Events of alternative splicing in head and neck cancer via RNA sequencing - an update

Background

Alternative splicing (AS) is a regulatory mechanism used to create many forms of mature messengers RNAs (mRNAs) from the same gene. Sequencing of RNA (RNA-Seq) is an advanced technology, which has been utilized by different studies to find AS mechanisms in head and neck cancer (HNC). Hitherto, there is no available review that could inform us of the major findings from these studies. Hence, we aim to perform a systematic literature search following PRISMA guidelines to study AS events in HNC identified through RNA-Seq studies.

Results

A total of five records were identified that utilized RNA-Seq data for identifying AS events in HNC. Five software was used in these records to identify AS events. Two genes influenced by AS i.e. MLL3 and RPS9 were found to be common in 4 out of 5 records. Likewise, 38 genes were identified to be similar in at least 3 records.

Conclusions

Alternative splicing in HNC is a multifaceted regulatory mechanism of gene expression. It can be studied via RNA-Seq using different bioinformatics tools. Genes MLL3, as well as RPS9, were repeatedly found to be associated with HNC, however needs further functional validation.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5794-y) contains supplementary material, which is available to authorized users.

Eleven novel SLC12A1 variants and an exonic mutation cause exon skipping in Bartter syndrome type I

INTRODUCTION

Bartter syndrome type I (BS1) has been rarely reported in large groups. On the other hand, the phenomenon of exon skipping, in which exonic mutations result in abnormal splicing, has been reported to be associated with various diseases. Specifically, mutations that result in the disruption of exonic splicing enhancers (ESEs) and/or the creation of exonic splicing silencers (ESSs) can promote exon skipping. However, the aberrant exon skipping caused by an exonic variant in such splicing regulatory elements (SREs) sequences has never been reported in the causal gene of SLC12A1 in BS1.

METHODS

We analyze the variants in nine Chinese families with BS1, including eight with antenatal BS (aBS) and one presenting as classical BS (cBS), by next-generation sequencing. Then we used bioinformatics programs to analyze all these variants found in this study and identify candidate mutations that may induce exon skipping. Furthermore, the effects of identified variants were classified according to the 2015 American College of Medical Genetics and Genomics (ACMG) standards and guidelines.

RESULTS

Fifteen different variants of SLC12A1 gene were identified, including 11 novel ones. Two of the nine probands were homozygotes, the rest seven ones were compound heterozygotes. One candidate variant (c.1435C>G), not only significantly reduced ESEs scores but also markedly increased ESSs scores, were further investigated by mini-gene splicing assay, and found this single-nucleotide substitution causes abnormal splicing in vitro (exclusion of exon 11). Finally, among 15 variants, 9, 3, and 3 were classified as "pathogenic variants", "likely pathogenic variants", "variants with uncertain significance", respectively.

CONCLUSION

These data would enrich the human gene mutation database (HGMD) and would provide valuable references to the genetic counseling and diagnosis of BS1 for Chinese population. Additionally, our results suggest that aberrant exon skipping is one previously unrecognized mechanism by which an exonic variant in SLC12A1 can lead to BS1.

SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation

BACKGROUND

In eukaryotes, most genes code for multiple transcript isoforms that are generated through the complex and tightly regulated process of RNA splicing. Despite arising from identical precursor transcripts, alternatively spliced RNAs can have dramatically different functions. Transcriptome complexity is elevated further by the production of circular RNAs (circRNAs), another class of mature RNA that results from the splicing of a downstream splice donor to an upstream splice acceptor. While there has been a rapid expansion of circRNA catalogs in the last few years through the utilization of next generation sequencing approaches, our understanding of the mechanisms and regulation of circular RNA biogenesis, the impact that circRNA generation has on parental transcript processing, and the functions carried out by circular RNAs remains limited.

RESULTS

Here, we present a visualization and analysis tool, SpliceV, that rapidly plots all relevant forward- and back-splice data, with exon and single nucleotide level coverage information from RNA-seq experiments in a publication quality format. SpliceV also integrates analysis features that assist investigations into splicing regulation and transcript functions through the display of predicted RNA binding protein sites and the configuration of repetitive elements along the primary transcript.

