Splicing Defects Research Articles

The Effects of Tail Truncations of Pre‐Messenger RNA Splicing Protein Dib1

The spliceosome is a multi‐megadalton ribonucleoprotein complex that catalyzes the removal of non‐coding introns and the ligation of coding exons from pre‐messenger RNA. This process is crucial in the transformation of pre‐messenger RNA into messenger RNA, a template that is readable by the ribosome and allows for the production of a functional protein. Significantly, the spliceosome is constructed anew on every pre‐mRNA. This construction entails over 140 protein factors that associate and dissociate throughout the splicing cycle, causing the conformational rearrangements and transesterification reactions necessary to yield the mature RNA template. Therefore, rather than a singular composition of proteins and RNAs being known as “the spliceosome,” this term actually refers to several different complexes which are distinct in their makeup and their role within the splicing cycle. Construction of a catalytic splicing complex occurs after a series of early assembly steps. Amongst the proteins involved in these early assembly steps is a 16.8 kDa protein, Dib1, that is present in the pre‐catalytic spliceosome but absent from the catalytically active conformation. The loss of Dib1 at this critical juncture hints at a potential role helping to facilitate the transition from pre‐catalytic to catalytic. Previous work on Dib1 has revealed that not only is it required for splicing, but the human ortholog, hDim1, has been shown to possess autocleavage activity in vitro where the last 14 amino acids are cleaved from its C‐terminal tail. Thus, we are interested in whether the C‐terminus impacts the function of the protein as it pertains to its role in splicing. In order to elucidate the importance of this region, we have constructed a series of C‐terminal truncations of varying lengths within Dib1 in order to assess any resulting splicing defects. These defects have been monitored through the use of growth assays and splicing assays to ascertain not only the overall importance of this region, but also the specific length required to ensure splicing abilities similar to wildtype Dib1 within the model organism S. cerevisiae. Overall, we observe that Dib1 can tolerate a large deletion before affecting cell growth and splicing.

Dissecting the phenotypic variability of osteogenesis imperfecta.

ABSTRACTOsteogenesis imperfecta (OI) is a heterogeneous family of collagen type I-related diseases characterized by bone fragility. OI is most commonly caused by single-nucleotide substitutions that replace glycine residues or exon splicing defects in the COL1A1 and COL1A2 genes that encode the α1(I) and α2(I) collagen chains. Mutant collagen is partially retained intracellularly, impairing cell homeostasis. Upon secretion, it assembles in disorganized fibrils, altering mineralization. OI is characterized by a wide range of clinical outcomes, even in the presence of identical sequence variants. Given the heterotrimeric nature of collagen I, its amino acid composition and the peculiarity of its folding, several causes may underlie the phenotypic variability of OI. A deep analysis of entries regarding glycine and splice site collagen substitution of the largest publicly available patient database reveals a higher risk of lethal phenotype for carriers of variants in α1(I) than in α2(I) chain. However, splice site variants are predominantly associated with lethal phenotype when they occur in COL1A2. In addition, lethality is increased when mutations occur in regions of importance for extracellular matrix interactions. Both extracellular and intracellular determinants of OI clinical severity are discussed in light of the findings from in vitro and in vivo OI models. Combined with meticulous tracking of clinical cases via a publicly available database, the available OI animal models have proven to be a unique tool to shed light on new modulators of phenotype determination for this rare heterogeneous disease.

ABCA4 c.859-25A>G, a Frequent Palestinian Founder Mutation Affecting the Intron 7 Branchpoint, Is Associated With Early-Onset Stargardt Disease.

