Splice-Modulating Oligonucleotide QR-110 Restores CEP290 mRNA and Function in Human c.2991+1655A&gt;G LCA10 Models

Dulla, Kalyan; Aguilà, Mònica; Lane, Amelia; Jovanović, Katarina; Parfitt, David A.; Schulkens, Iris A.; Chan, Hee Lam; Schmidt, Iris; Beumer, Wouter; Vorthoren, Lars; Collin, Rob W.J.; Garanto, Alejandro; Duijkers, Lonneke; Brugulat-Panes, Anna; Semo, Ma’ayan; Vugler, Anthony; Biasutto, Patricia; Adamson, Peter; Cheetham, Michael E.

doi:10.1016/j.omtn.2018.07.010

Cited by 140 publications

(145 citation statements)

References 49 publications

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“…For example, pathogenicity was proven when studying ABCA4 variants c.4539+2001G>A and c.4539+2028C>T in photoreceptor precursor cells derived from patient fibroblasts while no effect on splicing was detected in fibroblasts of the same patients (Albert et al, ). Moreover, a retina‐specific increase of a 128‐nt PE insertion was also observed for the most frequent Leber congenital amaurosis‐associated CEP290 variant, c.2991+1655A>G (den Hollander et al, ; Dulla et al, ).…”

Section: Discussionmentioning

confidence: 94%

Identification of splice defects due to noncanonical splice site or deep‐intronic variants in ABCA4

et al. 2019

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Pathogenic variants in the ATP‐binding cassette transporter A4 (ABCA4) gene cause a continuum of retinal disease phenotypes, including Stargardt disease. Noncanonical splice site (NCSS) and deep‐intronic variants constitute a large fraction of disease‐causing alleles, defining the functional consequences of which remains a challenge. We aimed to determine the effect on splicing of nine previously reported or unpublished NCSS variants, one near exon splice variant and nine deep‐intronic variants in ABCA4, using in vitro splice assays in human embryonic kidney 293T cells. Reverse transcription‐polymerase chain reaction and Sanger sequence analysis revealed splicing defects for 12 out of 19 variants. Four deep‐intronic variants create pseudoexons or elongate the upstream exon. Furthermore, eight NCSS variants cause a partial deletion or skipping of one or more exons in messenger RNAs. Among the 12 variants, nine lead to premature stop codons and predicted truncated ABCA4 proteins. At least two deep‐intronic variants affect splice enhancer and silencer motifs and, therefore, these conserved sequences should be carefully evaluated when predicting the outcome of NCSS and deep‐intronic variants.

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Section: Discussionmentioning

confidence: 94%

Identification of splice defects due to noncanonical splice site or deep‐intronic variants in ABCA4

et al. 2019

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“…Similarly, the HEK293T cells might lack retina‐specific splicing proteins (i.e., trans splicing factors) that are necessary for the recognition of a pseudoexon created by the c.212‐3599T>A variant. Pseudoexon insertion can be tissue specific, as was shown for the most frequent Leber congenital amaurosis‐associated CEP290 variant, c.2991+1655A>G (den Hollander et al, ; Dulla et al, ). Hence, variant c.212‐3599T>A that showed no effect on splicing in our study may still be proven to result in aberrant splicing when assessed in a retinal cell line.…”

Section: Discussionmentioning

confidence: 95%

Deep‐intronic variants in CNGB3 cause achromatopsia by pseudoexon activation

et al. 2019

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Our comprehensive cohort of 1100 unrelated achromatopsia (ACHM) patients comprises a considerable number of cases (~5%) harboring only a single pathogenic variant in the major ACHM gene CNGB3. We sequenced the entire CNGB3 locus in 33 of these patients to find a second variant which eventually explained the patients’ phenotype. Forty‐seven intronic CNGB3 variants were identified in 28 subjects after a filtering step based on frequency and the exclusion of variants found in cis with pathogenic alleles. In a second step, in silico prediction tools were used to filter out those variants with little odds of being deleterious. This left three variants that were analyzed using heterologous splicing assays. Variant c.1663–1205G>A, found in 14 subjects, and variant c.1663‐2137C>T, found in two subjects, were indeed shown to exert a splicing defect by causing pseudoexon insertion into the transcript. Subsequent screening of further unsolved CNGB3 subjects identified four additional cases harboring the c.1663–1205G>A variant which makes it the eighth most frequent CNGB3 variant in our cohort. Compound heterozygosity could be validated in ten cases. Our study demonstrates that whole gene sequencing can be a powerful approach to identify the second pathogenic allele in patients apparently harboring only one disease‐causing variant.

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“…Future trials are likely to involve the CEP290 gene, a major cause of Leber congenital amaurosis and JS (Maeder et al, ; Mookherjee et al, ). Alternatively, antisense oligonucleotides can augment gene function by blocking aberrant splicing (Cideciyan et al, ; Dulla et al, ) or by causing exons with deleterious variants to be skipped (Ramsbottom et al, ). These treatments are still in early development for JS, but have been used for other disorders in humans such as spinal muscular atrophy (Finkel et al, ).…”

Section: Methodsmentioning

confidence: 99%

Healthcare recommendations for Joubert syndrome

Bachmann‐Gagescu

Dempsey

Bulgheroni

et al. 2019

American J of Med Genetics Pt A

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Joubert syndrome (JS) is a recessive neurodevelopmental disorder defined by a characteristic cerebellar and brainstem malformation recognizable on axial brain magnetic resonance imaging as the "Molar Tooth Sign". Although defined by the neurological features, JS is associated with clinical features affecting many other organ systems, particularly progressive involvement of the retina, kidney, and liver. JS is a rare condition; therefore, many affected individuals may not have easy access to subspecialty providers familiar with JS (e.g., geneticists, neurologists, developmental pediatricians, ophthalmologists, nephrologists, hepatologists, psychiatrists, therapists, and educators). Expert recommendations can enable practitioners of all types to provide quality care to individuals with JS and know when to refer for subspecialty care. This need will only increase as precision treatments targeting specific genetic causes of JS emerge. The goal of these recommendations is to provide a resource for general practitioners, subspecialists, and families to maximize the health of individuals with JS throughout the lifespan.

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Splice-Modulating Oligonucleotide QR-110 Restores CEP290 mRNA and Function in Human c.2991+1655A>G LCA10 Models

Cited by 140 publications

References 49 publications

Identification of splice defects due to noncanonical splice site or deep‐intronic variants in ABCA4

Identification of splice defects due to noncanonical splice site or deep‐intronic variants in ABCA4

Deep‐intronic variants in CNGB3 cause achromatopsia by pseudoexon activation

Healthcare recommendations for Joubert syndrome

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