CONCLUSIONS

SpliceV is an easy-to-use splicing visualization tool, compatible with both Python 2.7 and 3+, and distributed under the GNU Public License. The source code is freely available for download at https://github.com/flemingtonlab/SpliceV and can be installed from PyPI using pip.

CRISPR/Cas9-generated mouse model of Duchenne muscular dystrophy recapitulating a newly identified large 430 kb deletion in the human DMD gene

Exon skipping is a promising strategy for Duchenne muscular dystrophy (DMD) disease-modifying therapy. To make this approach safe, ensuring that excluding one or more exons will restore the reading frame and that the resulting protein will retain critical functions of the full-length dystrophin protein is necessary. However, in vivo testing of the consequences of skipping exons that encode the N-terminal actin-binding domain (ABD) has been confounded by the absence of a relevant animal model. We created a mouse model of the disease recapitulating a novel human mutation, a large de novo deletion of exons 8-34 of the DMD gene, found in a Russian DMD patient. This mutation was achieved by deleting exons 8-34 of the X-linked mouse D md gene using CRISPR/Cas9 genome editing, which led to a reading frame shift and the absence of functional dystrophin production. Male mice carrying this deletion display several important signs of muscular dystrophy, including a gradual age-dependent decrease in muscle strength, increased creatine kinase, muscle fibrosis and central nucleation. The degrees of these changes are comparable to those observed in mdx mice, a standard laboratory model of DMD. This new model of DMD will be useful for validating therapies based on skipping exons that encode the N-terminal ABD and for improving our understanding of the role of the N-terminal domain and central rod domain in the biological function of dystrophin. Simultaneous skipping of exons 6 and 7 should restore the gene reading frame and lead to the production of a protein that might retain functionality despite the partial deletion of the ABD.

A novel splicing mutation of PTCH1 in a Chinese family with nevoid basal cell carcinoma syndrome

Nevoid basal cell carcinoma syndrome (NBCCS) is a rare autosomal dominant disease characterized by the development of multiple jaw keratocysts and basal cell carcinomas (BCC) and accompanied by diverse phenotypes. The establishment of diagnosis lies on the identification of a heterozygous germline pathogenic variant in the patched homolog 1 gene (PTCH1). PTCH1 has alternative splicing and selective initial coding exon, leading to three types of encoding proteins (PTCHL, PTCHM and PTCHS). The expression of each protein in NBCCS remains ambiguous, especially the importance of the first two exons in translation. Here, we report a Chinese NBCCS family of a novel PTCH1 heterozygous mutation (IVS 2, c.394+1G>T, g.10652G>T) identified by genomic sequencing and reverse-transcription-PCR as aberrant splicing. To the best of our knowledge, this is the first report of NBCCS with a splicing site mutation in intron 2 resulting in exon 2 skipping. Our finding suggests that exon 2 plays an important role in the development of NBCCS and further speculates that the role of longer isoforms PTCHL and PTCHM is crucial in NBCCS, while that of short isoform PTCHS might be dispensable.

A truncating MEIOB mutation responsible for familial primary ovarian insufficiency abolishes its interaction with its partner SPATA22 and their recruitment to DNA double-strand breaks

Background

Primary Ovarian Insufficiency (POI), a major cause of infertility, affects about 1–3% of women under forty years of age. Although there is a growing list of causal genetic alterations, POI remains mostly idiopathic.

Methods

We performed exome sequencing (WES) of two sisters affected with POI, one unaffected sister and their mother from a consanguineous family. We assessed the impact of the identified MEIOB variant with a minigene assay and by sequencing illegitimate transcripts from the proband's leukocytes. We studied its functional impact on the interaction between MEIOB with its partner SPATA22 and their localization to DNA double-strand breaks (DSB).

Findings

We identified a homozygous variant in the last base of exon 12 of MEIOB, which encodes a factor essential for meiotic recombination. This variant was predicted to strongly affect MEIOB pre-mRNA splicing. Consistently, a minigene assay showed that the variant induced exon 12 skipping, which was confirmed in vivo in the proband's leukocytes. Aberrant splicing leads to the production of a C-terminally truncated protein that cannot interact with SPATA22, abolishing their recruitment to DSBs.

