ASAH1 pathogenic variants associated with acid ceramidase deficiency: Farber disease and spinal muscular atrophy with progressive myoclonic epilepsy.

Farber disease and spinal muscular atrophy with progressive myoclonic epilepsy are a spectrum of rare lysosomal storage disorders characterized by acid ceramidase deficiency (ACD), resulting from pathogenic variants in N-acylsphingosine amidohydrolase 1 (ASAH1). Other than simple listings provided in literature reviews, a curated, comprehensive list of ASAH1 mutations associated with ACD clinical phenotypes has not yet been published. This publication includes mutations in ASAH1 collected through the Observational and Cross-Sectional Cohort Study of the Natural History and Phenotypic Spectrum of Farber Disease (NHS), ClinicalTrials.gov identifier NCT03233841, in combination with an up-to-date curated list of published mutations. The NHS is the first to collect retrospective and prospective data on living and deceased patients with ACD presenting as Farber disease, who had or had not undergone hematopoietic stem cell transplantation. Forty-five patients representing the known clinical spectrum of Farber disease (living patients aged 1-28 years) were enrolled. The curation of known ASAH1 pathogenic variants using a single reference transcript includes 10 previously unpublished from the NHS and 63 that were previously reported. The publication of ASAH1 variants will be greatly beneficial to patients undergoing genetic testing in the future by providing a significantly expanded reference list of disease-causing variants.

Arsenic Uptake by Muskmelon (Cucumis melo) Plants from Contaminated Water.

Arsenic is a carcinogenic element that occurs naturally in the environment. High levels of arsenic are found in water in some parts of the world, including Texas. The aims of this study were to determine the distribution of arsenic in muskmelon (Cucumis melo) plants accumulated from arsenic spiked water and to observe effects on plant biomass. Plants were grown and irrigated using water spiked with variable concentrations of arsenic. Inductively coupled plasma mass spectrometry was used to quantify arsenic in different parts of the plant and fruit. Under all conditions tested in this study, the highest concentrations of arsenic were found in the leaves, soil, and roots. Arsenic in the water had no significant effect on plant biomass. Fruits analyzed in this study had arsenic concentrations of 101 µg/kg or less. Consuming these fruits would result in less arsenic exposure than drinking water at recommended levels.

Succinic semialdehyde dehydrogenase deficiency: a metabolic and genomic approach to diagnosis.

Genomic sequencing offers an untargeted, data-driven approach to genetic diagnosis; however, variants of uncertain significance often hinder the diagnostic process. The discovery of rare genomic variants without previously known functional evidence of pathogenicity often results in variants being overlooked as potentially causative, particularly in individuals with undifferentiated phenotypes. Consequently, many neurometabolic conditions, including those in the GABA (gamma-aminobutyric acid) catabolism pathway, are underdiagnosed. Succinic semialdehyde dehydrogenase deficiency (SSADHD, OMIM #271980) is a neurometabolic disorder in the GABA catabolism pathway. The disorder is due to bi-allelic pathogenic variants in ALDH5A1 and is usually characterized by moderate-to-severe developmental delays, hypotonia, intellectual disability, ataxia, seizures, hyperkinetic behavior, aggression, psychiatric disorders, and sleep disturbances. In this study, we utilized an integrated approach to diagnosis of SSADHD by examining molecular, clinical, and metabolomic data from a single large commercial laboratory. Our analysis led to the identification of 16 patients with likely SSADHD along with three novel variants. We also showed that patients with this disorder have a clear metabolomic signature that, along with molecular and clinical findings, may allow for more rapid and efficient diagnosis. We further surveyed all available pathogenic/likely pathogenic variants and used this information to estimate the global prevalence of this disease. Taken together, our comprehensive analysis allows for a global approach to the diagnosis of SSADHD and provides a pathway to improved diagnosis and potential incorporation into newborn screening programs. Furthermore, early diagnosis facilitates referral to genetic counseling, family support, and access to targeted treatments-taken together, these provide the best outcomes for individuals living with either GABA-TD or SSADHD, as well as other rare conditions.

Assessing Prevalence and Carrier Frequency of Succinic Semialdehyde Dehydrogenase Deficiency.

Pathogenic variants in ALDH5A1 cause succinic semialdehyde dehydrogenase (SSADH) deficiency, with >180 cases reported worldwide. However, a nonspecific neurologic presentation and inconsistent variant nomenclature have limited diagnoses. In this study, pathogenic variants in ALDH5A1 were curated and variant prevalence assessed in the Genome Aggregation Database (gnomAD) to determine a minimum carrier frequency and to estimate disease prevalence. Stringent population variant analysis, including 98 reported disease-associated ALDH5A1 variants, indicates a pan-ethnic carrier frequency of ∼1/340, supporting a prevalence of SSADH deficiency of ∼1/460 000 worldwide, with highest carrier frequencies observed in East Asian and South Asian populations. Because heterozygous loss of function alleles are rare in gnomAD and >60% of reported disease-causing variants were missense changes that were not present in gnomAD, the pan-ethnic carrier frequency for SSADH deficiency is likely not fully represented in this study. Additional analyses to investigate the potential impact of more common ALDH5A1 variants with reduced but not deficient enzyme activity, including analysis in diverse populations, are needed to fully assess the prevalence of this ultra-rare disease.

The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways.

