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This article discusses the challenges and solutions discovered for implementing the Memento protocol in a variety of browser environments. It describes the design and deployment of the client technologies which have been developed: a web application that functioned as a browser, an add-on for FireFox called MementoFox, a plugin for Internet Explorer and an Android-based client application. The design and technical solutions identified during the development will be of interest to those considering implementation of a Memento based platform, especially on the client side, however the interactions are also important for building conformant server-side systems.

Infantile neuronal ceroid lipofuscinosis (CLN1 Batten Disease) is a devastating pediatric lysosomal storage disease caused by pathogenic variants in the CLN1 gene, which encodes the depalmitoylation enzyme, palmitoyl-protein thioesterase 1 (PPT1). CLN1 patients present with visual deterioration, psychomotor dysfunction, and recurrent seizures until neurodegeneration results in death, typically before fifteen years of age. Histopathological features of CLN1 include aggregation of lysosomal autofluorescent storage material (AFSM), as well as profound gliosis. The current management of CLN1 is relegated to palliative care. Here, we examine the therapeutic potential of a small molecule PPT1 mimetic, N-tert-butyl hydroxylamine (NtBuHA), in a Cln1 -/- mouse model. Treatment with NtBuHA reduced AFSM accumulation both in vitro and in vivo. Importantly, NtBuHA treatment in Cln1 -/- mice reduced neuroinflammation, mitigated epileptic episodes, and normalized motor function. Live cell imaging of Cln1 -/- primary cortical neurons treated with NtBuHA partially rescued aberrant synaptic calcium dynamics, suggesting a potential mechanism contributing to the therapeutic effects of NtBuHA in vivo. Taken together, our findings provide supporting evidence for NtBuHA as a potential treatment for CLN1 Batten Disease., Competing Interests: Declaration of competing interest AIS and DW have stock in Circumvent. NAN, CH, PR and RJ all receive compensation for their time and expertise from Circumvent., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Purpose: Sequencing-based genetic testing often identifies variants of uncertain significance (VUS) or fails to detect pathogenic variants altogether. We evaluated the utility of RNA sequencing (RNA-seq) to clarify VUS or identify missing variants in a clinical setting., Methods: Over a 2-year period, genetics providers at a single institution referred 26 cases for clinical RNA-seq. Cases had either no candidate variant identified by prior testing or a VUS suspected to impact splicing or expression. A committee reviewed each submission to ensure it met study criteria., Results: Among 26 cases, 8 could not be sequenced because of poor expression in an accessible tissue, 2 did not meet inclusion criteria, 3 were solved prior to collection, and 4 families declined participation or did not complete sample collection. For the 9 cases sequenced, the clinical laboratory reported two positive, four negative, and three "indeterminate." For all three indeterminate cases, original RNA-seq data was manually evaluated and deemed explanatory., Conclusion: Clinical RNA-seq can clarify VUS, especially splice variants, but laboratory-specific interpretation guidelines may lead to indeterminate results. Identifying individuals likely to benefit from RNA-seq and providing appropriate counseling poses unique challenges., Competing Interests: DEM holds stock options in MyOme, is on a scientific advisory board at Oxford Nanopore Technologies (ONT), is engaged in a research agreement with ONT, and has received travel support from ONT.