Interpretation

This truncating MEIOB variant is expected to provoke meiotic defects and a depleted follicular stock, as in Meiob^−/− mice. This is the first molecular defect reported in a meiosis-specific single-stranded DNA-binding protein (SSB) responsible for POI. We hypothesise that alterations in other SSB proteins could explain cases of syndromic or isolated ovarian insufficiency.

Fund

Université Paris Diderot, Fondation pour la Recherche Médicale, Fondation ARC contre le cancer, Commissariat à l'Energie Atomique and Institut Universitaire de France.

The assembly and evaluation of antisense oligonucleotides applied in exon skipping for titin-based mutations in dilated cardiomyopathy

The leading cause of genetic dilated cardiomyopathy (DCM) is due to mutations in the TTN gene, impacting approximately 15-20% of familial and 18% of sporadic DCM cases. Currently, there is potential for a personalized RNA-based therapeutic approach in titin-based DCM, utilizing antisense oligonucleotide (AON) mediated exon-skipping, which attempts to reframe mutated titin transcripts, resulting in shortened, functional protein. However, the TTN gene is massive with 363 exons; each newly identified TTN exon mutation provides a challenge to address when considering the potential application of AON mediated exon skipping. In the initial phase of this strategy, the mutated TTN exon requires specific AON design and evaluation to assess the exon skipping effectiveness for subsequent experiments. Here, we present a detailed protocol to effectively assemble and evaluate AONs for efficient exon-skipping in targeted TTN exons. We chose a previously identified TTN 1-bp deletion mutation in exon 335 as an exemplary target exon, which causes a frameshift mutation leading to truncated A-band titin in DCM. We designed two specific AONs to mask the Ttn exon 335 and confirmed successfully mediated exon skipping without disrupting the Ttn reading frame. In addition, we evaluated and confirmed AON-treated HL-1 cells show maintained store-operated calcium entry, fractional shortening as well as preserved sarcomeric formation in comparison to control samples, indicating the treated cardiomyocytes retain adequate, essential cell function and structure, proving the treated cells can compensate for the loss of exon 335. These results indicate our method offers the first systematic protocol in designing and evaluating AONs specifically for mutated TTN target exons, expanding the framework of future advancements in the therapeutic potential of antisense-mediated exon skipping in titin-based DCM.

In Vitro Evaluation of Exon Skipping in Disease-Specific iPSC-Derived Myocytes

Patient-derived disease-specific induced pluripotent stem cells (iPSCs) have opened the door to recreating pathological conditions in vitro using differentiation into diseased cells corresponding to each target tissue. To investigate muscular disease, we have established a myogenic differentiation protocol mediated by inducible MYOD1 expression that drives human iPSCs into myocytes. This highly reproducible differentiation protocol yields a homogenous skeletal muscle cell population, reaching efficiencies as high as 70-90%. Such high efficiency enables us to evaluate the efficacy of exon skipping in disease-specific myocytes. These disease-specific iPSC-derived myocytes can be applied not only for the validation of therapeutic efficacy of specific antisense oligonucleotide but also for the screening of exon skipping chemicals combined with the multiwell differentiation system.

Antisense-Mediated Splice Modulation to Reframe Transcripts

Numerous genetic disorders are caused by loss-of-function mutations that disrupt the open reading frame of the gene either by nonsense or by frameshift (insertion, deletion, indel, or splicing) mutations. Most of the time, the result is the absence of functional protein synthesis due to mRNA degradation by nonsense-mediated mRNA decay, or rapid degradation of a truncated protein. Antisense-based splicing modulation is a powerful tool that has the potential to treat genetic disorders by restoring the open reading frame through selective removal of the mutated exon, or by restoring correct splicing.We have developed this approach for a severe skin genetic disorder, recessive dystrophic epidermolysis bullosa, caused by mutations in the COL7A1 gene encoding type VII collagen. This gene is particularly suited for exon skipping approaches due to its unique genomic structure. It is composed of 118 exons, 83 of which are in frame. Moreover, these exons encode a single repetitive collagenous domain.Using this gene as an example, we describe general methods that demonstrate the feasibility and efficacy of the antisense-mediated exon skipping strategy to reframe transcripts.

