- Open Access
Pyruvate dehydrogenase complex deficiency: updating the clinical, metabolic and mutational landscapes in a cohort of Portuguese patients
Orphanet Journal of Rare Diseases volume 15, Article number: 298 (2020)
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.
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.
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.
Pyruvate dehydrogenase complex (PDC) deficiency, first described in 1970 by Blass et al. , is an inborn error of mitochondrial energy metabolism. The pyruvate oxidation route, that bridges the cytosolic glycolytic pathway and the mitochondrial tricarboxylic acid cycle , involves not only PDC but also pyruvate transport and the ancillary metabolic routes associated with various cofactors. PDC, which irreversibly decarboxylates pyruvate to acetyl coenzyme A, comprises three functional (E1 or pyruvate dehydrogenase, E2 or dihydrolipoamide transacetylase, and E3 or dihydrolipoyl dehydrogenase) and one structural (E3BP or E3 binding protein, formerly designated by protein X) components, and the regulatory PDC kinases and PDC phosphatases, which control the complex activity via phosphorylation/dephosphorylation . The E1 subunit catalyzes the first, rate-limiting and irreversible step of the reaction which takes place in two active sites formed at the interface between their two α and two β subunits, each requiring a thiamine pyrophosphate cofactor and magnesium ions for activity [4, 5].
The great majority (≈ 77%) of patients with PDC deficiency harbor mutations in the X-linked PDHA1 gene which encodes the E1α subunit. Hemizygous males are usually symptomatic whereas heterozygous females present variable expression due to random patterns of X-inactivation in different tissues, the clinical manifestations depending on the proportion of cells expressing the mutant E1α subunit. The remaining cases are caused by mutations in the genes encoding the remaining subunits: PDHB encoding E1β (4.3%), DLAT encoding E2 (1.5%), DLD encoding E3 (6.2%) and PDHX encoding E3BP (10.7%) .
The clinical presentation is extremely heterogeneous, ranging from a fatal lactic acidosis and progressive neurological and neuromuscular degradation in the neonatal period to a chronic neurological dysfunction and neurodegenerative condition. Inadequate removal of lactate but mainly of pyruvate  results in lactic acidemia which, together with the blood lactate/pyruvate ratio ≤ 20, is recognized as an important biomarker [8, 9]. The primary phenotypic manifestation corresponds to an impairment of neurological and/or developmental functions, leading to a wide range of symptoms and clinical features: hypotonia, seizures, ataxia, respiratory distress (like apnea and hypoventilation), facial dysmorphism, and peripheral neuropathy. Structural and functional brain abnormalities are also described, including ventriculomegaly and Leigh syndrome. According to their severity, the phenotypes can be divided into three main categories: neonatal, infantile and benign [10,11,12].
The therapeutic strategies target: (i) the metabolic pathway, bypassing energy production via a ketogenic diet [11, 13], (ii) the regulatory system of the dysfunctional PDC, using xenobiotic inhibitors [14, 15], or (iii) stimulation of the residual PDC activity with supplementation of cofactors [16, 17]. Nevertheless, none of these treatments is sufficiently effective and the responsiveness is markedly individual. Thus, the precise diagnosis, including the identification of the genetic defect and the phenotypic consequences, is becoming increasingly decisive for selecting the appropriate therapeutic strategy. Knowledge on the functional and structural impact of the identified mutations on the resulting PDC component variant provides relevant information for informed decisions on the therapeutic approaches.
In this study, we describe and discuss the profiles of thirteen Portuguese PDC deficient patients with reference to their clinical data, biochemical findings and results of DNA analysis, thus seeking to establish possible genotype–phenotype correlations. This is the first report on phenotypic and genotypic variability in a subset of PDC deficient patients diagnosed in Portugal.
The broad phenotypic spectrum of PDC deficiency, common to many other genetic mitochondrial disorders, often hampers the achievement of a rapid diagnosis. Patients were suspected to be PDC deficient based on clinical signs /symptoms and biochemical data, namely elevated plasma lactate (L) and pyruvate (P) levels with low L/P ratio and/or impaired PDC activity, but only those with genetic confirmation were considered in this study. Thus, a total of 13 individuals, all of European ancestry, were diagnosed (Table 1). The prevalence of PDC deficiency in Portugal is therefore estimated to be 1/790,000, comparable to the prevalence of 1/1,000,000 reported by Orphanet, the portal of rare diseases and orphan drugs, and also to the values calculated for the French population (1/827,000 – 1/1,135,000) [8, 18].
The 13 patients, seven males and six females, were born between 1983 and 2018, their current ages varying from 20 months to 36 years, with a median age of 15.5 years. Consanguinity was reported only in three families harboring PDHX mutations. Among this group of 13 patients, only two were siblings, born from a triplet pregnancy after in vitro fertilization (two affected males and one unaffected female) who carry a PDHA1 mutation. No affected relatives are known in any of these families.
