Unravelling the Genetic Basis of Propionic Acidemia Using Advanced Molecular Techniques

Background: Propionic acidemia (PA) is an inherited metabolic disease caused by propionyl-CoA carboxylase deficiency due to pathogenic variants in the PCCA and PCCB genes. Diagnosis of PA is challenging because of its non-specific clinical presentation but accurate and timely diagnosis is crucial for patient management.

Case Study: An 8-month-old patient presented with developmental delay following an acute metabolic crisis. Biochemical tests revealed elevated propionylcarnitine, glycine, 3-hydroxypropionic acid, methylmalonic acid, and unspecific metabolites. Targeted NGS of genes associated with inherited metabolic diseases, minigene expression assay, RNA analysis, and whole-genome sequencing was conducted to establish the diagnosis. Additionally, the U1-snRNA was modified to be exon-specific to prove the splicing disruption basis and for use as a potential therapeutic tool to correct splicing caused by one of the two identified variants.

Results: Targeted NGS of the coding exons of genes associated with inherited metabolic diseases identified only one variant of uncertain significance in the PCCA gene in a heterozygous state, NM_000282.4:c.183+4_183+7del, which is predicted to disrupt splicing. Functional assays showed that it prevented exon 2 recognition. However, since there was only one pathogenic variant in the heterozygous state, whole-genome sequencing was conducted which revealed a gross deletion involving PCCA exons 13-19 in the second allele. In vitro studies with the c.183+4_183+7del minigene and modified U1-snRNA showed enhanced PCCA exon 2 recognition and restoration of the wild-type splicing pattern.

Conclusion: This study highlights the usefulness of advanced molecular techniques in diagnosing inherited metabolic diseases when clinical and biochemical data are evident. Discovering the molecular basis of a disease may potentially lead to the development of targeted therapies for patients with inherited metabolic diseases.