Systemic Injection of Peptide-PMOs into Humanized DMD Mice and Evaluation by RT-PCR and ELISA

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder due to the lack of dystrophin production. The disease is characterized by muscle wasting, with the most common causes of death being respiratory failure or heart failure. Recently, exon skipping using a phosphorodiamidate morpholino oligomer (PMO) is used as an FDA approved treatment for DMD. Peptide-conjugated PMOs (PPMOs) are used to increase exon skipping efficacy in the heart and are a promising therapy for DMD. Researchers have previously relied on high-performance liquid chromatography (HPLC) or liquid chromatography-mass spectrometry (LC/MS) methods for detecting PPMO uptake, but an enzyme-linked immunosorbent assay (ELISA) has been shown to have greater sensitivity. Here, we present methodologies to determine the uptake efficiency of a PPMO into the heart and efficacy of exon 51 skipping by a PPMO injected retro-orbitally into a humanized DMD mouse model via ELISA and RT-PCR, respectively.

Exon 51 Skipping Quantification by Digital Droplet PCR in del52hDMD/mdx Mice

Duchenne muscular dystrophy (DMD) is a severe, neuromuscular disorder caused by mutations in the DMD gene, precluding synthesis of functional dystrophin protein. Antisense oligonucleotide (AON)-mediated exon skipping has been developed as a method to restore the reading frame, which allows the synthesis of internally truncated, but partially functional dystrophin proteins, as found in the less severe Becker muscular dystrophy (BMD). This approach is species specific, since AONs targeting human exons often will not have full homology to mouse exons. As such, mouse models with mutations in the murine Dmd gene are of limited use to study human specific AONs in vivo. However, our del52hDMD/mdx mouse model contains mutated copies of both the mouse (nonsense mutation in exon 23) and human (deletion of exon 52) dystrophin-encoding genes. This model allows for testing effects of treatment with human specific exon 51 or 53 targeting AONs on RNA, protein, histological, and functional levels. Therefore, the model can be used to optimize human specific AONs, e.g., by comparing dystrophin protein and exon skipping levels.Absolute quantification of exon skipping levels can be obtained by digital droplet PCR (ddPCR). This method compartmentalizes samples into thousands of droplets that represent individual micro PCR reactions, and can be either positive or negative after amplification depending on whether there was a template molecule present or not. This allows for precise determination of the copy numbers of template molecules. The protocol described here uses probes binding to exon-exon junctions (EEJs) of human DMD transcripts with and without skipping of exon 51. We report that this method is specific for human transcripts so that exon skipping levels can be quantified accurately by ddPCR in del52hDMD/mdx mice.

In Vivo Evaluation of Dystrophin Exon Skipping in mdx Mice

Dystrophin exon skipping in mdx mice has been the key model for the development of antisense therapy in vivo. Evaluation of exon skipping in this model involves the following two aspects: (1) efficiency and accuracy of exon skipping and levels of dystrophin expression determined by RT-PCR, immunochemistry, and western blotting; (2) therapeutic effects on muscle pathology and functions assessed by histology and functional assays including grip strength measurement, treadmill test, echocardiogram, and hemodynamics for cardiac functions. Here we describe some key considerations and the essential methodologies in detail for exon skipping in mdx mice.

Morpholino-Mediated Exon Skipping Targeting Human ACVR1/ALK2 for Fibrodysplasia Ossificans Progressiva

Fibrodysplasia ossificans progressiva (FOP) is a rare autosomal-dominant disorder characterized by progressive heterotopic ossification. More than 95% of cases are caused by a recurrent mutation (617G>A; R206H) of ACVR1/ALK2, a bone morphogenetic protein (BMP) type I receptor. Recent studies revealed that ACVR1^R206H induces heterotopic ossification by aberrant activation in response to activin A. Because ACVR1^R206H is a hyperactive receptor, a promising therapeutic strategy is to decrease the activity of ACVR1 in patients. Here, we describe a method to reduce ACVR1 expression in FOP patient cells by exon skipping in ACVR1 mRNAs using phosphorodiamidate morpholino oligomers (PMOs). This strategy can be applied to the screen to select antisense oligomers to knockdown not only ACVR1 but also genes which cause other autosomal-dominant genetic diseases.

