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Article history: Thiamine pyrophosphokinase (TPK) produces thiamine pyrophosphate, a cofactor for a number of enzymes,
Received 28 June 2014 including pyruvate dehydrogenase and 2-ketoglutarate dehydrogenase. Episodic encephalopathy type thiamine
Received in revised form 15 September 2014 metabolism dysfunction (OMIM 614458) due to TPK1 mutations is a recently described rare disorder. The mech-
Accepted 15 September 2014
anism of the disease, its phenotype and treatment are not entirely clear.
Available online 5 October 2014
We present two patients with novel homozygous TPK1 mutations (Patient 1 with p.Ser160Leu and Patient 2 with
Keywords:
p.Asp222His). Unlike the previously described phenotype, Patient 2 presented with a Leigh syndrome like non-
Thiamine episodic early-onset global developmental delay, thus extending the phenotypic spectrum of the disorder. We,
TPK1 therefore, propose that TPK deficiency may be a better name for the condition. The two cases help to further
Thiamine pyrophosphokinase refine the neuroradiological features of TPK deficiency and show that MRI changes can be either fleeting or pro-
TPK deficiency gressive and can affect either white or gray matter. We also show that in some cases lactic acidosis can be absent
Episodic encephalopathy type thiamine and 2-ketoglutaric aciduria may be the only biochemical marker. Furthermore, we have established the assays for
metabolism dysfunction TPK enzyme activity measurement and thiamine pyrophosphate quantification in frozen muscle and blood.
These tests will help to diagnose or confirm the diagnosis of TPK deficiency in a clinical setting.
Early thiamine supplementation prevented encephalopathic episodes and improved developmental progression
of Patient 1, emphasizing the importance of early diagnosis and treatment of TPK deficiency. We present evidence
suggesting that thiamine supplementation may rescue TPK enzyme activity.
Lastly, in silico protein structural analysis shows that the p.Ser160Leu mutation is predicted to interfere with TPK
dimerization, which may be a novel mechanism for the disease.
© 2014 Elsevier Inc. All rights reserved.
1. Introduction
Abbreviations: ATP, adenosine triphosphate; MRI, magnetic resonance imaging;
THDM5, episodic encephalopathy type thiamine metabolism dysfunction; TPK, thiamine Thiamine pyrophosphokinase (TPK, EC 2.7.6.2.) transfers a pyro-
pyrophosphokinase; TPP, thiamine pyrophosphate.
⁎ Corresponding author at: Manchester Centre for Genomic Medicine, St Mary's
phosphate group from adenosine triphosphate (ATP) to thiamine to
Hospital, University of Manchester, Manchester M13 9WL, UK. produce its active form, thiamine pyrophosphate (TPP) in the cytosol
E-mail address: Siddharth.Banka@manchester.ac.uk (S. Banka). [1]. TPP is a cofactor for enzymes important in a range of fundamental
http://dx.doi.org/10.1016/j.ymgme.2014.09.010
1096-7192/© 2014 Elsevier Inc. All rights reserved.
302 S. Banka et al. / Molecular Genetics and Metabolism 113 (2014) 301–306
2. Case histories
Human wild type TPK1 was expressed from the vector PRSET-
hTPK1 in Escherichia coli as reported previously [4]. Mutant TPK1
was amplified from patient cDNA and PCR amplification with the
Fig. 1. Axial T2 brain magnetic resonance imaging. A) Hyper-intense signals in the dentate
forward primer 5′-cgggatccgATGGAGCATGCCTTTACC-3′ that con- nucleus (P1, first episode, 30 months). B) Resolution of the earlier changes (P1, second ep-
tains a BamHI site and the reverse primer 5′-gaagatctTTAGCTTTTG isode, 32 months). C and D) Pyramidal tract signal changes in the medulla and left dentate
ATGGCCATGG-3′ that contains a BglII site. The mutant TPK1 was nucleus (P1, third episode, 36 months). E and F) Delayed myelination and altered density
cloned into this vector by replacing the wild type sequence. The in the basal ganglia (P2, 16 months). G and H) Enlarged extra-axial CSF spaces suggesting
cortical atrophy (P2, 41 months).
