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

Abstract

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.

Keywords: 2-pyrrolidinone; ALDH5A1; GABA catabolism; GABA-T (GABA transaminase); GHB (4-hydroxybutyric acid); SSADHD (succinic semialdehyde dehydrogenase deficiency); succinic semialdehyde dehydrogenase.

FIGURE 1

Overview of the gamma-aminobutyric acid (GABA) release, neurotransmission in the GABAergic-synapse and catabolism in the astrocyte mitochondria. Glutamate is one of the main sources of GABA formation via glutamic acid decarboxylase (GAD1). In response to electrophysiological activation, GABA is released into the presynaptic cleft where it binds three receptors, GABA_A, GABA_B, and GABA_C receptors. GABA is subsequently removed from the synaptic cleft by uptake in the astrocytes and catabolized in the astrocyte mitochondria to form succinic semialdehyde (SSA), gamma-hydroxybutyrate (GHB) and succinate. Succinate is subsequently channeled into the TCA cycle (Prepared using BioRender.com).

FIGURE 2

Biochemical pathway of GABA metabolism by GABA transaminase (GABA-T) and succinic semialdehyde dehydrogenase (SSADH). This is a two-step enzymatic pathway. In step 1, GABA is transaminated to form succinic semialdehyde by GABA-T. GABA can also be spontaneously converted to a stable lactam ring form, 2-pyrrolidinone, which is then converted to succinimide and succinamic acid or into 4-guanidinobutanoate via a transamidination reaction with arginine (Arg). In step 2, succinic semialdehyde is oxidized to form succinate by SSADH. Succinic semialdehyde may then be converted to gamma-hydroxybutyrate (GHB).

FIGURE 3

Summary of variants identified in SSADHD patients. All pathogenic or likely pathogenic variants detected in SSADHD patients in the BG/BCM cohort are depicted and labeled with variant frequency within the cohort. ClinVar pathogenic and likely pathogenic variants are also depicted.

FIGURE 4

Key plasma analytes in SSADHD and GABA-TD individuals compared to control reference population. Scatter plots (A) are shown for plasma analyses from individuals with SSADHD and GABA-TD as compared to the control reference population (GABA-TD data shown for comparison since, as previously reported by Kennedy et al., this disorder demonstrates clear defects in GABA metabolism in brain). SSADHD individuals in the pediatric age group (age ≤18 years) are indicated in red squares (n = 8), and those in adult age-group (age ≥19 years) are indicated in green squares (n = 5). Samples from GABA-TD individuals (n = 5) are indicated in blue circles for comparison. Control reference population (n = 395) is represented in open circles. Median with interquartile range is indicated for each analyte. Linear regression analysis of z-score levels by age of 2-pyrrolidinone (B), 4-guanidinobutanoate (C), and argininate (D) are shown, with difference in average z-scores of each group in inset. Dotted red lines indicate the z-score +2 on the y-axis and age 19 years on the x-axis.

FIGURE 5

Proposed algorithm for the diagnosis of SSADHD. Patients may be suspected as having a diagnosis of SSADH deficiency based on either clinical features, abnormalities on urine organic acids, or characteristic brain imaging. Based on this, we recommend patients have clinical metabolomic analysis, genomic sequencing of ALDH5A1 or the combination of the two tests as confirmation of the diagnosis. Genomic sequencing is now considered part of the first-line approach for evaluation of a child with developmental delays.