Journal of Clinical Medicine Case Report Utility of Whole Blood Thiamine Pyrophosphate Evaluation in TPK1-Related Diseases Enrico Bugiardini 1,2 , Simon Pope 3, René G. Feichtinger 4 , Olivia V. Poole 1,2, Alan M. Pittman 2, Cathy E. Woodward 5, Simon Heales 3, Rosaline Quinlivan 1,2,6, Henry Houlden 1,2, Johannes A. Mayr 4, Michael G. Hanna 1,2 and Robert D.S. Pitceathly 1,2,* 1 MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK 2 Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK 3 Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK 4 Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University,5020 Salzburg, Austria 5 Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK 6 Dubowitz Neuromuscular Centre, Great Ormond Street Hospital, London WC1N 3JH, UK * Correspondence: [email protected]; Tel.: +44-(0)2031087527 Received: 30 May 2019; Accepted: 3 July 2019; Published: 8 July 2019 Abstract: TPK1 mutations are a rare, but potentially treatable, cause of thiamine deficiency. Diagnosis is challenging given the phenotypic overlap that exists with other metabolic and neurological disorders. We report a case of TPK1-related disease presenting with Leigh-like syndrome and review the diagnostic utility of thiamine pyrophosphate (TPP) blood measurement. The proband, a 35-year-old male, presented at four months of age with recurrent episodes of post-infectious encephalopathy. He subsequently developed epilepsy, learning difficulties, sensorineural hearing loss, spasticity, and dysphagia. There was a positive family history for Leigh syndrome in an older brother. Plasma lactate was elevated (3.51 mmol/L) and brain MRI showed bilateral basal ganglia hyperintensities, indicative of Leigh syndrome. Histochemical and spectrophotometric analysis of mitochondrial respiratory chain complexes I, II+III, and IV was normal. Genetic analysis of muscle mitochondrial DNA was negative. Whole exome sequencing of the proband confirmed compound heterozygous variants in TPK1: c. 426G>C (p. Leu142Phe) and c. 258+1G>A (p.?). Blood TPP levels were reduced, providing functional evidence for the deleterious effects of the variants. We highlight the clinical and bioinformatics challenges to diagnosing rare genetic disorders and the continued utility of biochemical analyses, despite major advances in DNA sequencing technology, when investigating novel, potentially disease-causing, genetic variants. Blood TPP measurement represents a fast and cost-effective diagnostic tool in TPK1-related diseases. Keywords: mitochondrial diseases; TPK1; thiamine pyrophosphate; Leigh syndrome; thiamine deficiency 1. Introduction Genetic disorders of thiamine transport and metabolism are a rare but treatable cause of thiamine deficiency that usually present during childhood [1]. Four genetic defects are reported; three present with a predominantly neurological phenotype (SLC19A3, SLC25A19 and TPK1) and one with multisystem disease (SLC19A2), including megaloblastic anaemia, thrombocytopenia, diabetes, and hearing loss. Thiamine pyrophosphokinase 1 (hTPK1, EC2.7.6.2), encoded by TPK1, converts free thiamine to active thiamine pyrophosphate (TPP). Early recognition is therefore crucial given the potential benefits of thiamine supplementation. However, diagnosis of TPK1-related diseases is often J. Clin. Med. 2019, 8, 991; doi:10.3390/jcm8070991 www.mdpi.com/journal/jcm J.J. Clin.Clin. Med. 2019,, 8,, 991x FOR PEER REVIEW 22 of 99 delayed because of the clinical overlap with other metabolic diseases, including Leigh syndrome. delayedConsequently, because patients of the often clinical undergo overlap numerous with other investigations, metabolic diseases, including including muscle and Leigh skin syndrome. biopsies, Consequently,prior to receiving patients a molecular often undergo diagnosis. numerous Here, investigations,we describe a including case of TPK1 muscle-related and skin disease biopsies, that priorhighlights to receiving the potential a molecular applications diagnosis. of whole Here, blood we TPP describe measurement a case offorTPK1 diagnosis-related and disease subsequent that highlightsbiochemical the monitoring potential applications following thiamine of whole supplementation. blood TPP measurement for diagnosis and subsequent biochemical monitoring following thiamine supplementation. 