Direct Reprogramming of Human DMD Fibroblasts into Myotubes for In Vitro Evaluation of Antisense-Mediated Exon Skipping and Exons 45-55 Skipping Accompanied by Rescue of Dystrophin Expression

Antisense oligonucleotide-mediated exon skipping is a promising therapeutic approach for the treatment of various genetic diseases and a therapy which has gained significant traction in recent years following FDA approval of new antisense-based drugs. Exon skipping for Duchenne muscular dystrophy (DMD) works by modulating dystrophin pre-mRNA splicing, preventing incorporation of frame-disrupting exons into the final mRNA product while maintaining the open reading frame, to produce a shortened-yet-functional protein as seen in milder Becker muscular dystrophy (BMD) patients. Exons 45-55 skipping in dystrophin is potentially applicable to approximately 47% of DMD patients because many mutations occur within this "mutation hotspot." In addition, patients naturally harboring a dystrophin exons 45-55 in-frame deletion mutation have an asymptomatic or exceptionally mild phenotype compared to shorter in-frame deletion mutations in this region. As such, exons 45-55 skipping could transform the DMD phenotype into an asymptomatic or very mild BMD phenotype and rescue nearly a half of DMD patients. In addition, this strategy is potentially applicable to some BMD patients as well, who have in-frame deletion mutations in this region. As the degree of exon skipping correlates with therapeutic outcomes, reliable measurements of exon skipping efficiencies are essential to the development of novel antisense-mediated exon skipping therapeutics. In the case of DMD, researchers have often relied upon human muscle fibers obtained from muscle biopsies for testing; however, this method is highly invasive and patient myofibers can display limited proliferative ability. To overcome these challenges, researchers can generate myofibers from patient fibroblast cells by transducing the cells with a viral vector containing MyoD, a myogenic regulatory factor. Here, we describe a methodology for assessing dystrophin exons 45-55 multiple skipping efficiency using antisense oligonucleotides in human muscle cells derived from DMD patient fibroblast cells.

Optimization of 2',4'-BNA/LNA-Based Oligonucleotides for Splicing Modulation In Vitro

Antisense oligonucleotide-mediated splicing modulation is an attractive strategy for treating genetic disorders. In 2016, two splice-switching oligonucleotides (SSOs) were approved by the FDA. To date, various types of novel artificial nucleic acids have been developed, and their potential for splicing modulations has been demonstrated. To apply these novel chemistries to SSOs, it is necessary to determine the appropriate design for each artificial nucleic acid such as the length of the SSO and number of modifications. In this protocol, we focus on SSOs modified with 2'-O,4'-methylene-bridged nucleic acid (2',4'-BNA)/locked nucleic acid (LNA), which is an artificial nucleic acid that shows extremely high binding affinity to target RNA strands. We describe our typical protocol for the optimization of 2',4'-BNA-based SSOs.

Exon Skipping of FcεRIβ for Allergic Diseases

Mast cells are key effector cells in allergic inflammation and consequently are ideal targets for new therapeutics. The high-affinity IgE receptor complex, FcεRI, plays a critical role in mast cell and basophil activation by allergens to drive the immediate allergic inflammatory response. The β subunit of FcεRI is critical for trafficking the FcεRI complex to the cell membrane and amplifies the FcεRI signaling cascade. We have utilized splice switching antisense oligonucleotides to force expression of a truncated isoform of FcεRIβ, which we have shown does not associate with the FcεRI complex. This approach eliminates surface FcεRI expression in mast cells by targeting protein-protein interactions. Exon skipping has several therapeutic applications, and our findings demonstrate a novel application to alter receptor trafficking and dampen allergic inflammation. Here, we describe the methods of exon skipping in mast cells and the assays used to examine the responses of mast cells in vitro and in vivo.