PurposeThe effect of noncoding variants is often unknown in the absence of functional assays. Here, we characterized an ABCA4 intron 7 variant, c.859-25A>G, identified in Palestinian probands with Stargardt disease (STGD) or cone-rod dystrophy (CRD). We investigated the effect of this variant on the ABCA4 mRNA and retinal phenotype, and its prevalence in Palestine.MethodsThe ABCA4 gene was sequenced completely or partially in 1998 cases with STGD or CRD. The effect of c.859-25A>G on splicing was investigated in silico using SpliceAI and in vitro using splice assays. Homozygosity mapping was performed for 16 affected individuals homozygous for c.859-25A>G. The clinical phenotype was assessed using functional and structural analyses including visual acuity, full-field electroretinography, and multimodal imaging.ResultsThe smMIPs-based ABCA4 sequencing revealed c.859-25A>G in 10 Palestinian probands from Hebron and Jerusalem. SpliceAI predicted a significant effect of this putative branchpoint-inactivating variant on the nearby intron 7 splice acceptor site. Splice assays revealed exon 8 skipping and two partial inclusions of intron 7, each having a deleterious effect. Additional genotyping revealed another 46 affected homozygous or compound heterozygous individuals carrying variant c.859-25A>G. Homozygotes shared a genomic segment of 59.6 to 87.9 kb and showed severe retinal defects on ophthalmoscopic evaluation.ConclusionsThe ABCA4 variant c.859-25A>G disrupts a predicted branchpoint, resulting in protein truncation because of different splice defects, and is associated with early-onset STGD1 when present in homozygosity. This variant was found in 25/525 Palestinian inherited retinal dystrophy probands, representing one of the most frequent inherited retinal disease-causing variants in West-Bank Palestine.

Splicing Modulation as a Promising Therapeutic Strategy for Lysosomal Storage Disorders: The Mucopolysaccharidoses Example

Over recent decades, the many functions of RNA have become more evident. This molecule has been recognized not only as a carrier of genetic information, but also as a specific and essential regulator of gene expression. Different RNA species have been identified and novel and exciting roles have been unveiled. Quite remarkably, this explosion of novel RNA classes has increased the possibility for new therapeutic strategies that tap into RNA biology. Most of these drugs use nucleic acid analogues and take advantage of complementary base pairing to either mimic or antagonize the function of RNAs. Among the most successful RNA-based drugs are those that act at the pre-mRNA level to modulate or correct aberrant splicing patterns, which are caused by specific pathogenic variants. This approach is particularly tempting for monogenic disorders with associated splicing defects, especially when they are highly frequent among affected patients worldwide or within a specific population. With more than 600 mutations that cause disease affecting the pre-mRNA splicing process, we consider lysosomal storage diseases (LSDs) to be perfect candidates for this type of approach. Here, we introduce the overall rationale and general mechanisms of splicing modulation approaches and highlight the currently marketed formulations, which have been developed for non-lysosomal genetic disorders. We also extensively reviewed the existing preclinical studies on the potential of this sort of therapeutic strategy to recover aberrant splicing and increase enzyme activity in our diseases of interest: the LSDs. Special attention was paid to a particular subgroup of LSDs: the mucopolysaccharidoses (MPSs). By doing this, we hoped to unveil the unique therapeutic potential of the use of this sort of approach for LSDs as a whole.

A combinatorial approach increases SMN level in SMA model mice.

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by reduced expression of the survival motor neuron (SMN) protein. Current disease-modifying therapies increase SMN levels and dramatically improve survival and motor function of SMA patients. Nevertheless, current treatments are not cures and autopsy data suggest that SMN induction is variable. Our group and others have shown that combinatorial approaches that target different modalities can improve outcomes in rodent models of SMA. Here we explore if slowing SMN protein degradation and correcting SMN splicing defects could synergistically increase SMN production and improve the SMA phenotype in model mice. We show that co-administering ML372, which inhibits SMN ubiquitination, with an SMN-modifying antisense oligonucleotide (ASO) increases SMN production in SMA cells and model mice. In addition, we observed improved spinal cord, neuromuscular junction and muscle pathology when ML372 and the ASO were administered in combination. Importantly, the combinatorial approach resulted in increased motor function and extended survival of SMA mice. Our results demonstrate that a combination of treatment modalities synergistically increases SMN levels and improves pathophysiology of SMA model mice over individual treatment.

