Phenylketonuria: an update

Identification of deep intronic variants of PAH in phenylketonuria using full-length gene sequencing

BACKGROUND

Phenylketonuria (PKU) is an autosomal recessive congenital metabolic disorder caused by PAH variants. Previously, approximately 5% of PKU patients remained undiagnosed after Sanger sequencing and multiplex ligation-dependent probe amplification. To date, increasing numbers of pathogenic deep intronic variants have been reported in more than 100 disease-associated genes.

METHODS

In this study, we performed full-length sequencing of PAH to investigate the deep intronic variants in PAH of PKU patients without definite genetic diagnosis.

RESULTS

We identified five deep intronic variants (c.1199+502A>T, c.1065+241C>A, c.706+368T>C, c.706+531>C, and c.706+608A>C). Of these, the c.1199+502A>T variant was found at high frequency and may be a hotspot PAH variant in Chinese PKU. c.706+531T>C and c.706+608A>C are two novel variants that extend the deep intronic variant spectrum of PAH.

CONCLUSION

Deep intronic variant pathogenicity analysis can further improve the genetic diagnosis of PKU patients. In silico prediction and minigene analysis are powerful approaches for studying the functions and effects of deep intronic variants. Targeted sequencing after full-length gene amplification is an economical and effective tool for the detection of deep intron variation in genes with small fragments.

The spectrum of phenylalanine hydroxylase variants and genotype-phenotype correlation in phenylketonuria patients in Gansu, China

BACKGROUND

Phenylketonuria (PKU) is a common, congenital, autosomal recessive, metabolic disorder caused by Phenylalanine hydroxylase (PAH) variants.

METHODS

967 PKU patients from Gansu, China were genotyped by Sanger sequencing, multiplex ligation-dependent probe amplification, and whole exome sequencing. We analyzed the variants of PAH exons, their flanking sequences, and introns.

RESULTS

The detection of deep intronic variants in PAH gene can significantly improve the genetic diagnostic rate of PKU. The distribution of PAH variants among PKU subtypes may be related to the unique genetic background in Gansu, China.

CONCLUSION

The identification of PAH hotspot variants will aid the development of large-scale neonatal genetic screening for PKU. The five new PAH variants found in this study further expand the spectrum of PAH variants. Genotype-phenotype correlation analysis may help predict the prognosis of PKU patients and enable precise treatment regimens to be developed.

Identification of phenylketonuria patient genotypes using single-gene full-length sequencing

Background

Phenylketonuria (PKU) is a common, autosomal recessive inborn error of metabolism caused by PAH gene variants. After routine genetic analysis methods were applied, approximately 5% of PKU patients were still not diagnosed with a definite genotype.

Methods

In this study, for the first time, we identified PKU patients with unknown genotypes via single-gene full-length sequencing.

Results

The detection rate of PKU genotype increased from 94.6 to 99.4%, an increase of approximately 5%. The variants c.1199 + 502A > T and 1065 + 241C > A were found at a high frequency in Chinese PKU patients.

Conclusion

Our study suggest that single-gene full-length sequencing is a rapid, efficient and cost-effective tool to improve the genotype detection rate of PKU patients. Moreover, we provides additional case data to support pathogenicity of deep intronic variants in PAH.

Repeat-dose animal toxicity studies and genotoxicity study with deactivated alkaline serine protease (DASP), a protein low in phenylalanine (PHE)

Phenylketonuria (PKU) is an autosomal recessive inherited disorder affecting one in every 10,000 to 15,000 newborn children in the US each year. PKU patients' metabolism of an essential amino acid, phenylalanine (PHE), is impaired, resulting in concentrations of PHE in the circulating blood and brain that are potentially toxic. Individuals with PKU restrict dietary intakes of PHE by consuming medical foods formulated with low PHE concentrations. In this study, an alkaline serine protease (ASP) expressed in Bacillus licheniformis strain 2709, which is composed of >90% protein with a concentration of <0.25% PHE, was heat deactivated (becoming deactivated ASP (DASP)) and evaluated for safe use as an ingredient in foods, including medical foods. DASP was non-mutagenic with and without metabolic activation up to 5000 μg DASP/plate. 14-Day dietary studies supported a Maximum Tolerated Dose (MTD) of 115000 ppm DASP. In a 90-day dietary toxicity study, CRL SD CD® rats were administered 0, 28750, 57500, 115500 ppm DASP in the diet. No DASP-related adverse effects were observed at the high dose. As such, a No Observable Adverse Effect Level (NOAEL) of 115,500 ppm DASP or 6224.1 mg DASP/kg bw/day (males) and 7500.9 mg DASP/kg bw/day (females) was established.