final constructs were sequenced and the mutations, c.479CNT
(p.Ser160Leu, Patient 1) and c.664GNC (p.Asp222His, Patient 2)
were confirmed. and grown for 2 h. The cells were harvested by centrifugation, washed
once and resuspended in 20 ml lysis buffer/wash buffer (50 mmol/l
3.2. Expression and purification of TPK1 protein sodium phosphate, 300 mmol/l sodium chloride, 10 mmol/l imidazole,
pH 7.4). Cells were disrupted by sonication and crude protein extracts
The E. coli strain BL21(DE3)pLysS (Promega) was transformed with were obtained by collecting the supernatant after centrifugation for
either mutant or wild type TPK1 on pRSET B and grown on LB medium 5 min at 10,000 g. Sonication and all following steps were performed
containing 50 μl/ml chloramphenicol and 100 μl/ml ampicillin. For ex- under cooling with ice. Since the recombinant human TPK contains an
pression of the recombinant protein, 200 ml of this medium containing N-terminal His-tag we purified the crude extracts with HisPur cobalt
1 mmol/l isopropyl-β-D-thiogalactopyranoside (IPTG) was inoculated spin columns (1 ml columns, Pierce Biotechnology) according to the
with an overnight preculture at an optical density at 600 nm of 0.1 manufacturer's instructions. After washing with 50 resin volumes of
S. Banka et al. / Molecular Genetics and Metabolism 113 (2014) 301–306 303
buffer/wash buffer the His-tagged protein was eluted by 5 ml of addition of 5 μl of a freshly prepared solution of 10 mmol/l potassi-
50 mmol/l sodium phosphate, 300 mmol/l sodium chloride, and um ferricyanide in 15% NaOH.
150 mmol/l imidazole, pH 7.4. The buffer was replaced with
30 mmol/l NaCl and 30 mmol/l Tris, pH 7.5 followed by ultracentrifu-
gation in an Amicon Ultra-15 (Millipore) centrifugal filter unit with 4. Results
the molecular weight cut-off of 10 kDa.
TPK1 Sanger sequencing revealed novel homozygous c.479CNT
3.3. Measurement of TPK activity (p.Ser160Leu) and c.664GNC (p.Asp222His) mutations in P1 and P2
respectively (Fig. 2A). Both mutations affect highly conserved residues
The activity of TPK was determined in a mixture containing (Fig. S1). TPP levels were significantly decreased in patients' blood and
20 mmol/l Tris buffer (pH 7.5), 1 mmol/l ATP, 1 mmol/l MgCl2 and muscle samples (Table 1). Activities of the two recombinant mutant
variable concentrations of thiamin (10–1000 nmol/l). An equal TPK enzymes were significantly lower than that of the wild-type TPK
amount of either mutated or wild type recombinant purified TPK (Fig. 2B). Similar to what has been described previously [3] the immu-
(10 μl, approx. 10 ng) was added followed by incubation at 37 °C noblot analysis showed marked reduction in the level of the TPK protein
for 30 min. The reaction was stopped by adding 20 μl of 50% trichlo- in P2's muscle extract but, remarkably, not in P1's sample (Fig. 2C).
roacetic acid. Samples were then incubated on ice for 15 min and These results suggested that both the mutations were pathogenic and
centrifuged for 5 min at 10,000 g. The supernatants obtained after in contrast to the previously reported cases, loss of TPK activity in P1
centrifugation were transferred into new tubes, extracted twice is not due to lower enzyme levels but possibly another mechanism.
with 400 μl of water-saturated diethyl ether, centrifuged for 10 s at Inspection of the available human TPK1 structure (PDB code 3S4Y)
2500 g and finally incubated for 15 min at 37 °C to remove residual revealed that the p.Ser160Leu mutation likely disrupts the TPK dimer-
ether. The samples were centrifuged at 10,000 g for 5 min, and super- ization interface (Fig. 3A) thereby possibly affecting its enzyme activity.
natants were transferred into new tubes. Immediately prior to injec- Similar analysis for P2's mutation showed that the Asp222 residue is
tion into High-performance Liquid Chromatography (HPLC), 50 μl of close to the thiamine-binding domain at the C-terminus of the enzyme
the supernatants was derivatized to thiochrome products by the (Fig. 3B).
Fig. 2. Results of genetic and biochemical investigations. A) Sequencing chromatograms showing the homozygous c.479CNT mutation in P1 and c.664GNC in P2. B) TPK activity
analysis with recombinant TPK1 protein showing decreased enzyme activity for mutations seen in P1 and P2, most pronounced at lower thiamine concentrations. Polyacryl-
amide electrophoresis and staining with Coomassie brilliant blue showing the high purity of the purified recombinant proteins. C) Human TPK1 and GAPDH western blots in
muscle extracts showing no clear decrease of TPK levels in P1 when compared to controls (C1, C2, C3, C4). TPK levels are decreased in P2 and disease control (DC), a previously
published patient with p.[Arg60Lysfs*52] + [Asn219Ser] TPK1 mutations [3].