High Concentration or Combined Treatment of Antisense Oligonucleotides for Spinal Muscular Atrophy Perturbed SMN2 Splicing in Patient Fibroblasts

Spinal muscular atrophy (SMA) is caused by survival motor neuron 1 SMN1 deletion. The survival motor neuron 2 (SMN2) encodes the same protein as SMN1 does, but it has a splicing defect of exon 7. Some antisense oligonucleotides (ASOs) have been proven to correct this defect. One of these, nusinersen, is effective in SMA-affected infants, but not as much so in advanced-stage patients. Furthermore, the current regimen may exhibit a ceiling effect. To overcome these problems, high-dose ASOs or combined ASOs have been explored. Here, using SMA fibroblasts, we examined the effects of high-concentration ASOs and of combining two ASOs. Three ASOs were examined: one targeting intronic splicing suppressor site N1 (ISS-N1) in intron 7, and two others targeting the 3′ splice site and 5′ region of exon 8. In our experiments on all ASO types, a low or intermediate concentration (50 or 100 nM) showed better splicing efficiency than a high concentration (200 nM). In addition, a high concentration of each ASO created a cryptic exon in exon 6. When a mixture of two different ASOs (100 nM each) was added to the cells, the cryptic exon was included in the mRNA. In conclusion, ASOs at a high concentration or used in combination may show less splicing correction and cryptic exon creation.

Mutations in FgPrp6 suppressive to the Fgprp4 mutant in Fusarium graminearum

The pre-mRNA processing factor Prp6 is an essential component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP). In a previous study, mutations were identified in the PRP6 ortholog in four suppressors of Fgprp4 that was deleted of the only kinase FgPrp4 among the spliceosome components in the plant pathogenic fungus Fusarium graminearum. In this study, we identified additional suppressor mutations in FgPrp6 and determined the suppressive effects of selected mutations. In total, 12 mutations of FgPRP6 were identified in 20 suppressors of Fgprp4 by sequencing analysis. Whereas three mutation sites are in the linker region of FgPrp6, seven are in the first two HAT repeats. RNA-seq analysis showed that suppressor mutations on different sites caused different splicing efficiency recovery. The suppressive effects of E308K and R230H were verified. Similar to human and fission yeast, the FgPrp6 was phosphorylated by the FgPrp4 kinase. Interestingly, the conserved Prp4-phosphorylation sites T261, T219&T221, and predicted phosphorylation sites T199&T200 on FgPrp6 were dispensable for the function of FgPrp6 in hyphal growth and sexual reproduction but important in plant infection. They are required for the infectious growth of F. graminearum in wheat lemma. RNA-seq analysis of the wheat lemma infected with Fgprp6/FgPRP6Δ199–221-GFP or Fgprp6/FgPRP6Δ250–262-GFP showed that 28 and 35% introns had splicing defects, respectively, which may be responsible for their defects in plant infection.

RNA splicing to cytoskeleton: A new path to cardiomyocyte ploidy and division?

Mammalian cardiomyocytes (CMs) undergo polyploidization after birth, accompanied by the loss of CM proliferation and regenerative capacity, although why this occurs is still poorly understood. In this issue of Developmental Cell, Gan etal. show that premature CM polyploidization, through defective RNA splicing, is detrimental to ventricular wall growth.

Selection for increasing milk production of cattle: the value of genetic predictor markers