Key Potentially Inappropriate Drugs in Pediatrics: The KIDs List

OBJECTIVES

The safe use of medications in pediatric patients requires practitioners to consider the unique pharmacokinetics and pharmacodynamics of drugs prescribed in this age group. In an effort to create a standard of care for the safe use of medications in this population, a list of drugs that are potentially inappropriate for use in pediatric patients has been developed and titled the "KIDs List."

METHODS

A panel of 7 pediatric pharmacists from the Pediatric Pharmacy Association were recruited to evaluate primary, secondary, and tertiary literature; FDA Pediatric Safety Communications; the Lexicomp electronic database; and product information for drugs that should be considered potentially inappropriate for use in pediatric patients. Information was rated using predefined criteria. A PubMed search was conducted using the following terms: adverse drug events OR adverse drug reactions. The search was limited to humans; age <18 years; case reports, observational studies, or clinical trials; and English language. No date range was used. Results were used to create an evidence-based list of candidate drugs that was then peer-reviewed and subjected to a 30-day public comment period prior to being finalized.

RESULTS

A PubMed search yielded 4049 unique titles, of which 210 were deemed relevant for full review. Practitioner recommendations highlighted an additional 77 drugs. FDA Pediatric Safety Communications and the Lexicomp database yielded 22 and 619 drugs, respectively. After critical analysis, peer review, and public review the final KIDs List contains 67 drugs and/or drug classes and 10 excipients.

CONCLUSIONS

This extensive effort led to compilation of the first list of drugs that are potentially inappropriate for prescribing in all or in a select subgroup of pediatric patients. If avoidance is not clinically possible, the drug should be used with caution and accompanied by appropriate monitoring.

Current Status and Future Prospects of Clinically Exploiting Cancer-specific Metabolism-Why Is Tumor Metabolism Not More Extensively Translated into Clinical Targets and Biomarkers?

Tumor cells exhibit a specialized metabolism supporting their superior ability for rapid proliferation, migration, and apoptotic evasion. It is reasonable to assume that the specific metabolic needs of the tumor cells can offer an array of therapeutic windows as pharmacological disturbance may derail the biochemical mechanisms necessary for maintaining the tumor characteristics, while being less important for normally proliferating cells. In addition, the specialized metabolism may leave a unique metabolic signature which could be used clinically for diagnostic or prognostic purposes. Quantitative global metabolic profiling (metabolomics) has evolved over the last two decades. However, despite the technology’s present ability to measure 1000s of endogenous metabolites in various clinical or biological specimens, there are essentially no examples of metabolomics investigations being translated into actual utility in the cancer clinic. This review investigates the current efforts of using metabolomics as a tool for translation of tumor metabolism into the clinic and further seeks to outline paths for increasing the momentum of using tumor metabolism as a biomarker and drug target opportunity.

Construction of different calibration models by FTIR/ATR spectra and their application in screening of phenylketonuria

OBJECTIVE

To construct different calibration models by using FTIR/ATR spectra and apply them for the screening of phenylketonuria for the newborns.

METHOD

69 dried blood spots samples were collected, of which the concentrations of phenylalanine (Phe) and tyrosine (Tyr) were determined by tandem mass spectrometry method. The FTIR/ATR method was used to collect the spectra of the samples. After various pretreatments with the original spectra, such as smoothing, derivative, vector normalization, Concave rubberband correction, the new spectra were fed into different methods to construct calibration models for the Phe concentrations of the samples. The kernel function, consensus strategy and their combination were integrated into the popular partial least squares method. The obtained models were then assessed by calculating coefficient of determination, root mean square error, mean relative error, etc.

