Spurious Elevation of Multiple Urine Amino Acids by Ion-Exchange Chromatography in Patients with Prolidase Deficiency

Prolidase deficiency: A novel PEPD missense variant in exon 2

Prolidase deficiency is an autosomal recessive disease that causes impaired collagen degradation. Altered collagen homeostasis results in the intracellular accumulation of imidodipeptides, which contain proline and hydroxyproline. The many clinical manifestations of prolidase deficiency include dysmorphic facial features, skeletal deformities, hepatosplenomegaly, necrotizing skin ulcers, and recurrent infections. Current clinical knowledge of this genetic disease relies upon few case reports due to its extreme rarity. Diagnosis is dependent on the detection of a pathologic gene variant. Additional diagnostic confirmation may be provided by urine amino acid quantification or reduced in vitro prolidase activity. We present a case of prolidase deficiency caused by a novel variant manifested by skeletal malformations and lifelong multisystemic infections. Genetic testing revealed a homozygous missense variant in the PEPD gene at nucleotide position 200, whereby adenine was replaced by guanine (c.200A > G). The corresponding amino acid change replaced glutamine with arginine at codon 67 (p.Gln67Arg). After boiling the urine sample for hydrolysis, quantitative urine amino acids demonstrated a markedly elevated proline level, confirming the diagnosis. We also provide a discussion of the pathophysiology, clinical manifestations, diagnostic testing, and clinical management of this disease.

Quantitative analysis of the natural history of prolidase deficiency: description of 17 families and systematic review of published cases

PURPOSE

Prolidase deficiency is a rare inborn error of metabolism causing ulcers and other skin disorders, splenomegaly, developmental delay, and recurrent infections. Most of the literature is constituted of isolated case reports. We aim to provide a quantitative description of the natural history of the condition by describing 19 affected individuals and reviewing the literature.

METHODS

Nineteen patients were phenotyped per local institutional procedures. A systematic review following PRISMA criteria identified 132 articles describing 161 patients. Main outcome analyses were performed for manifestation frequency, diagnostic delay, overall survival, symptom-free survival, and ulcer-free survival.

RESULTS

Our cohort presented a wide variability of severity. Autoimmune disorders were found in 6/19, including Crohn disease, systemic lupus erythematosus, and arthritis. Another immune finding was hemophagocytic lymphohistiocytosis (HLH). Half of published patients were symptomatic by age 4 and had a delayed diagnosis (mean delay 11.6 years). Ulcers were present initially in only 30% of cases, with a median age of onset at 12 years old.

CONCLUSION

Prolidase deficiency has a broad range of manifestations. Symptoms at onset may be nonspecific, likely contributing to the diagnostic delay. Testing for this disorder should be considered in any child with unexplained autoimmunity, lower extremity ulcers, splenomegaly, or HLH.

Structural analysis of new compound heterozygous variants in PEPD gene identified in a patient with Prolidase Deficiency diagnosed by exome sequencing

Prolidase Deficiency (PD) is an autosomal recessive rare disorder caused by loss or reduction of prolidase enzymatic activity due to variants in the PEPD gene. PD clinical features vary among affected individuals: skin ulcerations, recurrent infections, and developmental delay are common. In this study, we describe a 16-year-old boy with a mild PD phenotype comprising chronic eczema, recurrent infections and elevated IgE. Whole exome sequencing analysis revealed three PEPD variants: c.575T>C p.(Leu192Pro) inherited from the mother, and c.692_694del p.(Tyr231del) and c.1409G>A p.(Arg470His), both inherited from the father. The variant p.(Tyr231del) has been previously characterized by high-resolution X-ray structure analysis as altering protein dynamics/flexibility. In order to study the effects of the other two prolidase variants, we performed site directed mutagenesis purification and crystallization studies. A high-resolution X-ray structure could only be obtained for the p.(Arg470His) variant, which showed no significant structural differences in comparison to WT prolidase. On the other hand, the p.(Leu192Pro) variant led to significant protein destabilization. Hence, we conclude that the maternal p.(Leu192Pro) variant was likely causally associated with the proband´s disease, together with the known pathogenic paternal variant p.(Tyr231del). Our results demonstrated the utility of exome sequencing to perform diagnosis in PD cases with mild phenotype.