All patients showed the first symptoms either in the neonatal period (five individuals, 38.5%) or during infancy (eight individuals, 61.6%) with a median age of 0.5 years. In some cases however, the diagnosis was only achieved later, mainly among the older patients who presented a less severe clinical picture (five individuals confirmed between 3.3 and 17 years); indeed, the most striking example is the deficiency in E3 (also designated by dihydrolipoamide dehydrogenase, DLD), which was only diagnosed when the patient was 17 years old.
All patients but one are alive; the deceased patient is a boy carrying the c.1132C>T mutation in PDHA1 (generating the p.R378C E1α variant); the death occurred at the age of 3.3 years and was caused by cardiorespiratory arrest.
In this cohort of 13 patients it was shown that patients carried mutations in three different genes: seven in the PDHA1 gene, five in the PDHX gene, and one in the DLD gene (Table 1). The mutational spectrum revealed ten different mutations: five in PDHA1, three in PDHX and two in DLD.
As expected for an X-linked disorder, most patients with mutations in PDHA1, are males (6/7) in families with no consanguinity, but it is interesting to notice that in all these patients mutations arrived by a de novo mechanism, confirmed by parental sequencing, and that mosaicism was absent. On the other hand, most patients with mutations in PDHX, displaying an autosomal recessive mode of inheritance, are females (4/5) and consanguinity was detected in three cases. Finally, the single patient with mutations in DLD, also displaying an autosomal recessive mode of inheritance, is a compound heterozygous female with no consanguinity reported in her family.
In this patient cohort, all five different PDHA1 mutations are missense (c.615C>G, c.757A>G, c.905G>A, c.1132C>T, and c.1133G>A), generating respectively the p.F205L, p.R253G, p.R302H, p.R378C and p.R378H E1α variants. The prevalence of missense mutations, in principle the less severe mutation type, strongly correlates with the majority of patients being males. On the contrary, the three mutations detected in PDHX gene (c.160+1G>A, c.483delC and c.850C>T), being nonsense (p.R284X) and frameshift (p.G26Vfs*7 and p.P161Pfs*17), usually result in absent protein, hence their highly deleterious consequences. Three out of the five patients are homozygous for the p.R284X variant, whereas one of the remaining patients is a compound heterozygote expressing the p.R284X and p.P161Pfs*17 variants, while the other is homozygous for the mutation generating the p.G26Vfs*7 variant. Regarding the two identified DLD mutations, both c.259C>T and c.803_804delAG are novel (Exome Variant, LOVD or ClinVar). The c.259C>T mutation generates the E3 p.P87S variant. Moreover, c.803_804delAG, originating a frameshift variant (p.Q268Rfs*3), is predicted to be very severe.
All patients, regardless of the carried mutation, were suspected of PDC deficiency due to their elevated plasma lactate and pyruvate levels: lactate ranging from 3.0 to 17.0 mmol·L−1 (median value 6.6 ± 3.9) and pyruvate from 0.27 to 0.81 mmol·L−1 (median value 0.398 ± 0.086). Lactate/pyruvate ratios as expected, with a single exception, were ≤ 16, i.e., in the normal range. PDC deficiency was confirmed by determination of PDC activity. Enzymatic assays were performed either in circulating lymphocytes (12 patients) or cultured fibroblasts (two patients), both tissues having been analyzed in patient 11. All patients had their enzymatic activities confirmed in a second independent sample and the results always matched. Interestingly, a single false negative result was found in the lymphocytes of a female patient later identified with a PDHA1 mutation. In our experience, the cut-off value for considering a primary PDC deficiency should be ≤ 30% of control activity and, indeed, all patients but one presented enzymatic activities ranging from 8.5% to 30% (median value 28.0 ± 7.9). The single exception was one of the siblings carrying the p.R378C variant in PDHA1, who presented 40% of normal control activity (Table 1), surprisingly the one whose symptoms manifested earliest in the neonatal period.
However, when stratifying the values of enzyme activity according to the affected PDC subunit, we observed some differences. Patients carrying PDHX mutations displayed higher and more similar values of relative activity (median value 29 ± 3.4%), whereas patients carrying PDHA1 mutations displayed a wider range of activity (median value 23.5 ± 10.7%), with half of them below 20%.
The clinical features observed in these patients’ cohort are displayed in Table 1 and, according to the most recently published data , can be roughly divided into two categories: one caused by PDHA1 and PDHX mutations, and the other caused by DLD mutations. Indeed, the clinical phenotypes manifested by patients carrying PDHA1 and PDHX mutations are quite variable and almost undistinguishable.