RESULT

After a careful comparison, the cKPLS model performed the best, and the result yielded were much more accurate and stable.

CONCLUSION

The present cKPLS model, due to the combination of the kernel function and the consensus strategy, can be successfully applied to the prediction of Phe concentration for the phenylketonuria newborns. Also, we believe that the cKPLS method will be of help for FTIR/ATR spectra calibration problems in other complex systems.

Modeling correlates of low bone mineral density in patients with phenylalanine hydroxylase deficiency

Phenylalanine hydroxylase (PAH) deficiency is an inherited metabolic disorder requiring life-long restriction of dietary protein and phenylalanine-free medical food. Low bone mineral density (BMD) is reported, but factors associated with BMD Z-score (standard deviations from normal) are unknown. We examined associations between clinical and dietary parameters and total BMD Z-score in PAH deficiency patients, and developed models to predict Z-score. Data collected from patients >4 years of age (n = 88; mean age = 18.8 y; 61 % female) included demographic, clinical, laboratory, and dietary intakes. Adjusted Spearman's correlation coefficients were calculated between parameters and TBMD Z-score, measured by dual energy x-ray absorptiometry (DXA). Parameters approaching significance (p-value < 0.10) were candidate predictors for four linear regression models predicting TBMD Z-score. To validate, model-predicted Z-scores were compared to DXA Z-scores. Mean TBMD Z-score was -0.326; 18 (20.4 %) had Z-score < -1. Z-scores were positively correlated with dietary vitamin D, calcium, and medical food intake and compliance with prescription, and negatively with dietary carbohydrate, sugar, caffeine intake, glycemic load, and prescribed medical food (grams protein/day; p-value < 0.05). The best model included medical food compliance, medical food intake, caffeine intake, and bone-specific alkaline phosphatase (r-square = 0.364). This model predicted Z-score category [normal or low (<-1)] with sensitivity = 66.7 %, likelihood ratio = 14.7, and AUC = 0.83 compared to DXA Z-score. No subjects had low BMD for chronological age (Z-score ≤ -2). Compliance with medical food prescription was the strongest predictor of TBMD Z-score. One model, if validated in a separate sample of patients with more cases of low BMD, showed potential to estimate TBMD Z-score using routine clinical patient parameters.

Aspectos clínicos e demográficos da fenilcetonúria no Estado da Bahia

OBJETIVO: Descrever as características clínicas e demográficas dos pacientes com diagnóstico de hiperfenilalaninemia acompanhados no Serviço de Referência em Triagem Neonatal da Bahia. MÉTODOS: Estudo transversal de 99 famílias (111 afetados) com fenótipo bioquímico de hiperfenilalaninemia, com coleta de dados em prontuários e em banco de dados laboratorial, incluindo aspectos demográficos e clínicos. RESULTADOS: A incidência de hiperfenilalaninemia na Bahia foi de um caso a cada 16.334 nascidos vivos, com cobertura de 91%. Dentre os pacientes acompanhados, 82% foram diagnosticados pela triagem neonatal e, em 11 famílias, havia mais de um caso. O fenótipo clássico da fenilcetonúria foi diagnosticado em 63 (57%) pacientes. Entre os triados, a mediana de idade na primeira consulta foi 39,5 dias e, deles, 34% apresentavam sintomatologia nesse momento; nenhum com atraso no desenvolvimento neuropsicomotor. A consanguinidade foi descrita em 32% dos casos e houve predomínio de pacientes classificados como brancos (63%). Os pais tinham baixa escolaridade e baixa renda. Dos 417 municípios da Bahia, 15% apresentavam pelo menos um caso, com concentração na região nordeste (10%) e na capital do Estado (14%). CONCLUSÕES: Os resultados evidenciaram idade tardia ao início do tratamento, o que pode comprometer os resultados do programa. Observou-se também presença de consanguinidade e recorrência familiar, reforçando a importância da investigação familiar para diagnosticar indivíduos com deficiência mental de etiologia não esclarecida que podem se beneficiar de tratamento.