Systemic Intravenous Administration of Antisense Therapeutics for Combinatorial Dystrophin and Myostatin Exon Splice Modulation

Using antisense oligonucleotides (AOs) to reframe mutated dystrophin, a recently developed therapeutic approach for Duchenne muscular dystrophy (DMD) named exon skipping, is considered among the most promising treatments for DMD patients. The development of this strategy is rapidly moving forward and the AO designed to skip exon 51 has received accelerated approval in the USA. However the strong complexity of the DMD pathology suggests that at least in older patients, where the muscle structure is almost completely compromised and the muscle is wasted and significantly infiltrated with fat and connective tissue, combined therapeutic approaches should be developed to approach the disease more effectively. Here we describe the methodology for the systemic intravenous delivery of AOs targeting dystrophin and myostatin in mdx mice, a DMD mouse model, in order to express dystrophin while downregulating myostatin, aiming for an increase in the muscle size and muscle strength. Furthermore the most relevant functional analyses to be performed in living mice and the most informative histopathological and molecular assays to evaluate the effect of this treatment are detailed.

Exon Skipping Using Antisense Oligonucleotides for Laminin-Alpha2-Deficient Muscular Dystrophy

Phosphorodiamidate morpholino oligomer (PMO)-mediated exon skipping is among the more promising approaches available for the treatment of several neuromuscular disorders, including Duchenne muscular dystrophy. The main weakness of this treatment arises from the low efficiency and sporadic nature of delivery of the neutrally charged PMO into muscle fibers, the mechanism of which is unknown.Recently, using wild-type and dystrophic mdx52 mice, we showed that muscle fibers took up PMO more efficiently during myotube formation. Interestingly, through in situ hybridization, we detected PMO mainly in embryonic myosin heavy chain-positive regenerating fibers. Next, we tested the therapeutic potential of PMO in laminin-alpha2 (laminin-α2) chain-null dy ^3K/dy ^3K mice, a model of merosin-deficient congenital muscular dystrophy 1A (MDC1A) with active muscle regeneration. We confirmed the recovery of the laminin-α2 chain following skipping of the mutated exon 4 in dy ^3K/dy ^3K mice, which prolonged the life span of the animals slightly. These findings support the theory that PMO entry into fibers is dependent on the developmental stage in myogenesis rather than on dystrophinless muscle membranes, and provide a platform for the future development of PMO-mediated therapies for a variety of muscular disorders, such as MDC1A, that involve active muscle regeneration. Herein, we describe the methods for PMO transfection/injection and evaluation of the efficacy of exon skipping in the laminin-α2-deficient dy ^3K/dy ^3K mouse model both in vitro and in vivo.

In Vivo Evaluation of Single-Exon and Multiexon Skipping in mdx52 Mice

Exon-skipping therapy is an emerging approach that uses synthetic DNA-like molecules called antisense oligonucleotides (ASOs) to splice out frame-disrupting parts of mRNA, restore the reading frame, and produce truncated yet functional proteins. Phosphorodiamidate morpholino oligomer (PMO) is one of the safest among therapeutic ASOs for patients and has recently been approved under the accelerated approval program by the US Food and Drug Administration (FDA) as the first ASO-based drug for Duchenne muscular dystrophy (DMD). Multi-exon skipping utilizing ASOs can theoretically treat 80-90% of patients with DMD. Here, we describe the systemic delivery of a cocktail of ASOs to skip exon 51 and exons 45-55 in the mdx52 mouse, an exon 52 deletion model of DMD produced by gene targeting, and the evaluation of their efficacies in vivo.

Exon Skipping by Ultrasound-Enhanced Delivery of Morpholino with Bubble Liposomes for Myotonic Dystrophy Model Mice

Abnormal splicing of the chloride channel 1 (CLCN1) gene causes myotonic dystrophy type 1 (DM1). Therefore, controlling the alternative splicing process of this gene by antisense oligonucleotides can be a promising treatment for DM1. In this study, we describe an efficient phosphorodiamidate morpholino oligomer (PMO) delivery method by ultrasound-mediated bubble liposomes, which is a known gene delivery tool with ultrasound exposure, to treat skeletal muscles in a DM1 mouse model, HSA^LR. Effective delivery of PMO using this technique can help control the alternative splicing of the Clcn1 gene via exon skipping and enhance the expression of Clcn1 protein in skeletal muscles and the amelioration of myotonia. Thus, exon skipping by PMO delivery with ultrasound-mediated BLs may be feasible in myotonic dystrophy model mice.