Concerning neurological features, all individuals presented development delay/psychomotor retardation, which ranged from severe (eight patients: 61.5%) to moderate (four patients: 30.8%) or very mild (one patient who attended normal school: 7.7%). Hypotonia was also observed in all individuals, with a single exception (Patient 11) who nevertheless could display it at an earlier age. Seizures were reported in half the individuals, especially those carrying PDHA1 mutations (5/7 patients: 71%). On the other hand, ocular manifestations were more frequent in individuals harboring PDHX mutations (4/5 patients: 80%). Microcephaly, dystonia and ataxia were also reported in half the patients of both these gene defects. As expected, facial dysmorphism was only detected in a single female patient carrying a PDHA1 mutation. The patient with DLD deficiency revealed moderate developmental delay/psychomotor retardation, seizures, hypotonia, dystonia and ataxia. Basal ganglia abnormalities were exclusively observed in patients carrying mutations in PDHA1. Cerebral atrophy, but not cerebellar atrophy, was detected mainly in patients carrying PDHX mutations. However, in patients carrying PDHA1 mutations, cerebral atrophy, when present, was always associated with cerebellar atrophy (Figs. 1 and 2). Patient 13, harboring DLD mutations, presented partial agenesis of corpus callosum.
All the patients are under therapeutic measures which include ketogenic diet, thiamine supplementation and antiepileptic drugs. Three patients with PDHA1 mutations (3/7: 43%) and three with PDHX mutations (3/5: 60%) are under ketogenic diet with clearly beneficial effects on childhood-onset epilepsy or paroxysmal dystonia. The rationale for the ketogenic diet is that ketone bodies generated by fatty acid oxidation serve as an alternative energy substrate to glucose as the glycolytic end product, pyruvate, is not optimally metabolized. The long-term thiamine supplementation, as PDC cofactor, is prescribed in almost all patients (11/13), and antiepileptic drugs only in those presenting seizures (Table 1). Finally, it is interesting to mention that three of the patients carrying mutations in the PDHA1 gene were under arginine aspartate supplementation, with beneficial effects at the physical and intellectual levels, especially Patient 2.
In silico analysis of missense mutations
Bioinformatic analysis using the PolyPhen-2 server  suggested that all mutations but one affecting E1α subunit are most probably damaging. The E1α p.R302H, p.R378C and p.R378H variants displayed a score of 1.000 (sensitivity 0.00 and specificity 1.00), p.F205L displayed a score of 0.919 (sensitivity 0.81 and specificity 0.94), and p.R253G displayed a score of 0.007 (sensitivity 0.96 and specificity 0.75) thus being considered benign. As for E3 subunit, the p.P87S variant is predicted to be most probably damaging, with a score of 0.996 (sensitivity 0.55 and specificity 0.98).
To complement the information of the PolyPhen-2 server, which solely bases its predictions on the polypeptide sequence and overlooks other structural and functional details, such as e.g. cofactor binding and interaction with other proteins, we obtained and thoroughly inspected structural models of each E1α variant. The models obtained for the E1α p.R253G, p.R378C, p.R378H and p.F205L variants have been recently described by our group, attempting to understand the molecular mechanisms underlying the pathogenicity of the corresponding mutations . All mutations result in putative loss of H-bonds, electrostatic or hydrophobic interactions between the side chains of the substituted amino acids and neighboring residues, with predicted effects on P-loop destabilization, inter-subunit interactions and proper oligomeric assembly, as well as interaction with other PDC components. Herein, we additionally generated a structural model of the E1α p.R302H variant (Fig. 3). R302 is located at one end of the P-loop A, its side chain being within electrostatic and H-bonding distance to the side chain or main chain carbonyl moieties of Y287, R288, Y289, H290 (active site residue) and G298, all residues belonging to the same P-loop. Upon substitution by a histidine residue, most of the possible interactions between its side chain and other residues in the P-loop are lost. The single remaining H bond is that between the side chain imidazole and the main chain carbonyl of G298. Therefore, in the p.R302H E1α variant, the net loss of four possible side chain interactions with other P-loop A residues (Fig. 3) is likely to contribute to a more disordered loop and consequently lower enzymatic activity. Notably, the degree of disorder in P-loop A has been negatively correlated with E1 enzymatic activity, since an ordered loop favors TPP binding, which itself promotes P-loop A order .
To further understand the pathogenicity of the DLD mutation generating the E3 p.P87S variant, a structural model was obtained (Fig. 4) based on the reported 3D crystallographic structure of another disease-causing E3 variant (PDB entry 6I4T) . As observed in Fig. 4, P87 is located in a helix that lines with the flavin adenine dinucleotide isoalloxazine ring and contains the active site disulfide composed of C45 and C50. Substitution of P87 by a serine is likely to alter the flexibility and thus the overall stability of the respective helix, possibly affecting the enzymatic activity.