Causes of delay in referral of patients with phenylketonuria to a specialized reference centre in Mexico

Objective

To expose causes leading to the delayed arrival of phenylketonuria (PKU) patients at a governmental reference centre (RC), and to describe their clinical characteristics.

Material and methods

PKU files registered during the past 18 years at the National Institute of Pediatrics in Mexico City were evaluated. Patients were classified into two groups according to their age at arrival: Group I (early reference), patients arriving during the first month of life; and Group II (late reference), those who arrived after thirty days of age. Time and causes of delay were documented.

Results

Of 57 recorded files, 10 were classified in Group I and 47 in Group II. Causes leading to the late arrival of Group II patients were absence of routine newborn screening (NBS), PKU not included in the routine NBS, sampling after the recommended age, false negative result, results without interpretation and/or instructions to follow, delayed notification of results, poor medical criteria of attending physician, difficulties in obtaining confirmatory tests, and administrative failures.

Conclusion

The main cause of late referral of PKU patients was the absence of PKU testing. As a developing country, Mexico still faces challenges in the proper functioning and expansion of the NBS programme. Most PKU patients arrived at the RC late, presenting with varying degrees of the clinical spectrum. Incorporating PKU testing into the already established Mexican NBS system and adding quality indicators to guarantee proper operation in all NBS phases is necessary to achieve the goal of identifying, referring, diagnosing, and treating patients promptly.

Newborn screening for neuropathic lysosomal storage disorders

Interest in newborn screening (NBS) for lysosomal storage disorders (LSDs) has increased significantly due to newly developed enzyme replacement therapy (ERT), the need for early diagnosis, and advances in technical developments. Since the central nervous system cannot be treated by ERT, neuronopathic LSDs are generally not the primary target of NBS. An exception is Krabbe disease, in which hematopoietic stem cell transplantation before the onset of symptoms has benefits. However, NBS for LSD relies on measuring enzyme activities, so the most severely affected individuals (usually patients with neuronopathic subtypes) will be detected together with patients with less severe disease. In the near future, NBS is likely to be developed for diseases such as Gaucher, Niemann-Pick A/B, and certain mucopolysaccharidoses. The ability to predict phenotypes (neuronopathic or not) by enzyme activity and genotyping will therefore be critical for adequate patient management. This article reviews the status of LSD screening and issues concerning detection of neuronopathic LSDs by screening.

A case of maternal PKU syndrome despite intensive patient counseling

We report on a 21-year-old woman with classic phenylketonuria, who presented at our outpatient clinic at week 14 of pregnancy. Despite intensive preconceptional counselling about the risk of raised Phenylalanine (Phe) levels for the offspring and nutritional consultations about the necessity to be on a Phe-restricted diet she had elevated blood Phe concentrations. Phe level could be lowered to the recommended range during a stay as an inpatient, but the patient was not able to maintain the recommended levels due to non-compliance. The patient delivered a newborn with classic maternal PKU syndrome (microcephaly, brachygnathia, congenital heart defect and psychomotoric retardation), which is nowadays rarely seen under preconceptional Phe-restricted diet. With more PKU patients reaching the childbearing age, intensive preconception counselling about maternal PKU syndrome is of pivotal importance for the women. However, a major factor in preventing Phe embryopathy is patient compliance in keeping the diet, which was insufficient in the case presented.

