive Transcriptional Profiling and Mouse Phenotyping Reveals Dispensable Role for Adipose Tissue Selective Long Noncoding RNA Gm15551
by Christoph Andreas Engelhard, Chien Huang, Sajjad Khani, Petr Kasparek, Jan Prochazka, Jan Rozman, David Pajuelo Reguera, Radislav Sedlacek and Jan-Wilhelm Kornfeld
Non-Coding RNA 2022, 8(3), 32; https://doi.org/10.3390/ncrna8030032 - 6 May 2022
Cited by 3 | Viewed by 3659
Abstract
Cold and nutrient-activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via the uncoupled respiration and secretion of endocrine factors, thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have [...] Read more.
Cold and nutrient-activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via the uncoupled respiration and secretion of endocrine factors, thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have recently been identified as fine-tuning regulators of cellular function. While certain lncRNAs have been functionally characterised in adipose tissue, their overall contribution in the activation of BAT remains elusive. We identified lncRNAs correlating to interscapular brown adipose tissue (iBAT) function in a high fat diet (HFD) and cold stressed mice. We focused on Gm15551, which has an adipose tissue specific expression profile, is highly upregulated during adipogenesis, and downregulated by β-adrenergic activation in mature adipocytes. Although we performed comprehensive transcriptional and adipocyte physiology profiling in vitro and in vivo, we could not detect an effect of gain or loss of function of Gm15551. Full article
(This article belongs to the Special Issue CRISPR/Cas Technology Applied to the Study of Non-coding RNAs in Human Disease)
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Review

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23 pages, 1486 KiB  
Review
CRISPR-Based Approaches for the High-Throughput Characterization of Long Non-Coding RNAs
by Joshua Hazan and Assaf Chanan Bester
Non-Coding RNA 2021, 7(4), 79; https://doi.org/10.3390/ncrna7040079 - 13 Dec 2021
Cited by 9 | Viewed by 5147
Abstract
Over the last decade, tens of thousands of new long non-coding RNAs (lncRNAs) have been identified in the human genome. Nevertheless, except for a handful of genes, the genetic characteristics and functions of most of these lncRNAs remain elusive; this is partially due [...] Read more.
Over the last decade, tens of thousands of new long non-coding RNAs (lncRNAs) have been identified in the human genome. Nevertheless, except for a handful of genes, the genetic characteristics and functions of most of these lncRNAs remain elusive; this is partially due to their relatively low expression, high tissue specificity, and low conservation across species. A major limitation for determining the function of lncRNAs was the lack of methodologies suitable for studying these genes. The recent development of CRISPR/Cas9 technology has opened unprecedented opportunities to uncover the genetic and functional characteristics of the non-coding genome via targeted and high-throughput approaches. Specific CRISPR/Cas9-based approaches were developed to target lncRNA loci. Some of these approaches involve modifying the sequence, but others were developed to study lncRNAs by inducing transcriptional and epigenetic changes. The discovery of other programable Cas proteins broaden our possibilities to target RNA molecules with greater precision and accuracy. These approaches allow for the knock-down and characterization of lncRNAs. Here, we review how various CRISPR-based strategies have been used to characterize lncRNAs with important functions in different biological contexts and how these approaches can be further utilized to improve our understanding of the non-coding genome. Full article
(This article belongs to the Special Issue CRISPR/Cas Technology Applied to the Study of Non-coding RNAs in Human Disease)
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Other

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15 pages, 763 KiB  
Concept Paper
Between the Devil and the Deep Blue Sea: Non-Coding RNAs Associated with Transmissible Cancers in Tasmanian Devil, Domestic Dog and Bivalves
by Nicholas C. Lister, Ashley M. Milton, Benjamin J. Hanrahan and Paul D. Waters
Non-Coding RNA 2021, 7(4), 72; https://doi.org/10.3390/ncrna7040072 - 10 Nov 2021
Cited by 2 | Viewed by 4521
Abstract
Currently there are nine known examples of transmissible cancers in nature. They have been observed in domestic dog, Tasmanian devil, and six bivalve species. These tumours can overcome host immune defences and spread to other members of the same species. Non-coding RNAs (ncRNAs) [...] Read more.
Currently there are nine known examples of transmissible cancers in nature. They have been observed in domestic dog, Tasmanian devil, and six bivalve species. These tumours can overcome host immune defences and spread to other members of the same species. Non-coding RNAs (ncRNAs) are known to play roles in tumorigenesis and immune system evasion. Despite their potential importance in transmissible cancers, there have been no studies on ncRNA function in this context to date. Here, we present possible applications of the CRISPR/Cas system to study the RNA biology of transmissible cancers. Specifically, we explore how ncRNAs may play a role in the immortality and immune evasion ability of these tumours. Full article
(This article belongs to the Special Issue CRISPR/Cas Technology Applied to the Study of Non-coding RNAs in Human Disease)
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