Special Issue "Aberrant Pre-mRNA Splicing in Disease"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (31 October 2017)

Special Issue Editor

Guest Editor
Dr. Michael Ladomery

Faculty of Health and Applied Sciences, University of the West of England, Bristol; Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
Website | E-Mail
Phone: +44-117-3283531
Interests: RNA biology in development and disease; RNA binding proteins; alternative splicing; splice factors; splice factor kinases

Special Issue Information

Dear Colleagues,

After the discovery of pre-mRNA splicing in the late 1970s, it became apparent that exons can be spliced together in different ways: in other words, pre-mRNA is alternatively spliced. The extent of alternative splicing in different species is remarkable; indeed, in humans, it is now thought that over 94% of our genes are alternatively spliced. Genes can even express dozens, if not hundreds of splice isoforms; alternative splicing is a major contributor to proteomic complexity. Alternative splicing affects all parts of mRNAs; not only the open reading frame altering the amino-acid sequence, but also the 5' and 3' UTRs influencing mRNA translation, localization and stability. Splice isoforms often encode functionally distinct proteins. Mutations that disrupt normal pre-mRNA splicing—as many as one in six mutations in humans—are associated with a wide range of diseases. The purpose of this Special Issue is to illustrate the growing prominence of alternative splicing in biomedical research.

Dr. Michael Ladomery
Guest Editor

Manuscript Submission Information

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Keywords

  • pre-mRNA splicing
  • alternative splicing
  • RNA-binding proteins
  • splice factors
  • splice factor kinases

Published Papers (6 papers)

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Research

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Open AccessArticle Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease
Genes 2018, 9(1), 15; doi:10.3390/genes9010015
Received: 9 November 2017 / Revised: 11 December 2017 / Accepted: 27 December 2017 / Published: 4 January 2018
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Abstract
Mutations in the OCRL gene are associated with both Lowe syndrome and Dent-2 disease. Patients with Lowe syndrome present congenital cataracts, mental disabilities and a renal proximal tubulopathy, whereas patients with Dent-2 disease exhibit similar proximal tubule dysfunction but only mild, or no
[...] Read more.
Mutations in the OCRL gene are associated with both Lowe syndrome and Dent-2 disease. Patients with Lowe syndrome present congenital cataracts, mental disabilities and a renal proximal tubulopathy, whereas patients with Dent-2 disease exhibit similar proximal tubule dysfunction but only mild, or no additional clinical defects. It is not yet understood why some OCRL mutations cause the phenotype of Lowe syndrome, while others develop the milder phenotype of Dent-2 disease. Our goal was to gain new insights into the consequences of OCRL exonic mutations on pre-mRNA splicing. Using predictive bioinformatics tools, we selected thirteen missense mutations and one synonymous mutation based on their potential effects on splicing regulatory elements or splice sites. These mutations were analyzed in a minigene splicing assay. Results of the RNA analysis showed that three presumed missense mutations caused alterations in pre-mRNA splicing. Mutation c.741G>T; p.(Trp247Cys) generated splicing silencer sequences and disrupted splicing enhancer motifs that resulted in skipping of exon 9, while mutations c.2581G>A; p.(Ala861Thr) and c.2581G>C; p.(Ala861Pro) abolished a 5′ splice site leading to skipping of exon 23. Mutation c.741G>T represents the first OCRL exonic variant outside the conserved splice site dinucleotides that results in alteration of pre-mRNA splicing. Our results highlight the importance of evaluating the effects of OCRL exonic mutations at the mRNA level. Full article
(This article belongs to the Special Issue Aberrant Pre-mRNA Splicing in Disease)
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Review