Purpose: Current newborn screening programs for Pompe disease (PD) and mucopolysaccharidosis type I (MPS I) suffer from a high false positive rate and long turnaround time for clinical follow up. This study aimed to develop a novel proteomics-based assay for rapid and accurate second-tier screening of PD and MPS I. A fast turnaround assay would enable the identification of severe cases who need immediate clinical follow up and treatment., Methods: We developed an immunocapture coupled with mass spectrometry-based proteomics (Immuno-SRM) assay to quantify GAA and IDUA proteins in dried blood spots (DBS) and buccal swabs. Sensitivity, linearity, reproducibility, and protein concentration range in healthy control samples were determined. Clinical performance was evaluated in known PD and MPS I patients as well as pseudodeficiency and carrier cases., Results: Using three 3.2 mm punches (~13.1 μL of blood) of DBS, the assay showed reproducible and sensitive quantification of GAA and IDUA. Both proteins can also be quantified in buccal swabs with high reproducibility and sensitivity. Infantile onset Pompe disease (IOPD) and severe MPS I cases are readily identifiable due to the absence of GAA and IDUA, respectively. In addition, late onset Pompe disease (LOPD) and attenuated MPS I patients showed much reduced levels of the target protein. By contrast, pseudodeficiency and carrier cases exhibited significant higher target protein levels compared to true patients., Conclusion: Direct quantification of endogenous GAA and IDUA peptides in DBS by Immuno-SRM can be used for second-tier screening to rapidly identify severe PD and MPS I patients with a turnaround time of <1 week. Such patients could benefit from immediate clinical follow up and possibly earlier treatment., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Abnormal accumulation of very-long-chain fatty acids (VLCFAs), defined as molecules with greater than 22 carbons, and branched-chain fatty acids, pristanic and phytanic acids, is characteristic of inborn errors of peroxisomal biogenesis or function. X-linked adrenoleukodystrophy, Zellweger spectrum disorders, rhizomelic chondrodysplasia punctata, and Refsum syndrome can be diagnosed biochemically by quantitation of these metabolites in plasma. Ratios of C24/C22 and C26/C22 can help improve detection of X-linked adrenoleukodystrophy. Analysis using gas-chromatography mass spectrometry (GC/MS) after acid/base hydrolysis, organic solvent extraction, and derivatization is an established method for clinical diagnostics. This chapter describes detailed steps to process plasma samples for GC/MS analysis., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: The metabolic demands associated with critical illness place patients at risk for nutrition deficits. Carnitine is a small molecule essential for fatty acid oxidation and gluconeogenesis. Secondary carnitine deficiency can have clinically significant complications and has been observed anecdotally in patients receiving extracorporeal membrane oxygenation (ECMO) therapy at our institution. Guidelines for monitoring and supplementing carnitine are lacking. This retrospective study determined whether critically ill pediatric patients receiving ECMO have an increased risk of carnitine deficiency., Methods: Acylcarnitine analysis was performed on residual specimens from patients who received ECMO therapy. The control data were a convenience sample gathered by chart review of patients who had been tested for carnitine during a hospitalization., Results: Acylcarnitines were measured in 217 non-ECMO patients and 81 ECMO patients. Carnitine deficiency, based on age-specific reference ranges, was observed in 41% of ECMO cases compared with 21% of non-ECMO cases. Multivariable analysis of age-matched patients identified that the odds of carnitine deficiency were significantly lower among patients on the floor compared with ECMO patients (odds ratio, 0.21; 95% CI, 0.10-0.44). Age-specific frequency of qualitative carnitine deficiency ranged from 15% (patients >5 years old) to 56% (patients 1 week to 1 month old) in ECMO patients and 15% (patients >5 years old) to 34% (patients 1-5 years old) in non-ECMO patients., Conclusion: In this study, ECMO patients were carnitine deficient more frequently compared with other inpatients, with the highest rates of deficiency among ECMO patients between 1 week and 1 month old., (© 2021 The Authors. Journal of Parenteral and Enteral Nutrition published by Wiley Periodicals LLC on behalf of American Society for Parenteral and Enteral Nutrition.)

