Regulating PCCA gene expression by modulation of pseudoexon splicing patterns to rescue enzyme activity in propionic acidemia

Ulrika Simone Spangsberg Petersen, Maja Dembic, Ainhoa Martínez-Pizarro, Eva Richard, Lise Lolle Holm, Jesper Foged Havelund, Thomas Koed Doktor, Martin Røssel Larsen, Nils J. Færgeman, Lourdes Ruiz Desviat, Brage Storstein Andresen*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Pseudoexons are nonfunctional intronic sequences that can be activated by deep-intronic sequence variation. Activation increases pseudoexon inclusion in mRNA and interferes with normal gene expression. The PCCA c.1285-1416A>G variation activates a pseudoexon and causes the severe metabolic disorder propionic acidemia by deficiency of the propionyl-CoA carboxylase enzyme encoded by PCCA and PCCB. We characterized this pathogenic pseudoexon activation event in detail and identified hnRNP A1 to be important for normal repression. The PCCA c.1285-1416A>G variation disrupts an hnRNP A1-binding splicing silencer and simultaneously creates a splicing enhancer. We demonstrate that blocking this region of regulation with splice-switching antisense oligonucleotides restores normal splicing and rescues enzyme activity in patient fibroblasts and in a cellular model created by CRISPR gene editing. Interestingly, the PCCA pseudoexon offers an unexploited potential to upregulate gene expression because healthy tissues show relatively high inclusion levels. By blocking inclusion of the nonactivated wild-type pseudoexon, we can increase both PCCA and PCCB protein levels, which increases the activity of the heterododecameric enzyme. Surprisingly, we can increase enzyme activity from residual levels in not only patient fibroblasts harboring PCCA missense variants but also those harboring PCCB missense variants. This is a potential treatment strategy for propionic acidemia.

Original languageEnglish
Article number102101
JournalMolecular Therapy Nucleic Acids
Issue number1
Number of pages46
Publication statusPublished - 12. Mar 2024


  • cryptic splicing
  • metabolic disorder
  • MT: Oligonucleotides: Therapies and Applications
  • PCCA
  • pre-mRNA splicing
  • propionic acidemia
  • propionyl-CoA carboxylase
  • pseudoexon
  • splice-switching antisense oligonucleotides
  • Targeted Augmentation of Nuclear Gene output (TANGO)


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