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Open AccessReview Muscle-Specific Mis-Splicing and Heart Disease Exemplified by RBM20
Genes 2018, 9(1), 18; doi:10.3390/genes9010018
Received: 20 November 2017 / Revised: 23 December 2017 / Accepted: 27 December 2017 / Published: 5 January 2018
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Abstract
Alternative splicing is an essential post-transcriptional process to generate multiple functional RNAs or proteins from a single transcript. Progress in RNA biology has led to a better understanding of muscle-specific RNA splicing in heart disease. The recent discovery of the muscle-specific splicing factor
[...] Read more.
Alternative splicing is an essential post-transcriptional process to generate multiple functional RNAs or proteins from a single transcript. Progress in RNA biology has led to a better understanding of muscle-specific RNA splicing in heart disease. The recent discovery of the muscle-specific splicing factor RNA-binding motif 20 (RBM20) not only provided great insights into the general alternative splicing mechanism but also demonstrated molecular mechanism of how this splicing factor is associated with dilated cardiomyopathy. Here, we review our current knowledge of muscle-specific splicing factors and heart disease, with an emphasis on RBM20 and its targets, RBM20-dependent alternative splicing mechanism, RBM20 disease origin in induced Pluripotent Stem Cells (iPSCs), and RBM20 mutations in dilated cardiomyopathy. In the end, we will discuss the multifunctional role of RBM20 and manipulation of RBM20 as a potential therapeutic target for heart disease. Full article
(This article belongs to the Special Issue Aberrant Pre-mRNA Splicing in Disease)
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Open AccessReview Signaling Pathways Driving Aberrant Splicing in Cancer Cells
Genes 2018, 9(1), 9; doi:10.3390/genes9010009
Received: 6 November 2017 / Revised: 7 December 2017 / Accepted: 18 December 2017 / Published: 29 December 2017
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Abstract
Aberrant profiles of pre-mRNA splicing are frequently observed in cancer. At the molecular level, an altered profile results from a complex interplay between chromatin modifications, the transcriptional elongation rate of RNA polymerase, and effective binding of the spliceosome to the generated transcripts. Key
[...] Read more.
Aberrant profiles of pre-mRNA splicing are frequently observed in cancer. At the molecular level, an altered profile results from a complex interplay between chromatin modifications, the transcriptional elongation rate of RNA polymerase, and effective binding of the spliceosome to the generated transcripts. Key players in this interplay are regulatory splicing factors (SFs) that bind to gene-specific splice-regulatory sequence elements. Although mutations in genes of some SFs were described, a major driver of aberrant splicing profiles is oncogenic signal transduction pathways. Signaling can affect either the transcriptional expression levels of SFs or the post-translational modification of SF proteins, and both modulate the ratio of nuclear versus cytoplasmic SFs in a given cell. Here, we will review currently known mechanisms by which cancer cell signaling, including the mitogen-activated protein kinases (MAPK), phosphatidylinositol 3 (PI3)-kinase pathway (PI3K) and wingless (Wnt) pathways but also signals from the tumor microenvironment, modulate the activity or subcellular localization of the Ser/Arg rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) families of SFs. Full article
(This article belongs to the Special Issue Aberrant Pre-mRNA Splicing in Disease)
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Open AccessReview Circular RNAs (circRNAs) in Health and Disease
Genes 2017, 8(12), 353; doi:10.3390/genes8120353
Received: 19 October 2017 / Revised: 22 November 2017 / Accepted: 22 November 2017 / Published: 28 November 2017
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Abstract
Splicing events do not always produce a linear transcript. Circular RNAs (circRNAs) are a class of RNA that are emerging as key new members of the gene regulatory milieu, which are produced by back-splicing events within genes. In circRNA formation, rather than being
[...] Read more.