The diagnosis of PDC deficiency is extremely challenging due to a phenotypic presentation that can be observed in many other neurological disorders, especially those causing abnormal mitochondrial metabolism [6, 23, 24]. Indeed, PDC deficiency can be included in the vaster group of pyruvate oxidation defects (POD) which also involves defects in genes coding for proteins participating in the whole pyruvate oxidation route, including cofactors, regulation of PDC and the mitochondrial pyruvate carrier . Nevertheless, in this study, we only included patients carrying mutations in the genes encoding the PDC subunits (PDHA1, PDHB, PDHX, DLAT and DLD). Accordingly, and comparing the prevalence rate we obtained versus the previously reported prevalence (respectively 1:790,000 and 1:1,000,000) we may assume that no significant number of patients were missed.
In such context, we aimed to present the first report on a cohort of PDC deficient Portuguese patients combining information on the associated clinical, biochemical, enzymatic and genotypic spectra. The mutational spectrum of PDC deficiency in this group of patients revealed ten different mutations affecting three genes, PDHA1 (five), PDHX (three) and DLD (two). Concerning the prevalence of the deficiency of each gene, these data generally agree with literature surveys [6, 9] and also with several studies focused on different populations [8, 25, 26]. However, the frequency of mutations in the PDHA1 gene is lower than the usually reported average of 75–80%, due to a high number of patients harboring mutations in the PDHX gene (38% in our cohort versus 10% in the literature).
The most striking evidence is the relatively high incidence of E3BP deficiency, mostly caused by a p.R284X E3BP variant, half the cases originating from the Azores Islands, thus denoting a founder effect. This E3BP variant was first described by our group  and, until now, only another Portuguese patient has been reported to carry this mutation . Furthermore, the mutational spectrum of E3BP deficiency in Portugal includes very severe mutations, leading to null alleles. Nevertheless, our older patients surprisingly reached adulthood, in line with the high proportion of long-term survival among reported E3BP deficient patients [8, 29, 30]. In general, an overwhelming majority of the mutations hitherto identified in the PDHX gene are, as in this work, deletions, nonsense mutations, point mutations at intron–exon boundaries, or even large intra-genic rearrangements, expected to result in a complete absence of E3BP protein [8, 30,31,32]. Despite this fact, the patients retain considerably significant PDC activity (20–30%), considering the expected impairment on PDC assembly. On the one hand, as a structural subunit devoid of enzymatic activity, E3BP does not directly contribute to the complex catalytic activity. On the other hand, the significantly truncated E3BP, if present at all in the cell, would likely compromise the structure of the E2/E3BP PDC core and binding of the E3 component. Both E2 and E3BP components have a similar structure and domain organization, despite only E2 being catalytically active . However, the possibility of the E2 core directly binding to the E3 enzyme may underlie the observed residual PDC activity [30,31,32, 34]. In their recent work, Prajapati and collaborators report a non-uniform stoichiometry of the E2/E3BP PDC core. The imbalanced distribution of E2 and E3BP constituents of the trimeric units results into structurally dynamic E1 and E3 clusters . Moreover, for one of the proposed models of E. coli, the PDC core is a fully functional E2 homotrimer operating in a “division-of-labor” mechanism, including binding of the E3 component [35, 36].
Concerning the mutational spectrum of E1α deficiency, five different PDHA1 mutations were identified, all but a single one (c.1132C>T, encoding the p.R378C variant) from non-consanguineous patients. Almost all mutations affect an arginine codon  and those located in exons 10 and 11 cause a severe phenotype, because the resulting protein variants present very low enzyme activity. On the contrary, the two mutations located in exon 7 originate moderate (c.615C>G, encoding the p.F205L variant) or very mild (c.757A>G, encoding the p.R253G variant) phenotypes. Interestingly, mutations affecting codon 378 are considered particularly lethal . Indeed, from our male patients carrying the p.R378C mutation, one deceased at three years of age and the twins, presently aged 8 years, display a severe clinical picture. However, a female patient bearing the p.R378H substitution reached the adulthood, probably due to a lyonization effect.
Regarding a possible genotype-dependent phenotypic presentation, our data is roughly suggestive of such a correlation. Effectively, the patients harboring the most deleterious mutations (c.905G>A and c.1132C>T in PDHA1 and all the mutations in PDHX) present the most severe phenotypes, involving serious psychomotor retardation, hypotonia and seizures, whereas those carrying less severe mutations accordingly display a better clinical outcome. The most puzzling observation concerns the female carrying mutations in DLD. Despite being a compound heterozygote bearing two severe mutations, her clinical course was reasonable until 2018 when she suffered an acute metabolic decompensation originating spastic tetraparesis with gait and language loss. Although she partially recovered language, she currently presents a moderate-to-severe psychomotor handicap. Despite the E3 subunit being common to other enzyme complexes such as α-ketoglutarate dehydrogenase and branched-chain amino acid dehydrogenase, this patient did not display the associated biochemical or clinical phenotypes.