Mining of integrated public transcriptomic and ChIP-Seq (cistromic) datasets can illuminate functions of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates community classifications of signaling pathway nodes (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules. We then mapped over 10,000 public transcriptomic or cistromic experiments to their pathway node or biosample of study. To enable prediction of pathway node-gene target transcriptional regulatory relationships through SPP, we generated consensus 'omics signatures, or consensomes, which ranked genes based on measures of their significant differential expression or promoter occupancy across transcriptomic or cistromic experiments mapped to a specific node family. Consensomes were validated using alignment with canonical literature knowledge, gene target-level integration of transcriptomic and cistromic data points, and in bench experiments confirming previously uncharacterized node-gene target regulatory relationships. To expose the SPP knowledgebase to researchers, a web browser interface was designed that accommodates numerous routine data mining strategies. SPP is freely accessible at https://www.signalingpathways.org .

Cyanobacterial signature genes.

A comparison of 8 cyanobacterial genomes reveals that there are 181 shared genes that do not have obvious orthologs in other bacteria. These signature genes define aspects of the genotype that are uniquely cyanobacterial. Approximately 25% of these genes have been associated with some function. These signature genes may or may not be involved in photosynthesis but likely they will be in many cases. In addition, several examples of widely conserved gene order involving two or more signature genes were observed. This suggests there may be regulatory processes that have been preserved throughout the long history of the cyanobacterial phenotype. The results presented here will be especially useful because they identify which of the many genes of unassigned function are likely to be of the greatest interest.

Quantitative segmentation of principal carotid atherosclerotic lesion components by feature space analysis based on multicontrast MRI at 1.5 T.

The purpose of this paper is to evaluate the capability of feature space analysis (FSA) for quantifying the relative volumes of principal components (thrombus, calcification, fibrous, normal intima, and lipid) of atherosclerotic plaque tissue in multicontrast magnetic resonance images (mc-MRI) acquired in a setup resembling clinical conditions ex vivo. Utilizing endogenous contrast, proton density, T1-weighted, and T2-weighted images were acquired for 13 carotid endarterectomy (CEA) tissues under near-clinical conditions (human 1.5 T GE Excite scanner with sequence parameters comparable to an in vivo acquisition). An FSA algorithm was utilized to segment and quantify the principal components of atherosclerotic plaques. Pilot in vivo mc-MRI images were analyzed in the same way as the ex vivo images for exploring the possible adaptation of this technique to in vivo imaging. Relative abundance of principal plaque components in CEA tissues as determined by mc-MRI/FSA were compared to those measured by histology. Mean differences +/- standard deviations were 5.8 +/- 4.1% for thrombus, 1.5 +/-1.4 % for calcification, 4.0 +/-2.8% for fibrous, 8.2 +/- 10% for normal intima, and 2.4 +/- 2.2% for lipid. Reasonable quantitative agreement between the classification results obtained with FSA and histological data was obtained for near-clinical imaging conditions. Combination of mc-MRI and FSA may have an application for determining atherosclerotic lesion composition and monitoring treatment in vivo.

Short-term tracking of atherosclerosis in operated and unoperated human carotid arteries by high resolution magnetic resonance imaging.

INTRODUCTION: A previous study demonstrated the efficacy of a phospholipid (PL) complexed with a protein (apoAI Milano) in causing 4.6% regression of atheroma volume as assessed by intravascular ultrasonography (IVUS) in a group of 47 patients with carotid atherosclerosis. The results of this study raised the question of whether the phospholipid alone could produce a similar effect. METHODS: To answer this question a trial of 39 subjects at five sites was designed. Patients with > 15% stenosis of at least one carotid artery as determined by US underwent intravenous PL (200 mg/kg) or placebo infusions weekly for 8 weeks. The wall/outer wall ratio, percent lipid-rich/necrotic core, and percent calcification were measured as a proportion of the vessel wall by magnetic resonance imaging (MRI) at 0, 4, 8, and 14 weeks. RESULTS: The substudy of seven of these patients evaluated at our site allowed comparison of the dimensions of five unoperated-unoperated carotid pairs and two operated-unoperated pairs. In patient 1, MRI measurements on unoperated left and unoperated right carotids tracked almost identically over the 14-week study. Both carotids showed similar increases in the volumes of the total wall (+61% vs. 56%), the normal wall (+51% vs. 49%), and plaque (+99% vs. 85%). Both carotids showed similar decreases in lumen volume (-11% vs. -17%). The other four unoperated-unoperated carotid pairs showed dimensional changes over 14 weeks similar to those of patient 1. In patient 2, who underwent left endarterectomy, the operated carotid had a total artery volume of 2300 mm(3), about twofold greater than the unoperated carotid (1100 mm(3)). Operated and unoperated carotid measurements tracked in parallel. The unoperated carotid had volume increases of 25% (+200 mm(3)) in total wall, +19% (+100 mm(3)) in normal wall, and 43% (+75 mm(3)) in plaque. The operated carotid lumen showed no significant changes. Patient 7, who also underwent left endarterectomy, exhibited carotid changes similar to those of patient 2. CONCLUSIONS: Individual unoperated carotid pairs have volumes that track almost identically. In unilateral operated carotid pairs, the operated artery has 1.5- to 2.0-fold greater volume than unoperated carotids. In each of our two unilaterally operated patients, the operated carotid had decreased plaque volume (-3%, -58%), whereas the unoperated carotid had increased plaque volume (+43%, +7%). Among the five unoperated patients, one pair had 85%/99% increase in plaque volume; one pair had -15%/-10% decrease; and the other three pairs had intermediate changes. This study provides additional support to the view that unoperated human carotid arteries are bilaterally symmetrical.