Splicing events do not always produce a linear transcript. Circular RNAs (circRNAs) are a class of RNA that are emerging as key new members of the gene regulatory milieu, which are produced by back-splicing events within genes. In circRNA formation, rather than being spliced in a linear fashion, exons can be circularised by use of the 3′ acceptor splice site of an upstream exon, leading to the formation of a circular RNA species. circRNAs have been demonstrated across species and have the potential to present genetic information in new orientations distinct from their parent transcript. The importance of these RNA players in gene regulation and normal cellular homeostasis is now beginning to be recognised. They have several potential modes of action, from serving as sponges for micro RNAs and RNA binding proteins, to acting as transcriptional regulators. In accordance with an important role in the normal biology of the cell, perturbations of circRNA expression are now being reported in association with disease. Furthermore, the inherent stability of circRNAs conferred by their circular structure and exonuclease resistance, and their expression in blood and other peripheral tissues in association with endosomes and microvesicles, renders them excellent candidates as disease biomarkers. In this review, we explore the state of knowledge on this exciting class of transcripts in regulating gene expression and discuss their emerging role in health and disease. Full article
(This article belongs to the Special Issue Aberrant Pre-mRNA Splicing in Disease)
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Open AccessReview Alternative Splicing of L-type CaV1.2 Calcium Channels: Implications in Cardiovascular Diseases
Genes 2017, 8(12), 344; doi:10.3390/genes8120344
Received: 11 October 2017 / Revised: 9 November 2017 / Accepted: 21 November 2017 / Published: 24 November 2017
PDF Full-text (2019 KB) | HTML Full-text | XML Full-text
Abstract
L-type CaV1.2 calcium channels are the major pathway for Ca2+ influx to initiate the contraction of smooth and cardiac muscles. Alteration of CaV1.2 channel function has been implicated in multiple cardiovascular diseases, such as hypertension and cardiac hypertrophy.
[...] Read more.
L-type CaV1.2 calcium channels are the major pathway for Ca2+ influx to initiate the contraction of smooth and cardiac muscles. Alteration of CaV1.2 channel function has been implicated in multiple cardiovascular diseases, such as hypertension and cardiac hypertrophy. Alternative splicing is a post-transcriptional mechanism that expands CaV1.2 channel structures to modify function, pharmacological and biophysical property such as calcium/voltage-dependent inactivation (C/VDI), or to influence its post-translational modulation by interacting proteins such as Galectin-1. Alternative splicing has generated functionally diverse CaV1.2 isoforms that can be developmentally regulated in the heart, or under pathophysiological conditions such as in heart failure. More importantly, alternative splicing of certain exons of CaV1.2 has been reported to be regulated by splicing factors such as RNA-binding Fox-1 homolog 1/2 (Rbfox 1/2), polypyrimidine tract-binding protein (PTBP1) and RNA-binding motif protein 20 (RBM20). Understanding how CaV1.2 channel function is remodelled in disease will provide better information to guide the development of more targeted approaches to discover therapeutic agents for cardiovascular diseases. Full article
(This article belongs to the Special Issue Aberrant Pre-mRNA Splicing in Disease)
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Open AccessReview Alternative Splicing in Breast Cancer and the Potential Development of Therapeutic Tools
Genes 2017, 8(10), 217; doi:10.3390/genes8100217
Received: 28 July 2017 / Revised: 22 August 2017 / Accepted: 22 August 2017 / Published: 5 October 2017
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Abstract
Alternative splicing is a key molecular mechanism now considered as a hallmark of cancer that has been associated with the expression of distinct isoforms during the onset and progression of the disease. The leading cause of cancer-related deaths in women worldwide is breast
[...] Read more.
Alternative splicing is a key molecular mechanism now considered as a hallmark of cancer that has been associated with the expression of distinct isoforms during the onset and progression of the disease. The leading cause of cancer-related deaths in women worldwide is breast cancer, and even when the role of alternative splicing in this type of cancer has been established, the function of this mechanism in breast cancer biology is not completely decoded. In order to gain a comprehensive view of the role of alternative splicing in breast cancer biology and development, we summarize here recent findings regarding alternative splicing events that have been well documented for breast cancer evolution, considering its prognostic and therapeutic value. Moreover, we analyze how the response to endocrine and chemical therapies could be affected due to alternative splicing and differential expression of variant isoforms. With all this knowledge, it becomes clear that targeting alternative splicing represents an innovative approach for breast cancer therapeutics and the information derived from current studies could guide clinical decisions with a direct impact in the clinical advances for breast cancer patients nowadays. Full article
(This article belongs to the Special Issue Aberrant Pre-mRNA Splicing in Disease)
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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.