Importance: Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by age of symptom onset less than 25 years and a variable presentation., Objective: To identify the genetic variants associated with juvenile ALS., Design, Setting, and Participants: In this multicenter family-based genetic study, trio whole-exome sequencing was performed to identify the disease-associated gene in a case series of unrelated patients diagnosed with juvenile ALS and severe growth retardation. The patients and their family members were enrolled at academic hospitals and a government research facility between March 1, 2016, and March 13, 2020, and were observed until October 1, 2020. Whole-exome sequencing was also performed in a series of patients with juvenile ALS. A total of 66 patients with juvenile ALS and 6258 adult patients with ALS participated in the study. Patients were selected for the study based on their diagnosis, and all eligible participants were enrolled in the study. None of the participants had a family history of neurological disorders, suggesting de novo variants as the underlying genetic mechanism., Main Outcomes and Measures: De novo variants present only in the index case and not in unaffected family members., Results: Trio whole-exome sequencing was performed in 3 patients diagnosed with juvenile ALS and their parents. An additional 63 patients with juvenile ALS and 6258 adult patients with ALS were subsequently screened for variants in the SPTLC1 gene. De novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient) were identified in 3 unrelated patients diagnosed with juvenile ALS and failure to thrive. A fourth variant (p.Leu39del) was identified in a patient with juvenile ALS where parental DNA was unavailable. Variants in this gene have been previously shown to be associated with autosomal-dominant hereditary sensory autonomic neuropathy, type 1A, by disrupting an essential enzyme complex in the sphingolipid synthesis pathway., Conclusions and Relevance: These data broaden the phenotype associated with SPTLC1 and suggest that patients presenting with juvenile ALS should be screened for variants in this gene.

Background: Deficiency of galactosylcerebrosidase (GALC) causes Krabbe disease. Historically, a diagnosis is made by measuring GALC enzymatic activity with a radioisotope assay. To improve the workflow and performance, we developed and clinically validated a leukocyte enzymatic assay using liquid chromatography tandem mass spectrometry (LC-MS/MS)., Materials: Extracted cell lysates were quantified and incubated with commercially available multiplexed substrates and internal standards. Liquid-liquid extraction was performed, and pre-analytical and analytical variability were evaluated and validated following clinical laboratory regulation guidelines., Results: Enzymatic reaction products were resolved from substrate breakdown products by a 3.5-minute column separation. Intra- and inter- assay imprecision were less than 15%. No matrix effects or carryover were observed. ACD anticoagulant tubes provide the best sample stability. Detection of product was linear with an R 2 of 0.99. Small differences in GALC activity were measurable near the anticipated disease range. Confirmed cases of Krabbe disease were well differentiated from carriers and non-Krabbe individuals (normal reference range)., Conclusion: An LC-MS/MS assay was developed, which can measure trace residual GALC activity in leukocytes and aid in the diagnosis of Krabbe disease. The multiplexed mixture allows for built-in sample quality control and enables a streamlined workflow for evaluation of multiple lysosomal storage diseases., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Background: Glutaric acidemia type I (GA1) is an organic acidemia that is often unrecognized in the newborn period until patients suffer an acute encephalopathic crisis, which can be mistaken for nonaccidental trauma. Presymptomatic identification of GA1 patients is possible by newborn screening (NBS). However, the biochemical "low-excretor" (LE) phenotype with nearly normal levels of disease metabolites can be overlooked, which may result in untreated disease and irreversible neurological sequelae. The LE phenotype is also a potential source of false negative (FN) NBS results that merits further investigation., Methods: Samples from six LE GA1 patients were analyzed by biochemical and molecular methods and newborn screen outcomes were retrospectively investigated., Results: Five LE GA1 patients were identified that had normal NBS results and three of these presented clinically with GA1 symptoms. One additional symptomatic patient was identified who did not undergo screening. Semiquantitative urine organic acid analysis was consistent with a GA1 diagnosis in two (33%) of the six patients, while plasma glutarylcarnitine was elevated in four (67%) of the six and urine glutarylcarnitine was elevated in four (80%) of five patients. Five GCDH variants were identified in these patients; three of which have not been previously linked to the biochemical LE phenotype., Conclusions: The data presented here raise awareness of potential FN NBS results for LE GA1 patients. The LE phenotype is not protective against adverse clinical outcomes, and the possibility of FN NBS results calls for high vigilance amongst clinicians, even in the setting of a normal NBS result., Competing Interests: The authors declare no potential conflict of interest., (© 2021 The Authors. JIMD Reports published by John Wiley & Sons Ltd on behalf of SSIEM.)