Russian dairy cattle breeding, developing in line with global trends, is based on the breeding of highly productive livestock, including the use of biotechnology for the transfer of embryos obtained from genetically valuable heifers and donor cows. From 2014 to 2020, Russian agricultural enterprises produced more than 90 thousand in vivo and in vitro cattle embryos with variations of the growth of their annual number in the range from 195 to 26762 pcs. (embryos in vitro), from 2746 to 14098 pcs. (embryos in vivo). Since keeping animals that do not have high productivity is economically unprofitable, it is necessary to exclude unproductive individuals from production. As a result, it is important to predict the highest milk production (proteins, fat, milk yield) of pre-implantation embryos obtained in veterinary practice for the purposes of embryo transfer, as well as in calves in the first weeks of their life after birth in high-yielding cows. There is a growing interest in the use of genetic markers to predict heritable traits of milk production. Against the backdrop of the rapid development of molecular genetic technologies, aimed at a deeper study of mammalian genes, new types of data are being discovered, in particular, data on functional gene mutations mediated by the mechanism of alternative splicing. Currently, a new direction of research of cattle has been outlined to study functional mutations (alternative splicing defects) that favorably or adversely affect phenotypes, including the milk production of cattle. The purpose of this study was to expand knowledge about the predictive value of molecular markers developed based on information about functional mutations in the milk production predictor genes GHR (growth receptor gene), LEPR (leptin receptor gene) and PRLR (prolactin receptor gene). These potentially important markers are shown to be promising for use in breeding aimed at increasing the productivity of dairy cattle.

Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading

MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. The nuclear protein RBV promotes the transcription of MIR genes into pri-miRNAs by enhancing the occupancy of RNA polymerase II (Pol II) at MIR gene promoters. RBV also promotes the loading of miRNAs into AGO1. In addition, RNA-seq revealed a global splicing defect in the mutant. Thus, this evolutionarily conserved, nuclear WD40 domain protein acts in miRNA biogenesis and RNA splicing.

Exon Skipping Through Chimeric Antisense U1 snRNAs to Correct Retinitis Pigmentosa GTPase-Regulator (RPGR) Splice Defect.

Inherited retinal dystrophies are caused by mutations in more than 250 genes, each of them carrying several types of mutations that can lead to different clinical phenotypes. Mutations in Retinitis Pigmentosa GTPase-Regulator (RPGR) cause X-linked Retinitis pigmentosa (RP). A nucleotide substitution in intron 9 of RPGR causes the increase of an alternatively spliced isoform of the mature mRNA, bearing exon 9a (E9a). This introduces a stop codon, leading to truncation of the protein. Aiming at restoring impaired gene expression, we developed an antisense RNA-based therapeutic approach for the skipping of RPGR E9a. We designed a set of specific U1 antisense snRNAs (U1_asRNAs) and tested their efficacy in vitro, upon transient cotransfection with RPGR minigene reporter systems in HEK-293T, 661W, and PC-12 cell lines.We thus identified three chimeric U1_asRNAs that efficiently mediate E9a skipping, correcting the genetic defect. Unexpectedly, the U1–5′antisense construct, which exhibited the highest exon-skipping efficiency in PC-12 cells, induced E9a inclusion in HEK-293T and 661W cells, indicating caution in the choice of preclinical model systems when testing RNA splicing-correcting therapies. Our data provide a proof of principle for the application of U1_snRNA exon skipping-based approach to correct splicing defects in RPGR.

Multiple Myeloma Patient Tumors With High Levels of Cereblon Exon-10 Deletion Splice Variant Upregulate Clinically Targetable Pro-Inflammatory Cytokine Pathways.

Immunomodulatory drugs (IMiDs), including lenalidomide and pomalidomide, are used in the routine treatment for multiple myeloma (MM) patients. Cereblon (CRBN) is the direct molecular target of IMiDs. While CRBN is not an essential gene for MM cell proliferation, the frequency of CRBN genetic aberrations, including mutation, copy number loss, and exon-10 (which includes a portion of the IMiD-binding domain) splicing, have been reported to incrementally increase in later-line patients. CRBN exon-10 splicing has also been shown to be associated with decreased progression-free survival in both newly diagnosed and relapsed refractory MM patients. Although we did not find significant general splicing defects among patients with CRBN exon-10 splice variant when compared to those expressing the full-length transcript, we identified upregulated TNFA signaling via NFKB, inflammatory response, and IL-10 signaling pathways in patients with exon-10 splice variant across various data sets—all potentially promoting tumor growth via chronic growth signals. We examined master regulators that mediate transcriptional programs in CRBN exon-10 splice variant patients and identified BATF, EZH2, and IKZF1 as the key candidates across the four data sets. Upregulated downstream targets of BATF, EZH2, and IKZF1 are components of TNFA signaling via NFKB, IL2/STAT5 signaling pathways, and IFNG response pathways. Previously, BATF-mediated transcriptional regulation was associated with venetoclax sensitivity in MM. Interestingly, we found that an EZH2 sensitivity gene expression signature also correlated with high BATF or venetoclax sensitivity scores in these tumors. Together, these data provide a rationale for investigating EZH2 inhibitors or venetoclax in combination with the next generation CRBN-targeting agents, such as CELMoDs, for patients overexpressing the CRBN exon-10 splice variant.