Irrespectively of our patients’ cohort size, the majority of our PDC deficient patients remarkably reached adulthood, as opposed to several other reports [9, 18, 25, 26]. Concerning the therapeutic measures to which these individuals are subjected, it is clear they are only palliative, since all patients but one continue presenting clinical features ranging from moderate to severe forms. The single exception is Patient 2 who seems to represent an exceptional case, because his treatment only encompasses thiamine (E1 subunit cofactor) and arginine aspartate supplementation . Arginine aspartate (Asparten®, Sargenor®) is an anti-asthenic over-the-counter medicine. Aspartate is considered an anaplerotic agent, whereas arginine has the ability to suppress aggregation during protein folding by binding to the folding intermediates through weak interactions, thus being considered a putative chemical chaperone [39,40,41]. This patient carries the PDHA1 c.757A>G mutation that originates the p.R253G E1α variant, whose in silico and in vitro analyses with the recombinant protein exhibited lower affinity for TPP and lower residual enzymatic activity, in addition to increased proneness to aggregation, in comparison with WT PDC-E1 . The same impairment on the affinity for TPP was observed in various PDHA1 missense mutations . Thiamine supplementation is thus likely to ameliorate the functional impact in terms of TPP affinity for several of these variants . Nevertheless, our observation of the serious regress of the clinical symptoms, while the arginine aspartate uptake was interrupted in Patient 2 , suggests that this patient benefits from both arginine aspartate and thiamine treatments.
In conclusion, the identification of the disease-causing mutations, together with the functional and structural characterization of the respective protein variants, allows getting insight on the severity of the clinical phenotype and the selection of the most appropriate therapy, namely the option for a ketogenic diet.
Materials and methods
Cohort of patients
This study included all PDC deficient patients whose diagnosis was confirmed at the molecular level: thirteen individuals comprising a pair of monozygous twin siblings, 6 being females and 7 males. Since patients originated from all regions of Portugal, this cohort can be considered representative of the whole population. The diagnosis of patients, suspected due to high lactate and pyruvate plasma levels and respective lactate/pyruvate ratio < 20, was confirmed by reduced PDC activity (ca < 30% of laboratory control mean: 1734 ± 455 (range: 1279 – 2189) pmol·min−1·mg protein−1; n = 70) in peripheral lymphocytes and/or cultured fibroblasts originating from skin biopsy, and also by identification of the causative mutation(s).
This study was approved by the local Ethics Committees and informed consents were obtained from the patients or their parents, who were also enrolled in the study, whenever necessary and possible. Declaration of Helsinki was also strictly observed.
The physicians following these patients completed a questionnaire involving a wide range of parameters, namely: general characteristics of the patients, clinical features, brain malformations, biochemical findings, genetic findings, and current therapy.
Sample collection and preparation
Blood samples were collected after overnight fasting by venipuncture into EDTA- and perchloric acid-containing tubes for plasma separation and quantification of lactate and pyruvate levels, respectively, and into heparin-containing tubes for peripheral blood mononuclear cells (PBMC) isolation.
PBMC were separated at room temperature on a Ficoll-Paque gradient. Fibroblasts were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% newborn calf serum and 1% antibiotic/antimycotic solution. Pelleted cells were resuspended in homogenization buffer (80 mM KH2PO4, pH 7.4, 2 mM EDTA). PBMC suspensions were immediately disrupted by sonication, whereas fibroblast suspensions were treated with 5 mM dichloroacetate for 15 min at 37 °C. The reaction was blocked by addition of a stopping solution (25 mM NaF, 25 mM EDTA, 4 mM DTT), and cells were disrupted by three freeze/thaw cycles.
PDC activity assay
Enzymatic activity was measured using a radiochemical method based on the release of 14CO2 from [1-14C]-pyruvate  with minor modifications (Johannes Mayr and Wolfgang Sperl, personal communication). Briefly, 100 µL of cell homogenates were incubated at 37 °C for 10 min in 100 µL of reaction buffer (32 mM phosphate buffer containing 4 mM MgCl2, 2 mM CaCl2, 0.5 mM NAD+, 0.5 mM TPP, 0.1 mM CoA and 5 mM carnitine; final concentrations); blanks were obtained by replacing the cell homogenate with homogenizing buffer. Then, the reaction was started by addition of 50 µL [1-14C]-pyruvate solution (0.5 mM, 0.067 µCi) and allowed to proceed for 30 min, after which the reaction was stopped by addition of 80 µL 6 N H2SO4. The released 14CO2 was trapped in filter paper saturated with benzethonium hydroxide, for 15 min post-incubation at room temperature and under gentle stirring, and its amount measured in a scintillation counter. All samples were analyzed in triplicates and PDC activity was expressed in pmol·min−1·mg protein−1.