304 S. Banka et al. / Molecular Genetics and Metabolism 113 (2014) 301–306
Fig. 3. Results of protein structural analysis for p.Ser160Leu and p.Asp222His. A) Structure of human TPK1 showing: the dimerization interface highlighted in red box (left panel); OH-
group of Ser160A in one subunit (green) forming a H-bond with Phe132B amide nitrogen of the neighboring dimeric subunit (blue); the snugly packed interface between Ser160A
(shown in surface representation) and Phe132B, which will preclude the substitution of a large non-polar amino acid at the Ser160 site, due to steric clash and loss of the H-bond
(right panel). B) Asp222 is towards the C-terminus of the TPK1 enzyme (PDB code 3S4Y), shown as a dimer (subunits A in green and B in blue). The Asp222 residue (magenta spheres)
is located at a surface-exposed loop, ~3–5 aa downstream from a β-strand that contributes to part of the thiamine binding site (thiamine shown in black line). Asp222 appears to stabilize
the conformation of the loop, and its substitution to Histidine may disrupt this conformation.
S. Banka et al. / Molecular Genetics and Metabolism 113 (2014) 301–306 305
developmental delay, brain malformations, episodic encephalopathy specifically for abnormal 2-ketoglutaric acid excretion. The biochemical
associated with lactic acidosis and alpha-ketoglutaric aciduria [8]. The profiles of our patients suggest that in vivo TPK deficiency primarily af-
second phenotype associated with SLC25A19 mutations is bilateral fects the function of PDHC and 2-ketoglutarate dehydrogenase complex.
striatal degeneration and progressive polyneuropathy (OMIM 613710) Of note, PDHC activity was found to be normal in muscle biopsy from P2
that is characterized by childhood onset of episodic encephalopathy because excess TPP is added in the standard laboratory assay. We have
with febrile illnesses resulting in transient neurologic dysfunction and previously shown that TPP depletion does not affect the stability of
slowly progressive axonal polyneuropathy [9]. The most recently iden- PDHC and TPP-unstimulated:TPP-stimulated PDHC activity ratios are a
tified condition in this group is episodic encephalopathy type thiamine better in vitro marker for PDHC dysfunction in TPK deficiency [3]. This
metabolism dysfunction caused by TPK1 mutations [3]. Some patients assay was not performed in either of the cases described here as the di-
with PDHC deficiency (OMIM 312170) and maple syrup urine disease agnosis was confirmed by other means.
(OMIM 248600) (caused by mutations in genes encoding catalytic com- We have established the laboratory methods to facilitate the confir-
ponents of the branched-chain alpha-ketoacid dehydrogenase com- mation of TPK deficiency. TPK enzyme activity has never been previous-
plex) are thiamine responsive [2]. ly measured for human mutations. The technique described here
Only five patients from three families with TPK1 mutations have establishes an assay for testing the pathogenicity of novel TPK1 muta-
been previously described [3]. While this manuscript was being tions and can be utilized in clinical settings. We have shown reduced
reviewed, another sibling pair with a novel homozygous TPK1 muta- TPP levels in a frozen muscle biopsy sample from P1 and determined
tion, detected via whole exome sequencing, was reported [10]. Clini- the reference range for the assay, thus demonstrating that frozen mus-
cal, radiological and biochemical features of all 9 patients (including cle tissue can be used to measure TPP levels. It is especially important in
the two reported in this paper) are summarized in Table S3. Our re- clinical settings because fresh muscle tissue may not always be avail-
port expands the known phenotype of the condition. In P1 the early able. To the best of our knowledge, previous TPP levels have only ever
development was slower than his siblings, but overall unremarkable. been measured in fresh muscle samples. Notably, TPP levels in frozen
His neurological episodes were triggered by infectious illnesses muscle were approximately two-fold higher than those in muscle ho-
followed by slow and incomplete recovery leading to a step-wise mogenate prepared from fresh tissue [3]. Higher amounts of thiamine
deterioration and regression, which is similar to the previously de- species in frozen muscle could be due to freezing and thawing resulting
scribed patients. There is an interesting partial overlap of this presen- in disintegration of the cell membranes.
tation with what is encountered in biotin or thiamine responsive basal Thiamine supplementation prevented further episodes of enceph-
ganglia disease, bilateral striatal degeneration and progressive alopathy in P1. One of the previously described patients with TPK de-
polyneuropathy, maple syrup urine disease and in some patients ficiency attends normal school and has normal development [3].
with PDHC deficiency. However, careful review of biochemical and Hence, TPK deficiency can be added to the list of thiamine responsive
neuroradiological features may help to distinguish between these disorders [2] and potentially a treatable inborn error of metabolism
phenotypes. Presenting features of P2 show that TPK1 mutations [13]. Lack of response to thiamine in P2 emphasizes the importance
may also result in a non-episodic early-onset global developmental of early diagnosis and treatment for better outcome. However, larger
delay. The phenotype described by Fraser et al.[10] is similar to that long-term studies will be needed to determine if thiamine supple-
of P2. The current nomenclature of episodic encephalopathy type thi- mentation truly results in improvement of developmental progres-
amine metabolism dysfunction for the disease should be therefore, sion in TPK deficiency. Ketogenic diet is recommended in PDHC
reconsidered. We propose that ‘TPK deficiency’ is a more appropriate deficiency because it provides alternative sources of acetyl-CoA [5].