Background: Patients with severe long-chain fatty acid oxidation disorders (LC-FAODs) experience serious morbidity and mortality despite traditional dietary management including medium-chain triglyceride (MCT)-supplemented, low-fat diets. Triheptanoin is a triglyceride oil that is broken down to acetyl-coenzyme A (CoA) and propionyl-CoA, which replenishes deficient tricarboxylic acid cycle intermediates. We report the complex medical and nutrition management of triheptanoin therapy initiated emergently for 3 patients with LC-FAOD., Methods: Triheptanoin (Ultragenyx Pharmaceutical, Inc, Novato, CA, USA) was administered to 3 patients with LC-FAOD on a compassionate-use basis. Triheptanoin was mixed with non-MCT-containing low-fat formula. Patients were closely followed with regular cardiac and laboratory monitoring., Results: Cardiac ejection fraction normalized after triheptanoin initiation. Patients experienced fewer hospitalizations related to metabolic crises while on triheptanoin. Patient 1 has tolerated oral administration without difficulty since birth. Patients 2 and 3 experienced increased diarrhea. Recurrent breakdown of the silicone gastrostomy tube occurred in patient 3, whereas the polyurethane nasogastric tube for patient 2 remained intact. Patient 3 experiences recurrent episodes of elevated creatine kinase levels and muscle weakness associated with illness. Patient 3 had chronically elevated C10-acylcarnitines while on MCT supplementation, which normalized after initiation of triheptanoin and discontinuation of MCT oil., Conclusions: Triheptanoin can ameliorate acute cardiomyopathy and increase survival in patients with severe LC-FAOD. Substituting triheptanoin for traditional MCT-based treatment improves clinical outcomes. MCT oil might be less effective in carnitine-acylcarnitine translocase deficiency patients compared with other FAODs and needs further investigation., (© 2020 American Society for Parenteral and Enteral Nutrition.)

Serine, a non-essential amino acid, has attracted clinical attention because of potential benefit in certain metabolic and neurological disorders. Despite the therapeutic potential, little is known about the pharmacokinetics of l-serine metabolism in humans. Here we present pharmacokinetic data at the time of treatment initiation as well as plasma serine levels during dose escalation from a single individual taking oral l-serine as part of a treatment regimen. Our results show that plasma serine levels rise and fall rapidly after oral l-serine intake, suggesting that the optimal dosing for oral l-serine supplementation is at least three times per day., Competing Interests: None., (© 2020 Published by Elsevier Inc.)

Organic acid analysis detects accumulation of organic acids in urine and other body fluids and is a crucial first-tier laboratory test for a broad spectrum of inborn errors of metabolism. It is also frequently ordered as follow-up for a positive newborn screen result, as recommended by American College of Medical Genetics and Genomics newborn screening ACTion sheets and algorithms. The typical assay is performed by gas chromatography-mass spectrometry. These technical standards were developed to provide guidance for laboratory practices in organic acid analysis, interpretation, and reporting. In addition, new diagnostic biomarkers for recently discovered organic acidurias have been added.

PTEN-induced putative kinase 1 (PINK1) is a mitochondria-targeted kinase whose mutations are a cause of Parkinson's disease. We set out to better understand PINK1's effects on mitochondrial proteins in vivo. Using an unbiased phosphoproteomic screen in Drosophila, we found that PINK1 mediates the phosphorylation of MCAD, a mitochondrial matrix protein critical to fatty acid metabolism. By mimicking phosphorylation of this protein in a PINK1 null background, we restored PINK1 null's climbing, flight, thorax, and wing deficiencies. Owing to MCAD's role in fatty acid metabolism, we examined the metabolic profile of PINK1 null flies, where we uncovered significant disruptions in both acylcarnitines and amino acids. Some of these disruptions were rescued by phosphorylation of MCAD, consistent with MCAD's rescue of PINK1 null's organismal phenotypes. Our work validates and extends the current knowledge of PINK1, identifies a novel function of MCAD, and illuminates the need for and effectiveness of metabolic profiling in models of neurodegenerative disease.