Preparation of genomic DNA, RNA and cDNA
Genomic DNA and, eventually, total RNA were isolated from peripheral blood leukocytes using the Puregene Cell and Tissue kit (Gentra Systems) and the Trizol method, respectively; 5 μg of total RNA were used for the reverse transcription reaction (Amersham First Strand cDNA Synthesis kit, GE Healthcare Bio-Science Corp.).
PCR amplification of PDC coding genes
The complete sequence of each gene was obtained by PCR amplification of individual exons, including intronic boundaries, or overlapping fragments of the respective cDNA. The PDC subunits under analysis together with their coding genes, approved symbols and reference sequences are listed in Additional file 1: Table S1, whereas primer sequences designed for each gene amplification are listed in Additional file 1: Table S2.
PCR and RT-PCR products were purified from solution or directly from agarose gels, using Isolate II PCR and Gel Kit (Bioline). PCR forward or reverse primers were added to the purified products from each individual sample and submitted to bi-directional Sanger sequencing. All chromatograms corresponding to PCR and RT-PCR fragments were analyzed with BLAST (NCBI).
In silico analysis of PDC-E1 mutations
To better establish genotype–phenotype correlations regarding the missense mutations in PDHA1, we undertook an in silico analysis of protein variants resulting from the described mutations. Besides evaluating the potential pathogenicity of the mutations using the PolyPhen-2 server , we sought to obtain structural models of the protein variants through two complementary strategies, previously described for the p.R253G, p.R378C, p.R378H, and p.F205L variants , and herein extended to p.R302H: i) submitting the sequence of the amino acid substituted variant to the SwissModel server and retrieving the corresponding model; and ii) using the Mutagenesis tool in Pymol (version 1.7)  employing the structure of WT PDC-E1 (PDB entry 3EXE) as template .
Data can be made available upon reasonable request to the corresponding authors.
Blass JP, Avigan J, Uhlendorf BW. A defect in pyruvate decarboxylase in a child with an intermittent movement disorder. J Clin Invest. 1970;49(3):423–32.
Patel MS, Harris RA. Mammalian alpha-keto acid dehydrogenase complexes: gene regulation and genetic defects. FASEB J. 1995;9(12):1164–72.
Patel MS, Korotchkina LG. Regulation of the pyruvate dehydrogenase complex. Biochem Soc Trans. 2006;34:217–22.
Cate RL, Roche TE, Davis LC. Rapid intersite transfer of acetyl groups and movement of pyruvate dehydrogenase component in the kidney pyruvate dehydrogenase complex. J Biol Chem. 1980;255(16):7556–62.
Berg A, Westphal AH, Bosma HJ, De Kok A. Kinetics and specificity of reductive acylation of wild-type and mutated lipoyl domains of 2-oxo-acid dehydrogenase complexes from Azotobacter vinelandii. Eur J Biochem. 1998;252(1):45–50.
Sperl W, Fleuren L, Freisinger P, Haack TB, Ribes A, Feichtinger RG, et al. The spectrum of pyruvate oxidation defects in the diagnosis of mitochondrial disorders. J Inherit Metab Dis. 2015;38(3):391–403.
Debray F-G, Mitchell GA, Allard P, Robinson BH, Hanley JA, Lambert M. Diagnostic accuracy of blood lactate-to-pyruvate molar ratio in the differential diagnosis of congenital lactic acidosis. Clin Chem. 2007;53(5):916–21.
Imbard A, Boutron A, Vequaud C, Zater M, de Lonlay P, de Baulny HO, et al. Molecular characterization of 82 patients with pyruvate dehydrogenase complex deficiency. Structural implications of novel amino acid substitutions in E1 protein. Mol Genet Metab. 2011;104(4):507–16.
Patel KP, O’Brien TW, Subramony SH, Shuster J, Stacpoole PW. The spectrum of pyruvate dehydrogenase complex deficiency: clinical, biochemical and genetic features in 371 patients. Mol Genet Metab. 2012;106(3):385–94.
Brown GK, Otero LJ, LeGris M, Brown RM. Pyruvate dehydrogenase deficiency. J Med Genet. 1994;31(11):875–9. https://doi.org/10.1136/jmg.31.11.875.
Wexler ID, Hemalatha SG, McConnell J, Buist NR, Dahl HH, Berry SA, et al. Outcome of pyruvate dehydrogenase deficiency treated with ketogenic diets. Studies in patients with identical mutations. Neurology. 1997;49(6):1655–61.
Robinson JN, Norwitz ER, Mulkern R, Brown SA, Rybicki F, Tempany CMC. Prenatal diagnosis of pyruvate dehydrogenase deficiency using magnetic resonance imaging. Prenat Diagn. 2001;21(12):1053–6. https://doi.org/10.1002/pd.187.