name. Interestingly, existence of two remarkably different pheno- In P2 ketogenic diet induced severe metabolic acidosis and resulted
types with mutations in SLC25A19 (congenital Amish microcephaly in an adverse outcome. The underlying mechanism for this response
and childhood onset encephalopathic disorder of bilateral striatal is unclear but metabolic acidosis is a known complication of ketogenic
degeneration and progressive polyneuropathy) is known. Similarly, diet [14]. Importantly, P2 did not receive thiamine supplementation
deficiency of PDHC, of which TPP is a cofactor, can present in either while on ketogenic diet (because the genetic diagnosis was not
chronic progressive or intermittent-relapsing forms [11]. known at the time of the start of dietary management). Of note, the
The signal changes seen in P1's left dentate nucleus during the first younger sibling described by Fraser et al. received ketogenic
presentation had completely resolved by the time of the second episode diet along with thiamine supplementation and was reported to
(Fig. 1). During the third episode changes were noticed in the pyramidal make some developmental progress. Based on our clinical experience,
tracts in the medulla and left dentate nucleus. In an appropriate clinical we recommend high dose thiamine supplementation as the mainstay
scenario, fleeting changes in the brain could be a clue to the diagnosis. of the treatment and to avoid use of ketogenic diet on its own.
A similar pattern has been described in PDHC [11]. This stresses the The p.Ser160Leu mutation reveals a possible novel disease mecha-
importance of performing and repeating neuroimaging during acute nism for TPK deficiency. In all previously described patients, the muta-
clinical episodes. Interestingly, the location of the signal changes tions resulted in a significant decrease in the amount of protein. In
seen in P1 matches the expression pattern of TPK in the rat brain contrast, in silico analysis suggests that the loss of the enzyme activity
[12]. P2's neuroimaging showed Leigh syndrome like altered basal in P1 could be due to impaired dimerization of TPK. This could not be ex-
ganglia density, delayed myelination and progressive cortical atrophy perimentally verified because of lack of a specific antibody suitable for
(Fig. 1). Similar features were seen in the two siblings described by non-denatured TPK protein. Additionally, it is important to note that
Fraser et al.[10]. Comparison of MRI images of our patients with we used an E. coli based system to express the mutant proteins. The sta-
those described previously [3] suggests that the neuroradiological bility of the protein may differ in human cells.
changes in TPK deficiency are variable and can be either fleeting or Remarkably, we found that in vitro TPK activity could be significant-
progressive and can affect either white or gray matter. ly rescued by increasing the concentration of thiamine (Fig. 2B) close to
Lactic acidosis was noted in P2 and has been seen in previously de- the serum level that can be reached by intensive supplementation with
scribed cases [3,10]. However, investigations in P1 show that the lactate thiamine (unpublished observation). Similar results were observed
levels in blood and cerebrospinal fluid, even during an episode, may not with P2's mutation. This may represent a common basis for the clinical
be reliable. 2-Ketoglutaric aciduria was observed in both patients de- response to thiamine in TPK deficiency.
scribed here. 2-Ketoglutaric aciduria was also described in the siblings In summary, we have reported novel clinical and biological insights
reported by Fraser et al. and in the younger patient the lactic acid levels into a rare disease. It is important for clinicians to be aware of this treat-
were only mildly elevated. 2-Ketoglutaric acid may, therefore, be a good able disorder and there is a need for more work to improve the under-
marker for the disease. Repeated analyses may be needed to check standing of TPK deficiency.
306 S. Banka et al. / Molecular Genetics and Metabolism 113 (2014) 301–306
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Conflicts of interest 431216.
[8] R.I. Kelley, D. Robinson, E.G. Puffenberger, K.A. Strauss, D.H. Morton, Amish lethal
microcephaly: a new metabolic disorder with severe congenital microcephaly and
None of the authors declare any conflicts of interest.
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10.1002/ajmg.10529.
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Centre. This work was supported by the Marie Curie Initial Training pyrophosphokinase deficiency causes a Leigh disease like phenotype in a sibling
Network MEET supported by the European Union (LM, HP, JAM) and pair: identification through whole exome sequencing and management strategies,
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the E-Rare project GENOMIT FWF I 920-B13 (VL, FAZ, RGF, WS). 12.007.
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