Titin mutations and muscle disease

The introduction of next-generation sequencing technology has revealed that mutations in the gene that encodes titin (TTN) are linked to multiple skeletal and cardiac myopathies. The most prominent of these myopathies is dilated cardiomyopathy (DCM). Over 60 genes are linked to the etiology of DCM, but by far, the leading cause of DCM is mutations in TTN with truncating variants in TTN (TTNtvs) associated with familial DCM in ∼ 20% of the cases. Titin is a large (3-4 MDa) and abundant protein that forms the third myofilament type of striated muscle where it spans half the sarcomere, from the Z-disk to the M-line. The underlying mechanisms by which titin mutations induce disease are poorly understood and targeted therapies are not available. Here, we review what is known about TTN mutations in muscle disease, with a major focus on DCM. We highlight that exon skipping might provide a possible therapeutic avenue to address diseases that arise from TTNtvs.

A novel antisense oligonucleotide anchored on the intronic splicing enhancer of hTERT pre-mRNA inhibits telomerase activity and induces apoptosis in glioma cells

INTRODUCTION

Alternative splicing of hTERT pre-mRNA is an important step in the regulation of telomerase activity, but the regulation mechanisms and functions remain unclear.

METHODS

RT-PCR analysis was used to detect hTERT splicing in glioma cell lines and brain tissues. TRAP assay was used to detect the telomerase activity. Then, we designed and synthesized 2'-O-methyl-RNA phosphorothioate AONs and transfected them into glioma cells to detect the changes in telomerase activity. MTT assay, plate colony formation assay, western blotting and Annexin V/PI assay were used to detect cell proliferation and apoptosis. At last, bioinformatics analyses were used to predict the expression and function of splicing protein SRSF2 in gliomas.

RESULTS

hTERT splicing occurs both in glioma cell lines and glioma patients' tissues. The telomerase activity was related to the expression level of the full-length hTERT, rather than the total hTERT transcript level. AON-Ex726 was complementary to the sequence of the intronic splicing enhancer (ISE) in intron six, and significantly altered the splicing pattern of hTERT pre-mRNA, reducing the expression level of the full-length hTERT mRNA and increasing the expression level of the -β hTERT mRNA. After transfection with AON-Ex726, the level of apoptosis was increased, while telomerase activity and cell proliferation were significantly decreased. By bioinformatic predictions, we found the AON-Ex726 anchoring sequence in ISE overlaps the binding site of SRSF2 protein, which is up-regulated during the development of gliomas.

CONCLUSIONS

Our findings provided new targets and important clues for the gene therapy of gliomas by regulating the alternative splicing pattern of hTERT pre-mRNA.

Genetic neuromuscular disorders: living the era of a therapeutic revolution. Part 2: diseases of motor neuron and skeletal muscle

This is the second part of a two-part document intended to discuss recent therapeutic progresses in genetic neuromuscular disorders. The present review is for diseases of motor neuron and skeletal muscle, some of which reached recently the most innovative therapeutic approaches. Nusinersen, an SMN2 mRNA splicing modifier, was approved as first-ever therapy of spinal muscular atrophy (SMA) by FDA in 2016 and by EMA in 2017. The orally administered small-molecule risdiplam, which increases SMN protein levels similarly but also in peripheral organs, is tested in ongoing phase 2 and 3 trials. After positive results with phase 1 treatment with AAV9-SMN, the first gene therapy for SMA, a phase 3 clinical trial is ongoing. Ataluren is the first approved drug for Duchenne muscular dystrophy (DMD) patients with premature stop codon mutations and its indication has been recently extended since the age of 2 years. Exon skipping technology was and is currently tested in many phase 3 trials, and eteplirsen received a conditional approval by FDA for patients amenable to exon 51 skipping, but not by EMA. Many other compounds with different mechanisms of action are now tested in DMD by phase 2 and 3 trials, including phase 1 gene therapy. Other innovative approaches are under investigation, i.e., gene therapy in X-linked myotubular myopathy and Pompe disease, and antisense oligonucleotides in myotonic dystrophy type 1. Positive evidences are discussed about lamotrigine and ranolazine in non-dystrophic myotonias, chaperons in Pompe disease, and nucleosides in mitochondrial DNA depletion induced by thymidine kinase 2 deficiency.

