Pyruvate dehydrogenase complex deficiency: updating the clinical, metabolic and mutational landscapes in a cohort of Portuguese patients

Abstract

Background: The pyruvate dehydrogenase complex (PDC) catalyzes the irreversible decarboxylation of pyruvate into acetyl-CoA. PDC deficiency can be caused by alterations in any of the genes encoding its several subunits. The resulting phenotype, though very heterogeneous, mainly affects the central nervous system. The aim of this study is to describe and discuss the clinical, biochemical and genotypic information from thirteen PDC deficient patients, thus seeking to establish possible genotype-phenotype correlations.

Results: The mutational spectrum showed that seven patients carry mutations in the PDHA1 gene encoding the E1α subunit, five patients carry mutations in the PDHX gene encoding the E3 binding protein, and the remaining patient carries mutations in the DLD gene encoding the E3 subunit. These data corroborate earlier reports describing PDHA1 mutations as the predominant cause of PDC deficiency but also reveal a notable prevalence of PDHX mutations among Portuguese patients, most of them carrying what seems to be a private mutation (p.R284X). The biochemical analyses revealed high lactate and pyruvate plasma levels whereas the lactate/pyruvate ratio was below 16; enzymatic activities, when compared to control values, indicated to be independent from the genotype and ranged from 8.5% to 30%, the latter being considered a cut-off value for primary PDC deficiency. Concerning the clinical features, all patients displayed psychomotor retardation/developmental delay, the severity of which seems to correlate with the type and localization of the mutation carried by the patient. The therapeutic options essentially include the administration of a ketogenic diet and supplementation with thiamine, although arginine aspartate intake revealed to be beneficial in some patients. Moreover, in silico analysis of the missense mutations present in this PDC deficient population allowed to envisage the molecular mechanism underlying these pathogenic variants.

Conclusion: The identification of the disease-causing mutations, together with the functional and structural characterization of the mutant protein variants, allow to obtain an insight on the severity of the clinical phenotype and the selection of the most appropriate therapy.

Keywords: Genotype–phenotype correlation; Lactic acidosis; Mutational analysis; Neurological dysfunction; Pyruvate dehydrogenase complex deficiency.

Fig. 1

Magnetic resonance images of brain lesions of an 8 month old patient carrying a PDHA1 mutation. Hyperintense bilateral and symmetrical lesions in the thalami, globus pallidus and putamina, on T2 weighted images, hypointense on T1 and with diffusion restriction suggestive of acute lesions; there is no diffusion restriction suggestive of chronic lesions. a axial T2, b axial T1 IR, c axial DWI, d axial ADC

Fig. 2

Magnetic resonance spectroscopy of a patient carrying a PDHA1 mutation. Spectroscopy with TE = 135 ms in left thalamus; slight reduction of NAA, increased choline and lactate

Fig. 3

In silico analysis of pyruvate dehydrogenase complex E1 p.R302H variant. Top left panel, cartoon and ribbon representation of the heterotetrameric PDC E1 crystallographic structure (PDB entry 3EXE). E1α subunit represented in green; E1β represented in blue; E1α phosphorylation loop A represented in orange. The corresponding E1α′ and E1β′ subunits are represented as a gray ribbon. Residues that are substituted in variants identified in Portuguese PDC deficient patients with mutations in PDHA1, encoding the PDH E1α subunit, are represented in sticks. Top right panel, scheme representing the possible impact of substituted residues in pathogenic E1α variants: p.R253G substitution located near phosphorylation loop A (orange shape); p.F205L substitution possibly affecting αα′ interface (each E1α subunit represented in different shades of green); p.R302H substitution located in phosphorylation loop A close to the TPP cofactor binding site; p.R378C/H substitutions located close to the αβ interface (each E1β subunit represented in different shades of blue), and possibly affecting the interaction with a domain of the PDC E2 component. Bottom panel, zoom-in on the region surrounding R302 (left), showing its possible interactions with neighbouring residues (Y287, R288, Y289, H290 and G298), only the latter being retained upon substitution by H in the p.R302H variant (right). Structural model of PDC-E1 p.R302H variant was obtained by loading the structure of WT PDC-E1 (PDB entry 3EXE) into Pymol and applying the mutagenesis tool to generate all possible rotamers of the substituting amino acid side chain

Fig. 4

In silico analysis of pyruvate dehydrogenase complex E3 p.P87S variant. Cartoon representation of homodimeric PDC E3 crystallographic structure (PDB entry 6I4T; one monomer represented in blue, the other in grey). Flavin adenine dinucleotide (FAD) cofactor in yellow sticks. Right panel, zoom-in on the location of the P87S substitution. P87 is located in an α-helix which contains the active site cysteine residues C80 and C85. Substitution of P by S will likely affect the helix structure and disturb the proximity between the active site disulphide and the FAD cofactor. Structural model of PDC-E1 p.R302H variant was obtained by loading the structure of WT PDC-E3 (PDB entry 6IT4) into Pymol and applying the mutagenesis tool to generate all possible rotamers of the substituting amino acid side chain