Reversal of RNA toxicity in myotonic dystrophy via a decoy RNA-binding protein with high affinity for expanded CUG repeats.

Myotonic dystrophy type 1 (DM1) is an RNA-dominant disease whose pathogenesis stems from the functional loss of muscleblind-like RNA-binding proteins (RBPs), which causes the formation of alternative-splicing defects. The loss of functional muscleblind-like protein 1 (MBNL1) results from its nuclear sequestration by mutant transcripts containing pathogenic expanded CUG repeats (CUGexp). Here we show that an RBP engineered to act as a decoy for CUGexp reverses the toxicity of the mutant transcripts. In vitro, the binding of the RBP decoy to CUGexp in immortalized muscle cells derived from a patient with DM1 released sequestered endogenous MBNL1 from nuclear RNA foci, restored MBNL1 activity, and corrected the transcriptomic signature of DM1. In mice with DM1, the local or systemic delivery of the RBP decoy via an adeno-associated virus into the animals' skeletal muscle led to the long-lasting correction of the splicing defects and to ameliorated disease pathology. Our findings support the development of decoy RBPs with high binding affinities for expanded RNA repeats as a therapeutic strategy for myotonic dystrophies.

Massively parallel reporter assays discover de novo exonic splicing mutants in paralogs of Autism genes.

To determine the contribution of defective splicing in Autism Spectrum Disorders (ASD), the most common neurodevelopmental disorder, a high throughput Massively Parallel Splicing Assay (MaPSY) was employed and identified 42 exonic splicing mutants out of 725 coding de novo variants discovered in the sequencing of ASD families. A redesign of the minigene constructs in MaPSY revealed that upstream exons with strong 5’ splice sites increase the magnitude of skipping phenotypes observed in downstream exons. Select hits were validated by RT-PCR and amplicon sequencing in patient cell lines. Exonic splicing mutants were enriched in probands relative to unaffected siblings -especially synonymous variants (7.5% vs 3.5%, respectively). Of the 26 genes disrupted by exonic splicing mutations, 6 were in known ASD genes and 3 were in paralogs of known ASD genes. Of particular interest was a synonymous variant in TNRC6C - an ASD gene paralog with interactions with other ASD genes. Clinical records of 3 ASD patients with TNRC6C variant revealed respiratory issues consistent with phenotypes observed in TNRC6 depleted mice. Overall, this study highlights the need for splicing analysis in determining variant pathogenicity, especially as it relates to ASD.

Small Molecule Screening Discovers Compounds that Reduce FMRpolyG Protein Aggregates and Splicing Defect Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome.