2. Case Presentation 2. Case Presentation The proband, the fourth child of healthy unrelated parents, was an uncomplicated pregnancy and Thedelivery proband, and thereached fourth all child early of healthymotor mileston unrelatedes parents,without was delays. an uncomplicated An older brother pregnancy had been and deliverydiagnosed and with reached Leigh all syndrome early motor in milestonesthe early childh withoutood, delays. while Antwo older older brother siblings had were been healthy. diagnosed He withpresented Leigh with syndrome a post-viral in the encephalopathy early childhood, aged while four two months older siblings following were varicella-zoster healthy. He presented infection withand at a post-viralnine months encephalopathy sensorineural agedhearing four loss months was detected. following He varicella-zoster subsequently experienced infection and recurrent at nine monthsepisodes sensorineural of encephalopathy hearing associated loss was detected.with interc Heurrent subsequently infection experiencedand was diagnosed recurrent with episodes learning of encephalopathydifficulties and seizures. associated At with 22 ye intercurrentars he was infectionevaluated and in wasa specialist diagnosed mitochondrial with learning clinic. diffi Atculties this andtime, seizures. he required At 22 yearsfulltime he wasuse evaluatedof a wheelchair in a specialist and, despite mitochondrial improved clinic. seizure At this control time, he with required dual fulltimeanticonvulsant use of atherapy, wheelchair continued and, despite to experience improved seizure daily controlepisodes with of dualfocal anticonvulsant impaired awareness. therapy, continuedNeurological to examination experience daily revealed episodes optic disc of focal atroph impairedy and sensorineural awareness. hearing Neurological loss. In examination limbs, there revealedwas a spastic optic increase disc atrophy in tone, and hyper-reflexia, sensorineural and hearing bilateral loss. extensor In limbs, plantar there wasresponses. a spastic Laboratory increase intests, tone, including hyper-reflexia, CPK, fasting and bilateral acylcarnitine extensor profile, plantar and responses. very long Laboratory chain fatty tests, acids, including were normal. CPK, fastingPlasma acylcarnitinelactate was elevated profile, (3.51 and verymmol/L, long reference chain fatty range acids, 0.5–2.22 were mmol/L). normal. PlasmaBrain MRI lactate revealed was elevatedbilateral, (3.51symmetrical mmol/L, T2 reference hyperintensities range 0.5–2.22 in the mmol corpus/L). striatum Brain MRI and revealed severe bilateral,cerebellar symmetrical and moderate T2 hyperintensitiesbrainstem volume in loss, the corpus without striatum signal abnormalities and severe cerebellar (Figure and1). The moderate cervical brainstem spinal cord volume displayed loss, withoutnormal signalimaging abnormalities appearances. (Figure 1). The cervical spinal cord displayed normal imaging appearances. Figure 1. Brain MRI. (A) Axial image demonstrates bilateral, symmetrical T2-weighted high signal intensitiesFigure 1. Brain within MRI. the corpus(A) Axial striatum image (arrows). demonstrates (B) Sagittal bilateral, image symmetrical shows cerebellar T2-weighted atrophy high (asterisk). signal intensities within the corpus striatum (arrows). (B) Sagittal image shows cerebellar atrophy (asterisk). Pyruvate dehydrogenase complex (PDC) activity in cultured fibroblasts, and histological, histochemical,Pyruvate dehydrogenase and mitochondrial complex respiratory (PDC) chainactivity enzyme in cultured analyses fibroblasts, of skeletal and muscle histological, tissue, washistochemical, normal. Sanger and mitochondrial sequencing ofrespiratory the entire chain mitochondrial enzyme analyses genome of andskeletal molecular muscle analysis tissue, was for largenormal. scale Sanger mitochondrial sequencing DNA of the rearrangements entire mitochondr usingial longgenome range and PCR molecular were negative. analysis Wholefor large exome scale sequencingmitochondrial was DNA performed rearrangements using the using proband’s long genomicrange PCR DNA were extracted negative. from Whole peripheral exome sequencing leukocytes (AppendixA). Variants with a minor allele frequency (MAF) of 0.01 reported in gnomAD [2] and was performed using the proband’s genomic DNA extracted from≥ peripheral leukocytes (Appendix 1000A). Variants Genomes with databases, a minor andallele synonymous frequency (MAF) and deep of ≥0.01 intronic reported variants, in gnomAD were excluded. [2] and 1000 Recessive Genomes and X-linkeddatabases, inheritance and synonymous patterns were and prioritiseddeep intronic (Supplementary variants, were Figure excluded. S1). First, Recessive a list of genes and encodingX-linked mitochondrial-localizedinheritance patterns were proteins prioritised (n = 1158, (Supplementary Mitocarta) [3] was Figure analysed. S1). First, A variant a list in ofNDUFA1 genes (c.94Gencoding>C; p.Gly32Arg),mitochondrial-localized previously proteins