Sofou K, Dahlin M, Hallböök T, Lindefeldt M, Viggedal G, Darin N. Ketogenic diet in pyruvate dehydrogenase complex deficiency: short- and long-term outcomes. J Inherit Metab Dis. 2017;40(2):237–45.
Fouque F, Brivet M, Boutron A, Vequaud C, Marsac C, Zabot M-T, et al. Differential effect of DCA treatment on the pyruvate dehydrogenase complex in patients with severe PDHC deficiency. Pediatr Res. 2003;53(5):793–9.
Ferriero R, Brunetti-Pierri N. Phenylbutyrate increases activity of pyruvate dehydrogenase complex. Oncotarget. 2013;4(6):804–5.
Pastoris O, Savasta S, Foppa P, Catapano M, Dossena M, Ornella P. Pyruvate dehydrogenase deficiency in a child responsive to thiamine treatment. Acta Paediatr Int J Paediatr. 1996;85(5):625–8.
Naito E, Ito M, Yokota I, Saijo T, Matsuda J, Ogawa Y, et al. Thiamine-responsive pyruvate dehydrogenase deficiency in two patients caused by a point mutation (F205L and L216F) within the thiamine pyrophosphate binding region. Biochim Biophys Acta Mol Basis Dis. 2002;1588(1):79–84.
DeBrosse SD, Okajima K, Zhang S, Nakouzi G, Schmotzer CL, Lusk-Kopp M, et al. Spectrum of neurological and survival outcomes in pyruvate dehydrogenase complex (PDC) deficiency: Lack of correlation with genotype. Mol Genet Metab. 2012;107(3):394–402.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248–9.
Pavlu-Pereira H, Silva MJ, Tomé CS, Florindo C, Tavares de Almeida I, Leandro P, et al. Structural and functional impact of clinically relevant E1α variants causing pyruvate dehydrogenase complex deficiency. Submitted manuscript, under review 2020
Whitley MJ, Arjunan P, Nemeria NS, Korotchkina LG, Park Y-H, Patel MS, et al. Pyruvate dehydrogenase complex deficiency is linked to regulatory loop disorder in the αV138M variant of human pyruvate dehydrogenase. J Biol Chem. 2018;293(34):13204–13.
Szabo E, Wilk P, Nagy B, Zambo Z, Bui D, Weichsel A, et al. Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants. Hum Mol Genet. 2019;28:3339–54.
Ciara E, Rokicki D, Halat P, Karkucińska-Więckowska A, Piekutowska-Abramczuk D, Mayr J, et al. Difficulties in recognition of pyruvate dehydrogenase complex deficiency on the basis of clinical and biochemical features. The role of next-generation sequencing. Mol Genet Metab Rep. 2016;7:70–6.
Shin HK, Grahame G, McCandless SE, Kerr DS, Bedoyan JK. Enzymatic testing sensitivity, variability and practical diagnostic algorithm for pyruvate dehydrogenase complex (PDC) deficiency. Mol Genet Metab. 2017;122(3):61–6.
Barnerias C, Saudubray JM, Touati G, De Lonlay P, Dulac O, Ponsot G, et al. Pyruvate dehydrogenase complex deficiency: Four neurological phenotypes with differing pathogenesis. Dev Med Child Neurol. 2010;52(2):e1–9. https://doi.org/10.1111/j.1469-8749.2009.03541.x.
Quintana E, Gort L, Busquets C, Navarro-Sastre A, Lissens W, Moliner S, et al. Mutational study in the PDHA1 gene of 40 patients suspected of pyruvate dehydrogenase complex deficiency. Clin Genet. 2010;77(5):474–82. https://doi.org/10.1111/j.1399-0004.2009.01313.x.
Pinheiro A, Silva MJ, Pavlu-Pereira H, Florindo C, Barroso M, Marques B, et al. Complex genetic findings in a female patient with pyruvate dehydrogenase complex deficiency: null mutations in the PDHX gene associated with unusual expression of the testis-specific PDHA2 gene in her somatic cells. Gene. 2016;591(2):417–24.
Nogueira C, Silva L, Pereira C, Vieira L, Leão Teles E, Rodrigues E, et al. Targeted next generation sequencing identifies novel pathogenic variants and provides molecular diagnoses in a cohort of pediatric and adult patients with unexplained mitochondrial dysfunction. Mitochondrion. 2019;1(47):309–17.
Marsac C, Stansbie D, Bonne G, Cousin J, Jehenson P, Benelli C, et al. Defect in the lipoyl-bearing protein X subunit of the pyruvate dehydrogenase complex in two patients with encephalomyelopathy. J Pediatr. 1993;123(6):915–20.
Brown RM, Head RA, Morris AA, Raiman JJA, Walter JH, Whitehouse WP, , et al. Pyruvate dehydrogenase E3 binding protein (protein X) deficiency. Dev Med Child Neurol. 2007;48(9):756–60. https://doi.org/10.1111/j.1469-8749.2006.tb01362.x.
