Deep-intronic ABCA4 variants explain missing heritability in Stargardt disease and allow correction of splice defects by antisense oligonucleotides.

ATP-Binding Cassette Transporters / genetics Adolescent Adult Aged Child Exons / genetics HEK293 Cells Humans Introns / genetics Middle Aged Mutation / genetics Oligonucleotides, Antisense / genetics Pedigree Polymorphism, Single Nucleotide / genetics Protein Isoforms / genetics RNA Splicing / genetics Stargardt Disease / genetics Young Adult

ABCA4 Stargardt disease antisense oligonucleotide deep-intronic variant missing heritability

Journal

Genetics in medicine : official journal of the American College of Medical Genetics

ISSN: 1530-0366

Titre abrégé: Genet Med

Pays: United States

ID NLM: 9815831

Informations de publication

Date de publication:
08 2019

Historique:

received: 19 04 2018

accepted: 07 12 2018

pubmed: 16 1 2019

medline: 7 2 2020

entrez: 16 1 2019

Statut: ppublish

Résumé

Using exome sequencing, the underlying variants in many persons with autosomal recessive diseases remain undetected. We explored autosomal recessive Stargardt disease (STGD1) as a model to identify the missing heritability. Sequencing of ABCA4 was performed in 8 STGD1 cases with one variant and p.Asn1868Ile in trans, 25 cases with one variant, and 3 cases with no ABCA4 variant. The effect of intronic variants was analyzed using in vitro splice assays in HEK293T cells and patient-derived fibroblasts. Antisense oligonucleotides were used to correct splice defects. In 24 of the probands (67%), one known and five novel deep-intronic variants were found. The five novel variants resulted in messenger RNA pseudoexon inclusions, due to strengthening of cryptic splice sites or by disrupting a splicing silencer motif. Variant c.769-784C>T showed partial insertion of a pseudoexon and was found in cis with c.5603A>T (p.Asn1868Ile), so its causal role could not be fully established. Variant c.4253+43G>A resulted in partial skipping of exon 28. Remarkably, antisense oligonucleotides targeting the aberrant splice processes resulted in (partial) correction of all splicing defects. Our data demonstrate the importance of assessing noncoding variants in genetic diseases, and show the great potential of splice modulation therapy for deep-intronic variants.

Identifiants

DOI: 10.1038/s41436-018-0414-9 PMID: 30643219 PMC: PMC6752325

pubmed: 30643219

doi: 10.1038/s41436-018-0414-9

pii: S1098-3600(21)01619-1

pmc: PMC6752325

doi:

Substances chimiques

ABCA4 protein, human 0

ATP-Binding Cassette Transporters 0

Oligonucleotides, Antisense 0

Protein Isoforms 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

Pagination

1751-1760

Subventions

Organisme : Department of Health

ID : RG65966

Pays : United Kingdom

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