Tentative Title: Modulation of VEGF-A splicing as a novel treatment in chronic kidney disease
Putative Authors: Megan Stevens1 and Sebastian Oltean1
Affiliations: 1Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, EX1 2LU, UK

Abstract: Vascular endothelial growth factor A (VEGF-A) is a prominent pro-angiogenic and pro-permeability factor in the kidney. Alternative splicing of the terminal exon of VEGF-A through the use of an alternative 3’ splice site gives rise to a functionally different family of isoforms, termed VEGF-Axxxb, which are known to be anti-angiogenic and anti-permeability. Dysregulation of the VEGF-Axxx/VEGF-Axxxb isoform balance has recently been reported in several kidney pathologies, including diabetic nephropathy (DN) and Denys-Drash syndrome. Using mouse models of kidney disease where the VEGF-A isoform balance is disrupted, several reports have shown that VEGF-A165b treatment/over-expression in the kidney is therapeutically beneficial. Furthermore, inhibition of certain splice factor kinases involved in the regulation of VEGF-A terminal exon splicing has provided some mechanistic insight into how VEGF-A splicing could be regulated in the kidney. This review highlights the importance for further investigation into the novel area of VEGF-A splicing in chronic kidney disease pathogenesis and how future studies may allow for the development of splicing modifying therapeutic drugs.

Tentative Title: Splicing regulation of canonical NO-cGMP signaling pathway in vascular inflammation.
Putative Authors: Gilbert J. Cote1, Emil Martin2, Iraida G. Sharina2
Affiliations: 1Department of Endocrine Neoplasia and Hormonal Disorders, MD Anderson Cancer Center, Houston, Texas, USA
2Department of Internal Medicine/Cardiology, McGovern School Of Medicine, Houston , Texas, USA

Abstract: More than 30 years passed since nitric oxide (NO), a gaseous free radical, was acknowledged as a critical physiologic signaling molecule. It originated with the discovery that “canonical” NO signal transduction through the secondary messenger cGMP mediates smooth muscle relaxation in vascular tissue and, therefore, important in regulation of blood pressure. Since then the list of known NO-directed functions has grown exponentially and includes, presently, regulation of smooth muscle in gastrointestinal system, neurotransmission and neuromodulation, inhibition of platelet aggregation and adhesion, immune defense, regulation of cellular respiration and cytotoxicity, and mitochondrial biogenesis. An alternative splicing of the enzymes of NO signaling pathway is started to emerge as one of multiple regulatory mechanisms governing NO signaling. Alternative splicing enriches transcriptome diversity and allows cells to meet the new challenges of extracellular environment. One of the main interests of our laboratory is an understanding of how the splicing of NO/cGMP enzymes participates in cellular adaptation to oxidative stress persisting in human blood vessels. In this review we will summarize the available information on splicing regulation of major enzymes of NO/cGMP pathway, including nitric oxide synthases (NOSs), heterodimeric soluble guanylyl cyclase (sGC) and cGMP-dependent protein kinase (PKG). We will discuss putative genetic mechanisms participating in this process. We will also highlight the evidence accumulated from different laboratories suggesting that the splicing of NO/cGMP enzymes is very complex and is strongly affected by various environmental cues and, specifically, by the changes in extra- and intracellular oxidative balance. Despite that our understanding of the mechanisms governing this process remains very limited and awaits systematic investigation, future studies promise to bring new exciting insights into the role that alternative splicing plays in NO/cGMP biology.

Tentative Title: Splicing analysis of exonic OCRL mutations causing Lowe syndrome or Dent-2 disease
Putative Authors: Suarez-Artiles L, Perdomo-Ramirez A, E. Ramos-Trujillo, Claverie-Martin F
Affiliations: Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain

Abstract: Mutations in the OCRL gene are associated with both Lowe syndrome and Dent-2 disease. Patients with Lowe syndrome present congenital cataracts, mental disabilities and a renal proximal tubulopathy, whereas patients with Dent-2 disease exhibit similar proximal tubule dysfunction but only mild, or no additional clinical defects. It is not yet understood why some OCRL mutations cause the phenotype of Lowe syndrome, while others develop the milder phenotype of Dent-2 disease. Our goal was to gain new insights into the consequences of OCRL exonic mutations on pre-mRNA splicing.
Thirteen missense mutations and one synonymous mutation located mainly in poorly defined exons and potentially affecting splicing regulatory elements or splice sites were selected. Their effects on splicing were studied using bioinformatics tools and a minigene assay. Specific mutations were introduced by site-directed mutagenesis, and the RNA was analysed by RT-PCR and DNA sequencing.
We found that three presumed missense mutations caused alterations in pre-mRNA splicing. Mutation p.W247C generated a splicing silencer and disrupted a splicing enhancer resulting in skipping of exon 9, while mutations p.A861T and p.A861P abolished a donor splice site and resulted in skipping of exon 23.
In conclusion, these results highlight the importance to evaluate the effects of missense mutations at the mRNA level in Lowe syndrome. Our findings also allowed the detection of previously unpredicted splicing regulatory elements in OCRL exon 9.