Clinical Genetics of Prolidase Deficiency: An Updated Review

Prolidase is a ubiquitous enzyme that plays a major role in the metabolism of proline-rich proteins. Prolidase deficiency is a rare autosomal recessive inborn metabolic and multisystemic disease, characterized by a protean association of symptoms, namely intellectual disability, recurrent infections, splenomegaly, skin lesions, auto-immune disorders and cytopenia. To our knowledge, no published review has assembled the different clinical data and research studies over prolidase deficiency. The aim of this study is to summarize the actual state of the art from the descriptions of all the patients with a molecular diagnosis of prolidase deficiency reported to date regarding the clinical, biological, histopathological features, therapeutic options and functional studies.

Prolidase deficiency diagnosed by whole exome sequencing in a child with pulmonary capillaritis

Diffuse alveolar haemorrhage (DAH) is rare in the paediatric population and the biological mechanisms remain poorly understood [1]. We retrospectively studied 12 children at our centre, identified from our pathology database, with idiopathic DAH between 2005–2017 who had undergone lung biopsy (SickKids ethics approval number: 1000029185). Two children in this cohort were offered clinical whole exome sequencing (WES) as an investigational diagnostic procedure based on a family history of lung disease. Both children who underwent WES, including the one presented here and one who we had previously reported [2], had single gene mutations that explained the pathogenesis of their pulmonary haemorrhage.

The case of a young boy with pulmonary haemorrhage who was ultimately diagnosed on whole exome sequencing with a rare condition called prolidase deficiency. This case demonstrates the utility of modern genomic testing in paediatric rare lung disease.http://ow.ly/rDGz30o8pcd

Aminoacidopathies: Prevalence, Etiology, Screening, and Treatment Options

Inborn errors of metabolism (IEMs) are a group of inherited metabolic disorders which are caused by mutations in the specific genes that lead to impaired proteins or enzymes production. Different metabolic pathways are perturbed due to the deficiency or lack of enzymes. To date, more than 500 IEMs have been reported with most of them being untreatable. However, fortunately 91 such disorders are potentially treatable, if diagnosed at an earlier stage of life. IEMs have been classified into different categories and one class of IEMs, characterized by the physiological disturbances of amino acids is called as aminoacidopathies. Out of 91 treatable IEM, thirteen disorders are amino acid related. Aminoacidopathies can be detected by chromatography and mass spectrometry based analytical techniques (e.g., HPLC, GC-MS, LC-MS/MS) for amino acid level changes, and through genetic assays (e.g., PCR, TaqMan Genotyping, DNA sequencing) at the mutation level in the corresponding genes. Hence, this review is focused to describe thirteen common aminoacidopathies namely: Phenylketonuria (PKU), Maple Syrup Urine Disease (MSUD), Homocystinuria/Methylene Tetrahydrofolate Reductase (MTHFR) deficiency, Tyrosinemia type II, Citrullinemia type I and type II, Argininosuccinic aciduria, Carbamoyl Phosphate Synthetase I (CPS) deficiency, Argininemia (arginase deficiency), Hyperornithinemia-Hyperammonemia-Homocitrullinuria (HHH) syndrome, N-Acetylglutamate Synthase (NAGS) deficiency, Ornithine Transcarbamylase (OTC) deficiency, and Pyruvate Dehydrogenase (PDH) complex deficiency. Furthermore, the etiology, prevalence and commonly used analytical techniques for screening of aminoacidopathies are briefly described. This information would be helpful to researchers and clinicians especially from developing countries to initiate newborn screening programs for aminoacidopathies.