Identification of exon skipping events associated with Alzheimer's disease in the human hippocampus

BACKGROUND

At least 90% of human genes are alternatively spliced. Alternative splicing has an important function regulating gene expression and miss-splicing can contribute to risk for human diseases, including Alzheimer's disease (AD).

METHODS

We developed a splicing decision model as a molecular mechanism to identify functional exon skipping events and genetic variation affecting alternative splicing on a genome-wide scale by integrating genomics, transcriptomics, and neuroimaging data in a systems biology approach. In this study, we analyzed RNA-Seq data of hippocampus brain tissue from Alzheimer's disease (AD; n = 24) and cognitively normal elderly controls (CN; n = 50) and identified three exon skipping events in two genes (RELN and NOS1) as significantly associated with AD (corrected p-value < 0.05 and fold change > 1.5). Next, we identified single-nucleotide polymorphisms (SNPs) affecting exon skipping events using the splicing decision model and then performed an association analysis of SNPs potentially affecting three exon skipping events with a global cortical measure of amyloid-β deposition measured by [18F] Florbetapir position emission tomography (PET) scan as an AD-related quantitative phenotype. A whole-brain voxel-based analysis was also performed.

RESULTS

Two exons in RELN and one exon in NOS1 showed significantly lower expression levels in the AD participants compared to CN participants, suggesting that the exons tend to be skipped more in AD. We also showed the loss of the core protein structure due to the skipped exons using the protein 3D structure analysis. The targeted SNP-based association analysis identified one intronic SNP (rs362771) adjacent to the skipped exon 24 in RELN as significantly associated with cortical amyloid-β levels (corrected p-value < 0.05). This SNP is within the splicing regulatory element, i.e., intronic splicing enhancer. The minor allele of rs362771 conferred decreases in cortical amyloid-β levels in the right temporal and bilateral parietal lobes.

CONCLUSIONS

Our results suggest that exon skipping events and splicing-affecting SNPs in the human hippocampus may contribute to AD pathogenesis. Integration of multiple omics and neuroimaging data provides insights into possible mechanisms underlying AD pathophysiology through exon skipping and may help identify novel therapeutic targets.

Exon skipping-rich transcriptomes of animals reflect the significance of exon-shuffling in metazoan proteome evolution

ᅟ

Animals are known to have higher rates of exon skipping than other eukaryotes. In a recent study, Grau-Bové et al. (Genome Biology 19:135, 2018) have used RNA-seq data across 65 eukaryotic species to investigate when and how this high prevalence of exon skipping evolved. They have found that bilaterian Metazoa have significantly increased exon skipping frequencies compared to all other eukaryotic groups and that exon skipping in nearly all animals, including non-bilaterians, is strongly enriched for frame-preserving events. The authors have hypothesized that “the increase of exon skipping rates in animals followed a two-step process. First, exon skipping in early animals became enriched for frame-preserving events. Second, bilaterian ancestors dramatically increased their exon skipping frequencies, likely driven by the interplay between a shift in their genome architectures towards more exon definition and recruitment of frame-preserving exon skipping events to functionally diversify their cell-specific proteomes.”

Here we offer a different explanation for the higher frequency of frame-preserving exon skipping in Metzoa than in all other eukaryotes. In our view these observations reflect the fact that the majority of multidomain proteins unique to metazoa and indispensable for metazoan type multicellularity were assembled by exon-shuffling from ‘symmetrical’ modules (i.e. modules flanked by introns of the same phase), whereas this type of protein evolution played a minor role in other groups of eukaryotes, including plants. The higher frequency of ‘symmetrical’ exons in Metazoan genomes provides an explanation for the enrichment for frame-preserving events since skipping or inclusion of ‘symmetrical’ modules during alternative splicing does not result in a reading-frame shift.

Reviewers

This article was reviewed by Manuel Irimia, Ashish Lal and Erez Levanon. The reviewers were nominated by the Editorial Board.