This corrects the article DOI: 10.1038/gim.2017.84.

KRAS is a regulator of the nutrient stress response in non-small-cell lung cancer (NSCLC). Induction of the ATF4 pathway during nutrient depletion requires AKT and NRF2 downstream of KRAS. The tumor suppressor KEAP1 strongly influences the outcome of activation of this pathway during nutrient stress; loss of KEAP1 in KRAS mutant cells leads to apoptosis. Through ATF4 regulation, KRAS alters amino acid uptake and asparagine biosynthesis. The ATF4 target asparagine synthetase (ASNS) contributes to apoptotic suppression, protein biosynthesis, and mTORC1 activation. Inhibition of AKT suppressed ASNS expression and, combined with depletion of extracellular asparagine, decreased tumor growth. Therefore, KRAS is important for the cellular response to nutrient stress, and ASNS represents a promising therapeutic target in KRAS mutant NSCLC., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Purpose: Maple Syrup Urine Disease (MSUD) is a rare disorder of branched-chain amino acid catabolism associated with encephalopathy from accumulation of leucine. Leucine is closely monitored during normal growth and particularly during acute illness. As most hospitals do not have access to rapid plasma amino acid quantification, the initial management is often empirical. A model describing the reduction of plasma leucine in hyperleucinemic patients on leucine-free formula would help to guide management and optimize testing frequency., Methods: We retrospectively reviewed charts from 15 MSUD patients comprising 29 episodes of hyperleucinemia that were managed with leucine-free formula. Episodes were categorized by clinical presentation., Results: Upon leucine restriction, plasma leucine concentrations fell exponentially at a rate proportional to approximately 50% of the starting value over each 24-hour period. Recovery appears to be sensitive to clinical status and triggering event of the hyperleucinemic episode. Patients with upper respiratory infections generally recovered slowly, while cases of dietary non-adherence resolved more quickly., Conclusion: This general model may help anticipate leucine levels during clinical management of MSUD patients when using nutritional support and leucine-free formula. The response of individual patients may vary depending on clinical status and triggering factors., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Disclaimer: These ACMG Standards and Guidelines are intended as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these Standards and Guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of others that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, clinical laboratory geneticists should apply their professional judgment to the specific circumstances presented by the patient or specimen. Clinical laboratory scientists and geneticists are encouraged to document in the patient's record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these Standards and Guidelines. They also are advised to take notice of the date any particular guideline was adopted, and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.Biotinidase deficiency is an autosomal recessively inherited disorder of biotin recycling that is associated with neurologic and cutaneous consequences if untreated. Fortunately, the clinical features of the disorder can be ameliorated or prevented by administering pharmacological doses of the vitamin biotin. Newborn screening and confirmatory diagnosis of biotinidase deficiency encompasses both enzymatic and molecular testing approaches. These guidelines were developed to define and standardize laboratory procedures for enzymatic biotinidase testing, to delineate situations for which follow-up molecular testing is warranted, and to characterize variables that can influence test performance and interpretation of results.

Hawkinsinuria is a rare disorder of tyrosine metabolism that can manifest with metabolic acidosis and growth arrest around the time of weaning off breast milk, typically followed by spontaneous resolution of symptoms around 1 year of age. The urinary metabolites hawkinsin, quinolacetic acid, and pyroglutamic acid can aid in identifying this condition, although their relationship to the clinical manifestations is not known. Herein we describe clinical and laboratory findings in two fraternal twins with hawkinsinuria who presented with failure to thrive and metabolic acidosis. Close clinical follow-up and laboratory testing revealed previously unrecognized hypoglycemia, hypophosphatemia, combined hyperlipidemia, and anemia, along with the characteristic urinary metabolites, including massive pyroglutamic aciduria. Treatment with N-acetyl-L-cysteine (NAC) restored normal growth and normalized or improved most biochemical parameters. The dramatic response to NAC therapy supports the idea that glutathione depletion plays a key role in the pathogenesis of hawkinsinuria.