Expansion of CGG trinucleotide repeats in 5' untranslated region of the FMR1 gene is the causative mutation of neurological diseases such as fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and ovarian disorder such as fragile X-associated primary ovarian insufficiency (FXPOI). CGG repeats containing FMR1 transcripts form the toxic ribonuclear aggregates, abrupt pre-mRNA splicing, and cause repeat-associated non-AUG translation, leading to the disease symptoms. Here, we utilized a small molecule library of ~ 250,000 members obtained from the National Cancer Institute (NCI) and implemented a shape-based screening approach to identify the candidate small molecules that mitigate toxic CGG RNA-mediated pathogenesis. The compounds obtained from screening were further assessed for their affinity and selectivity towards toxic CGG repeat RNA by employing fluorescence-binding experiment and isothermal calorimetry titration assay. Three candidate molecules B1, B4, and B11 showed high affinity and selectivity for expanded CGG repeats RNA. Further, NMR spectroscopy, gel mobility shift assay, CD spectroscopy, UV-thermal denaturation assay, and molecular docking affirmed their high affinity and selectivity for toxic CGG RNAs. Next, these lead compounds selectively improved the pre-mRNA alternative splicing defects with no perturbation in global splicing efficacy and simultaneouslyreduced the FMR1polyG protein aggregate formation without affecting the downstream expression of the gene. Taken together these findings, we addressed compound B1, B4, and B11 as potential lead molecules for developing promising therapeutics against FXTAS. Herein, this study, we have utilized shape similarity approach to screen the NCI library and found out the potential candidate which improves the pre-mRNA splicing defects and reduces FMR1polyG aggregations.

MRNA analysis revealed a novel pathogenic EIF2S3 variant causing MEHMO syndrome

EIF2S3 pathogenic variants have been shown to cause MEHMO syndrome - a rare X-linked intellectual disability syndrome. In most cases, DNA diagnostics of MEHMO syndrome is performed using exome sequencing. We describe two cousins with profound intellectual disability, severe microcephaly, microgenitalism, hypoglycemia, epileptic seizures, and hypertrichosis, whose clinical symptoms allowed us to suspect MEHMO syndrome. To confirm this diagnosis, we designed an mRNA analysis for the EIF2S3 gene. It is a cost-effective method to detect coding sequence variants in multi-exonic genes, as well as splicing defects and allelic imbalance. Our mRNA sequence analysis revealed a novel EIF2S3 variant c.820C>G in both cousins. We also found the same variant in female family members in the heterozygous state. To investigate the pathogenicity of the c.820C>G variant, we performed expression analysis, which showed that the DDIT3 transcript level was significantly increased in the patient relative to the controls. We, thus, demonstrate that mRNA analysis is an efficient tool for performing genetic testing in patients with distinct phenotypic features.

RNA Studies Demonstrate that the LDLR c.2389+4A>G Intronic Variant Causes Familial Hypercholesterolemia through an RNA Splicing Impact

Lead Author's Financial Disclosures H.Z. is an employee of Ambry Genetics. Study Funding None. Background/Synopsis Familial hypercholesterolemia (FH) is an inherited disorder characterized by high plasma levels of low-density lipoprotein cholesterol (LDL-C). Mutations in the low-density lipoprotein receptor (LDLR) gene are the most common cause of FH. However, not all alterations in LDLR are pathogenic; some represent benign genetic variation, and the clinical significance of any given variant is not always clear. Variants of uncertain significance (VUS) require additional studies to elucidate their pathogenicity. Objective/Purpose We sought to further characterize an intronic LDLR alteration originally classified as a VUS in a large family with clinical FH. Methods We performed multigene panel testing for four genes associated with FH (APOB, LDLR, LDLRAP1, and PCSK9) on the proband of a large family with a strong family history of high cholesterol and premature death; additional affected and unaffected family members were genotyped by Sanger sequencing for an identified intronic LDLR variant. The splicing impact of the LDLR variant was ascertained by RT-PCRseq performed on three affected individuals. Results Panel testing detected LDLR c.2389+4A>G in the proband. No other pathogenic variants, likely pathogenic variants, or VUSs were identified. Subsequent familial testing indicated that LDLR c.2389+4A>G cosegregates with disease. RNA studies demonstrated that this alteration causes skipping of exon 16, which is predicted to result in the in-frame deletion of 26 amino acids. This deletion removes part of the transmembrane domain and is expected to disrupt the ability of LDLR to insert into the membrane, resulting in loss of receptor function. Other pathogenic alterations impacting the same donor splice site have been shown to have a similar impact on splicing (LDLR c.2389G>T and LDLR c.2389+1G>T; Bourbon M et al. J. Med. Genet., 2009 May;46:352-7; Holla ØL et al. Mol. Genet. Metab., 2009 Apr;96:245-52). Conclusions The LDLR c.2389+4A>G intronic variant is a pathogenic mutation that results in a splice defect and cosegregates with disease. In this case, RNA and family studies resulted in a reclassification from a VUS to a pathogenic mutation and confirmed the molecular cause of the multigenerational FH. Clinical management recommendations exist for individuals with a confirmed FH diagnosis, and an accurate genetic diagnosis can improve patient outcomes through tailored treatments (Brown E et al. J. Clin. Lipidol.,2020 Jul-Aug;14:398-413). Our findings highlight the utility of familial testing and RNA studies in clarifying the classification of DNA variants. H.Z. is an employee of Ambry Genetics.