Avaliação do Serviço de Referência em Triagem Neonatal para hipotireoidismo congênito e fenilcetonúria no Estado de Mato Grosso, Brasil

OBJETIVO: Avaliar o Serviço de Referência em Triagem Neonatal para hipotireoidismo congênito e fenilcetonúria no Estado de Mato Grosso. MÉTODOS: Estudo transversal, utilizando-se dados secundários dos exames realizados no período de janeiro de 2003 a dezembro de 2004. RESULTADOS: Foram feitos 66.337 testes de triagem com uma cobertura populacional inferior a 70%. A prevalência de fenilcetonúria foi de 1:33.068 nascidos vivos, e de hipotireoidismo congênito foi de 1:9.448 nascidos vivos. Apenas 22% das amostras foram coletadas na idade recomendada; a maioria realizou o teste de triagem entre 8 e 30 dias de vida. A mediana da idade na coleta do teste foi de 12 dias. Verificou-se que o serviço teve dificuldades na reconvocação dos casos suspeitos e dificuldades financeiras na obtenção dos insumos laboratoriais. CONCLUSÕES: A idade na coleta e o atraso na fase de confirmação diagnóstica foram os principais motivos para o atraso do início do tratamento dos casos detectados pelo serviço.

Use of Amniotic Membrane Graft and Corneal Transplantation in a Patient With Bilateral Keratomalacia Induced by Uncontrolled Phenylketonuria

PURPOSE

To report a patient with a rare complication of bilateral keratomalacia induced by uncontrolled phenylketonuria (PKU) that was successfully treated with amniotic membrane transplantation in 1 eye and penetrating keratoplasty in the second eye.

METHODS

Case report and literature review.

RESULTS

A 9-month-old girl with uncontrolled PKU was referred to our clinic because of bilateral keratomalacia. Slit-lamp examination of the right eye revealed 2 large corneal erosions with stromal thinning on the nasal and inferior regions of the right cornea. Left eye examination revealed a large area of melting involving two thirds of the cornea with corneal perforation and iris bulging on the temporal side and no anterior chamber. She underwent amniotic membrane transplantation on her right cornea and penetrating keratoplasty on her left cornea. Treatment after surgery included antibiotic and steroid eye drops and a special diet regimen with partial phenylalanine intake. Examination under anesthesia 4 months after surgery revealed intact cornea in her right eye and a clear corneal graft with a deep anterior chamber on her left eye. Intraocular pressure was normal in both eyes.

CONCLUSIONS

Bilateral keratomalacia, although a rare ophthalmic manifestation of PKU, can cause a severe corneal injury that may threaten the eyeball integrity. Surgical treatments with amniotic membrane graft and corneal transplantation, along with the appropriate diet treatment, were found to be effective procedures, yielding rapid healing of the corneal surface.

[Mass neonatal screening using biological testing]

Implementation of a generalized screening program for neonatal diseases obeys precise guidelines. The disease must be severe, recognizable at an early stage, accessible to an effective treatment, detected with a non expansive and widely applicable test and it must represent an important health problem. In case of positive results, treatment or prevention shall be offered immediately and any screening program has to be regularly evaluated. There is in France since 1978 a national screening program that depends on a private association ("Association française pour le dépistage et la prévention des handicaps de l'enfant") and is supervised by the "Caisse nationale d'assurance maladie" and the "Direction Générale de la Sante". Presently, five diseases are included in the screening program: phenylketonuria, hypothyroidism, congenital adrenal hyperplasia, cystic fibrosis and sickle cell disease, the latter only in at risk newborns. Toxoplasmosis represents a particular problem because screening takes place only in children of mothers that have not been controlled during their pregnancy or in case of seroconversion. Neonatal screening of phenylketonuria and hypothyrodism is unanimously recommended. That of congenital adrenal hyperplasia is approved in most countries. The cases of sickle cell disease and cystic fibrosis are more complex because: 1) all the children that carry the mutations are not affected with a severe disease; 2) there is no curative treatment; 3) parents given information are made anxious, sometimes wrongly if the disease is mild or asymptomatic. The supporters of the screening insist on the interest of an early diagnosis which makes longer the life time of these children, the possibility for the parents to utilize prenatal screening in case of a future pregnancy, and the information given to the heterozygous carriers following a familial screening. The question is raised of the extension of neonatal screening to other diseases. This is now possible due to technical progresses such as the tandem mass spectrometry that can detect about 50 diseases in an only testing. In addition of its cost and of the difficulty to ensure an efficient organization, increasing the number of the screened diseases will raise ethical problems including how the parents will be informed of an incurable disease or a late-onset disease or an entirely asymptomatic disease. It is unanimously admitted that only mendelian diseases should be detected excluding genetic polymorphisms. Analysis of the present situation suggests the following developments: 1) to actualize the guidelines for deciding of a new neonatal screening; 2) to experiment on a local scale any new screening before its extension to the whole country; 3) to create an evaluation committee including paediatricians and epidemiologists and to evaluate on the long term the future of the children; 4) to precisely define the conditions in which the heterozygous carriers will be informed following a familial investigation; 5) to store in a resource biological centre the blood samples in order to utilize this bank for epidemiology studies.