Adenosine deaminases acting on RNA (ADARs) are editing enzymes that convert adenosine to inosine in duplex RNA, a modification reaction with wide-ranging consequences in RNA function. Understanding of the ADAR reaction mechanism, the origin of editing-site selectivity, and the effect of mutations is limited by the lack of high-resolution structural data for complexes of ADARs bound to substrate RNAs. Here we describe four crystal structures of the human ADAR2 deaminase domain bound to RNA duplexes bearing a mimic of the deamination reaction intermediate. These structures, together with structure-guided mutagenesis and RNA-modification experiments, explain the basis of the ADAR deaminase domain's dsRNA specificity, its base-flipping mechanism, and its nearest-neighbor preferences. In addition, we identified an ADAR2-specific RNA-binding loop near the enzyme active site, thus rationalizing differences in selectivity observed between different ADARs. Finally, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.

Background: In May 2003, the National Institute for Clinical Excellence published controversial clinical guidelines that intended to restrict the indications for the use of electroconvulsive therapy (ECT) in the United Kingdom., Objective: We investigated whether the guideline had affected the rate of usage of ECT in the City of Edinburgh and set this in the context of ECT usage in the City since 1993., Method: We calculated the annual rate of ECT usage using a case register and contemporaneous and coterminous population data, reporting separately rates for young people (younger than 18 years), the general adult population, and older adults (aged 65 years of age and older)., Results: No young person was treated after 1998. There were similar significant falls in the rates of usage in both the general adult and older age population (-60%). There was no suggestion that the fall had accelerated after May 2003., Conclusions: No early effect of the guidance was found in the rate of ECT usage in the City of Edinburgh, but the passage of time will be required to assess any longer term effect.

Background: Magnetic seizure therapy, in which seizures are elicited with a high-frequency magnetic field, is under development as a new treatment for major depressive disorder. Its use may be justified if it produces the antidepressant effects of electroconvulsive therapy (ECT), coupled with limited cognitive side-effects., Aims: To evaluate the usefulness of a new 100 Hz magnetic seizure therapy device., Method: We induced seizures with 100 Hz magnetic transcranial stimulation in 11 patients with major depressive disorder during one session of a regular course of ECT. Recovery times after seizures induced by magnetic seizure therapy and ECT were compared., Results: Seizures could be elicited in 10 of the 11 patients. Stimulation over the vertex produced tonic-clonic activity on 9 out of 11 occasions. Stimulation over the prefrontal midpoint elicited seizures on 3 out of 7 occasions. The mean duration of magnetically induced seizures was 31.3 s, ranging from 10 to 86 s. All patients had an exceptionally quick recovery of orientation: mean of 7 min 12 s (s.d.=2 min 7 s, range 4 min 20 s to 9 min 41 s). The recovery times were on average 15 min 35 s shorter with magnetic seizure therapy than with ECT in the same patients (paired-samples t-test: P<0.0001). Patients reported feeling less confused after magnetic seizure therapy. Side-effects were confined to myoclonic movements, associated with the use of etomidate., Conclusions: The new 100 Hz magnetic stimulator elicits seizures in the majority of patients when administered over the vertex. Magnetic seizure therapy was associated with shorter recovery times and less confusion following treatment. Subsequent work will be required to assess the safety and effectiveness of magnetic seizure therapy in the treatment of depression.

Nucleoside mediated Claisen condensation of malonates has been achieved under biomimetic weak acid conditions, pH 3or 4, 0.15 M NaCl, and 0.125 M Mg(2+). The result illustrates the catalyzing property of end-nucleosides of t-RNA in the RNA world.