Molecular diagnoses in the congenital malformations caused by ciliopathies cohort of the 100 000 genomes project

AbstractPurposeTo improve molecular diagnostic rates for participants recruited to the UK 100 000 Genomes Project suspected to have congenital malformations caused by ciliopathies.MethodsBespoke variant filtering and analysis strategy.ResultsEighty‐three pre‐screened probands were recruited in the following disease categories: Bardet‐Biedl syndrome (n = 45), Joubert syndrome (n = 14) and Rare Multisystem Ciliopathy Disorders (n = 24). We determined a research molecular diagnosis for n = 43/83 (51.8%) of probands, n = 33 (39.8%) classified as confident or probable diagnoses. The diagnosis rate is 19.3% higher than the n = 27/83 (32.5%) previously reported by Genomics England. Interestingly, 19/43 (44.2%) of diagnoses are not ciliopathies. 4 patients have causative variants in eye disease genes not directly linked to cilia (PRPF8, RHO, PROM1, OPA1) and 15 in genes causative of non‐ciliopathy multisystemic conditions. This may reflect difficulties in clinical recognition of ciliopathies and highlights the importance of looking beyond the initial panel. n = 11/83 probands (13.3%) had at least one causative variant outside of the Tiers 1 and 2 variant annotation categories (defined by the Genomics England Rare Disease Tiering Process), which would otherwise be excluded in standard diagnostic strategies. These include 4 SVs and 3 predicted by SpliceAI to cause non‐canonical splicing defects. We found two homozygous truncating variants in the candidate ciliopathy genes LRRC45 and CFAP45 in a single proband. Identification of further individuals with ciliopathy phenotypes with pathogenic variants in these genes would strengthen confidence in their status as ciliopathy disease genes.ConclusionsThis study shows the value of research collaborations to improve interpretation of genomic data. Improved integration of SV and splice variant analysis tools, such as SpliceAI, will be essential to maximise the diagnostic potential of WGS data beyond coding variants in exons of virtual panels of genes.

Development and Use of Cellular Systems to Assess and Correct Splicing Defects.

A significant proportion of mutations underlying genetic disorders affect pre-mRNA splicing, generally causing partial or total skipping of exons, and/or inclusion of pseudoexons. These changes often lead to the formation of aberrant transcripts that can induce nonsense-mediated decay, and a subsequent lack of functional protein. For some genetic disorders, including inherited retinal diseases (IRDs), reproducing splicing dynamics in vitro is a challenge due to the specific environment provided by, e.g. the retinal tissue, cells of which cannot be easily obtained and/or cultured. Here, we describe how to engineer splicing vectors, validate the reliability and reproducibility of alternative cellular systems, assess pre-mRNA splicing defects involved in IRD, and finally correct those by using antisense oligonucleotide-based strategies.

Effect of Small Molecules on Repeat RNA Toxicity in Animal Models

Repeat RNAs exhibit "RNA toxicity" by trapping RNA-binding proteins, thereby suppressing the proteins' native functions. The mismatch-binding molecules created in this study bound with high affinity and specificity to the slip-out structure formed by repeat DNA and RNA sequences, induced the shortening of repeat DNA length, and alleviated compound eye degeneration and splicing defects in animal models of Huntington's disease, spinocerebellar ataxia type 31, and myotonic dystrophy type 1.