Tentative Title: Signaling pathways driving aberrant splicing in cancer cells
Putative Authors: Peter Jordan
Affiliations: Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisboa, Portugal

Abstract: Aberrant profiles of pre-messenger RNA splicing are frequently observed in cancer. At the molecular level, an altered profile reflects differences in splice site choices, which are mediated by the binding of splicing factors (SFs) to gene-specific splice-regulatory sequence elements. Change in expression levels of key SFs can trigger aberrant splicing but, in addition, oncogenic signal transduction pathways can affect the ratio of nuclear versus cytoplasmic SF localization. Here, we will review currently known mechanisms by which cancer cell signaling, including the MAPK, PI3K and Wnt pathways, modulates the activity or localization of the SR protein and hnRNP family of SFs.


Tentative Title: Alternative splicing of alpha- and beta-synuclein genes plays differential roles in neurodegenerative disease
Putative Authors: Ana-Gámez-Valero, MSc, Katrin Beyer, PhD
Affiliations: Dept Pathology, Research Institute Germans Trias i Pujol, Badalona, Barcelona, Spain

Abstract: The synuclein family is composed of three members, two of which, alpha- and beta-synuclein, play a major role in the development of synucleinopathies including Parkinson’s disease (PD) as most important movement disorder, dementia with Lewy bodies (DLB) as second most frequent cause of dementia after Alzheimer’s disease and multiple system atrophy. Whereas abnormal oligomerization and fibrillation of alpha-synuclein are now well recognized as initial steps in the development of synucleinopathies, beta-synuclein is thought to be a natural alpha-synuclein antiaggregant.
Alpha- synuclein is encoded by the SNCA gene and beta-synuclein by SNCB. Both genes show an elevated homology and undergo complex splicing events. On the one hand, in-frame splicing of coding exons gives rise to at least three shorter transcripts with predictable changes in function of the correspondent protein isoforms. Another type of alternative splicing is the alternative inclusion of at least four initial exons in the case of SNCA and two in the case of SNCB. Finally, different lengths of 3’UTRs have been also reported for both genes. SNCB only expresses in the brain, but some of the numerous SNCA transcripts are also brain-specific.

Tentative Title: Impact, characterization and rescue of pre-mRNA splicing mutations in lysosomal storage disorders.
Putative Authors: Andrea Dardis1 and Emanuele Buratti2
Affiliations: 1Regional Coordinator Centre for Rare Diseases, Academic Hospital “Santa Maria della Misericordia”, Udine, Italy
2International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy

Abstract: Lysosomal storage disorders (LSDs) represent a group of more than 50 severe metabolic diseases caused by the deficiency of specific lysosomal hydrolases, activators, carriers or lysosomal integral membrane proteins, leading to the abnormal accumulation of substrates within the lysosomes. Numerous mutations have been described in each disease causing gene; among them about 5-19 % affect the pre-mRNA splicing process.
In the last decade, several strategies to rescue/increase normal splicing of mutated transcripts have been developed and LSDs represent excellent candidates for this type of approach: (i) most of them are inherited in an autosomic recessive manner and patients affected by late onset phenotypes often retain a quite fair residual enzymatic activity; thus, even a small recovery of normal splicing may be beneficial in clinical settings; (ii) most LSDs still lack effective treatments or are currently treated with extremely expensive approaches; (iii) in few LSDs a single splicing mutation accounts for up to 40-70% of pathogenic alleles.
At present, numerous preclinical studies support the feasibility of reverting the pathological phenotype by partially rescuing splicing defects in LSDs. This review provides an overview of the impact of splicing mutations in LSDs and the related therapeutic approaches currently under investigation in these disorders.

 

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