Exon identity influences splicing induced by exonic variants and in silico prediction efficacy

Functional analysis of the CTNS gene exonic variants predicted to affect splicing

Cystinosis is a severe, monogenic systemic disease caused by variants in CTNS gene. Currently, there is growing evidence that exonic variants in many diseases can affect pre-mRNA splicing. The impact of CTNS gene exonic variants on splicing regulation may be underestimated due to the lack of routine studies at the RNA level. Here, we analyzed 59 exonic variants in the CTNS gene using bioinformatics tools and identified candidate variants that may induce splicing alterations by minigene assays. We identified six exonic variants that induce splicing alterations by disrupting the ratio of exonic splicing enhancers/exonic splicing silencers (ESEs/ESSs) or by interfering with the recognition of classical splice sites, or both. Our results help in the correct molecular characterization of variants in cystinosis and inform emerging therapies. Furthermore, our work suggests that the combination of in silico and in vitro assays facilitates to assess the effects of DNA variants driving rare genetic diseases on splicing regulation and will enhance the clinical utility of variant functional annotation.

Identification of a Splicing Variant c.3813-3A>G in NPHP3 by Reanalysis of Whole Exome Sequencing in a Chinese Boy with Nephronophthisis

Nephronophthisis is an autosomal recessive cystic kidney disease characterized by tubular injury and commonly results in kidney failure. We reported a case of 4-year-old Chinese boy presented with severe anemia, kidney, and liver dysfunction. Whole exome sequencing (WES) was performed to identify the candidate variant with a negative result initially. After complete collection of clinical information, reanalysis of WES identified a homozygous NPHP3 variant c.3813-3A>G (NM_153240.4). The effect on mRNA splicing of the intronic variant was predicted through software (three in silico splice tools). Furthermore, in vitro minigene assay was conducted to validate the predicted deleterious effects of the intronic variant. All of the splice prediction programs and minigene assay indicated that the variant had an impact on the normal splicing pattern of NPHP3. Our study confirmed the effect of the c.3813-3A>G variant on NPHP3 splicing in vitro, which gives additional evidence for the clinical significance of the variant and provides a basis for genetic diagnosis of nephronophthisis 3. In addition, we think that it is essential to reanalyze WES data after the complete clinical information collection to avoid missing some important candidate variants.

The multi-faceted nature of 15 CFTR exonic variations: Impact on their functional classification and perspectives for therapy

BACKGROUND

The majority of variants of unknown clinical significance (VUCS) in the CFTR gene are missense variants. While change on the CFTR protein structure or function is often suspected, impact on splicing may be neglected. Such undetected splicing default of variants may complicate the interpretation of genetic analyses and the use of an appropriate pharmacotherapy.

METHODS

We selected 15 variants suspected to impact CFTR splicing after in silico predictions on 319 missense variants (214 VUCS), reported in the CFTR-France database. Six specialized laboratories assessed the impact of nucleotide substitutions on splicing (minigenes), mRNA expression levels (quantitative PCR), synthesis and maturation (western blot), cellular localization (immunofluorescence) and channel function (patch clamp) of the CFTR protein. We also studied maturation and function of the truncated protein, consecutive to in-frame aberrant splicing, on additional plasmid constructs.

RESULTS

Six of the 15 variants had a major impact on CFTR splicing by in-frame (n = 3) or out-of-frame (n = 3) exon skipping. We reclassified variants into: splicing variants; variants causing a splicing defect and the impairment of CFTR folding and/or function related to the amino acid substitution; deleterious missense variants that impair CFTR folding and/or function; and variants with no consequence on the different processes tested.

CONCLUSION

The 15 variants have been reclassified by our comprehensive approach of in vitro experiments that should be used to properly interpret very rare exonic variants of the CFTR gene. Targeted therapies may thus be adapted to the molecular defects regarding the results of laboratory experiments.

Splicing mutations in the CFTR gene as therapeutic targets

The marketing approval, about ten years ago, of the first disease modulator for patients with cystic fibrosis harboring specific CFTR genotypes (~5% of all patients) brought new hope for their treatment. To date, several therapeutic strategies have been approved and the number of CFTR mutations targeted by therapeutic agents is increasing. Although these drugs do not reverse the existing disease, they help to increase the median life expectancy. However, on the basis of their CFTR genotype, ~10% of patients presently do not qualify for any of the currently available CFTR modulator therapies, particularly patients with splicing mutations (~12% of the reported CFTR mutations). Efforts are currently made to develop therapeutic agents that target disease-causing CFTR variants that affect splicing. This highlights the need to fully identify them by scanning non-coding regions and systematically determine their functional consequences. In this review, we present some examples of CFTR alterations that affect splicing events and the different therapeutic options that are currently developed and tested for splice switching.