Aspectos clínicos da fenilcetonúria em serviço de referência em triagem neonatal da Bahia

OBJETIVOS: descrever as características clínicas dos pacientes com hiperfenilalaninemia acompanhados no Serviço de Referência em Triagem Neonatal (SRTN) do estado da Bahia. MÉTODOS: estudo descritivo transversal, tendo como amostra todos os pacientes com diagnóstico conhecido de Hiperfenilalaninemia residentes no estado da Bahia e acompanhados no SRTN até setembro de 2005. Tal população é composta de 46 famílias, num total de 51 pacientes. A análise dos dados foi descritiva, incluindo medidas de tendência central e dispersão. RESULTADOS: houve discreto predomínio do gênero feminino (52,9%). A maioria dos pacientes (78,4%) teve seu diagnóstico estabelecido através da triagem neonatal, tendo, portanto, tratamento precoce. Consangüinidade foi registrada em 32,6% das famílias. A média de início do tratamento entre os pacientes diagnosticados pela triagem neonatal foi de 56,6 37,8 dias, enquanto que entre os pacientes com diagnóstico tardio, foi de 7,1 anos. CONCLUSÕES: o estudo descreve um grupo de pacientes representativo de uma patologia incluída no Programa Nacional de Triagem Neonatal (PNTN), sendo, portanto, de relevância para a saúde pública. Entre os dados clínicos, chama a atenção a média de idade do início do tratamento, superior ao recomendado na literatura, alertando para a necessidade de um maior enfoque no diagnóstico precoce.

SINGLE NUCLEOTIDE POLYMORPHISMS THAT INFLUENCE LIPID METABOLISM: Interaction with Dietary Factors

Cardiovascular disease (CVD) risk is the result of complex interactions between genetic and environmental factors. During the past few decades, much attention has focused on plasma lipoproteins as CVD risk factors. The current evidence supports the concept that gene-environment interactions modulate plasma lipid concentrations and potentially CVD risk. The findings from studies examining gene-diet interactions and lipid metabolism have been highly promising. Several loci (i.e., APOA1, APOA4, APOE, and LIPC) are providing proof-of-concept for the potential application of genetics in the context of personalized nutritional recommendations for CVD prevention. However, the incorporation of these findings to the clinical environment is not ready for prime time. There is a compelling need for replication using a higher level of scientific evidence. Moreover, we need to evolve from the simple scenarios examined nowadays (i.e., one single dietary component, single nucleotide polymorphism, and risk factor) to more realistic situations involving interactions between multiple genes, dietary components, and risk factors. In summary, there is need for both large population studies and well-standardized intervention studies.

Nutritional genomics

Nutritional genomics has tremendous potential to change the future of dietary guidelines and personal recommendations. Nutrigenetics will provide the basis for personalized dietary recommendations based on the individual's genetic make up. This approach has been used for decades for certain monogenic diseases; however, the challenge is to implement a similar concept for common multifactorial disorders and to develop tools to detect genetic predisposition and to prevent common disorders decades before their manifestation. The preliminary results involving gene-diet interactions for cardiovascular diseases and cancer are promising, but mostly inconclusive. Success in this area will require the integration of different disciplines and investigators working on large population studies designed to adequately investigate gene-environment interactions. Despite the current difficulties, preliminary evidence strongly suggests that the concept should work and that we will be able to harness the information contained in our genomes to achieve successful aging using behavioral changes; nutrition will be the cornerstone of this endeavor.