Byron O, Lindsay JG. The pyruvate dehydrogenase complex and related assemblies in health and disease. In: Harris J, Marles-Wright J, editors. Sub-cellular biochemistry. Berlin: Springer; 2017. https://doi.org/10.1007/978-3-319-46503-6_19.
Gray LR, Tompkins SC, Taylor EB. Regulation of pyruvate metabolism and human disease. Cell Mol Life Sci. 2014;71(14):2577–604.
Harris RA, Bowker-Kinley MM, Wu P, Jeng J, Popov KM. Dihydrolipoamide dehydrogenase-binding protein of the human pyruvate dehydrogenase complex. DNA-derived amino acid sequence, expression, and reconstitution of the pyruvate dehydrogenase complex. J Biol Chem. 1997;272(32):19746–51.
Vijayakrishnan S, Callow P, Nutley MA, McGow DP, Gilbert D, Kropholler P, et al. Variation in the organization and subunit composition of the mammalian pyruvate dehydrogenase complex E2/E3BP core assembly. Biochem J. 2011;437(3):565–74.
Prajapati S, Haselbach D, Wittig S, Patel MS, Chari A, Schmidt C, et al. Structural and functional analyses of the human PDH complex suggest a “division-of-labor” mechanism by local E1 and E3 clusters. Structure. 2019;27(7):1124-1136.e4.
Song J, Jordan F. Interchain acetyl transfer in the E2 component of bacterial pyruvate dehydrogenase suggests a model with different roles for each chain in a trimer of the homooligomeric component. Biochemistry. 2012;51(13):2795–803.
Vitkup D, Sander C, Church GM. The amino-acid mutational spectrum of human genetic disease. Genome Biol. 2003;4(11):R72.
Silva MJ, Pinheiro A, Eusébio F, Gaspar A, Tavares de Almeida I, Rivera I. Pyruvate dehydrogenase deficiency: identification of a novel mutation in the PDHA1 gene which responds to amino acid supplementation. Eur J Pediatr. 2009;168(1):17–22.
Arakawa T, Tsumoto K. The effects of arginine on refolding of aggregated proteins: not facilitate refolding, but suppress aggregation. Biochem Biophys Res Commun. 2003;304(1):148–52.
Tsumoto K, Umetsu M, Kumagai I, Ejima D, Philo JS, Arakawa T. Role of arginine in protein refolding, solubilization, and purification. Biotechnol Prog. 2004;20:1301–8. https://doi.org/10.1021/bp0498793.
Baynes BM, Wang DIC, Trout BL. Role of arginine in the stabilization of proteins against aggregation. Biochemistry. 2005;44(12):4919–25.
Clot JP, Benelli C, Fouque F, Bernard R, Durand D, Postel-Vinay MC. Pyruvate dehydrogenase activity is stimulated by growth hormone (GH) in human mononuclear cells: a new tool to measure GH responsiveness in man. J Clin Endocrinol Metab. 1992;74(6):1258–62. https://doi.org/10.1210/jcem.74.6.1592868.
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018;46(W1):W296-303.
We acknowledge Dra. Carla Conceição, from the Radiology Department of Hospital D. Estefânia, Lisboa, for her contribution with the NMR images.
This work was supported by Fundação para a Ciência e Tecnologia (strategic project UID/DTP/04138/2019 and grant SFRH/BD/91729/2012), by iNOVA4Health Research Unit (LISBOA-01-0145-FEDER-007344), which is cofunded by Fundação para a Ciência e Tecnologia/ Ministério da Ciência e do Ensino Superior, through national funds, and by FEDER under the PT2020 Partnership Agreement.
Ethical approval and consent to participate
All procedures were in accordance with the ethical standards of responsible committee on human experimentation, institutional and national, and with Principles of the Declaration of Helsinki. Informed consent was obtained from all patients or their parents/guardians.
Consent for publication
Consent was obtained from all patients for publication.
The Authors declare they have no conflict of interest.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
List of the analyzed PDC components showing the type of enzymatic activity, the Enzyme Commission (EC) number, the gene symbol, the HUGO identification, the reference sequences and the chromosomal localization (Table S1) and list of primers used in this study (Table S2).
About this article
Cite this article
Pavlu-Pereira, H., Silva, M.J., Florindo, C. et al. Pyruvate dehydrogenase complex deficiency: updating the clinical, metabolic and mutational landscapes in a cohort of Portuguese patients. Orphanet J Rare Dis 15, 298 (2020). https://doi.org/10.1186/s13023-020-01586-3
- Pyruvate dehydrogenase complex deficiency
- Neurological dysfunction
- Lactic acidosis
- Mutational analysis
- Genotype–phenotype correlation