Childhood onset amyotrophic lateral sclerosis associated with SPTLC2 gain-of-function pathogenic variants: clinical, genetic, and biochemical insights

Amyotrophic lateral sclerosis (ALS) is an etiologically heterogeneous, severe, progressive motor neuron disease characterized by the degeneration of upper and lower motor neurons. A childhood onset monogenic form of ALS caused by unrestrained sphingolipid synthesis by serine palmitoyltransferase (SPT) secondary to variants in serine palmitoyltransferase long chain base subunit 1 (SPTLC1) gene has been recently established. We report a cohort of eight independent patients with neonatal to juvenile-onset ALS with de-novo recurrent variants in SPTLC2. The cohort consists of six patients carrying a dominantly acting variant c.778G>A [p.Glu260Lys] previously presented by us, and two patients carrying a newly identified, dominantly acting variant, c.203T>G [p.Met68Arg]. All patients presented with early-childhood onset progressive weakness, with signs and symptoms of upper and lower motor neuron degeneration and without a component of sensory neuropathy. Three patients had progressive academic difficulties, and the most severely affected patient (neonatal onset, died at age 7 years) was also diagnosed with an autism spectrum disorder. In silico mapping based on the cryo-EM structure of SPT shows that the SPTLC2 E260 residue and the M68 residue interact with the SPT negative regulatory subunit ORMDL3. Biochemical investigations in patients’ plasma and fibroblasts showed excess canonical sphingolipid biosynthesis, similar to SPTLC1-associated ALS. SPTLC2 is thus the second SPT-associated gene that underlies monogenic, childhood-onset ALS and further establishes alterations of sphingolipid metabolism in motor neuron disease pathogenesis. Understanding the common pathogenesis of these two SPT-related forms paves the way for targeted therapeutic approaches to dampen SPT overactivity. Of note, serine supplementation should be avoided as it would exacerbate the excess sphingolipid synthesis. Amyotrophic lateral sclerosis (ALS) is an etiologically heterogeneous, severe, progressive motor neuron disease characterized by the degeneration of upper and lower motor neurons. A childhood onset monogenic form of ALS caused by unrestrained sphingolipid synthesis by serine palmitoyltransferase (SPT) secondary to variants in serine palmitoyltransferase long chain base subunit 1 (SPTLC1) gene has been recently established. We report a cohort of eight independent patients with neonatal to juvenile-onset ALS with de-novo recurrent variants in SPTLC2. The cohort consists of six patients carrying a dominantly acting variant c.778G>A [p.Glu260Lys] previously presented by us, and two patients carrying a newly identified, dominantly acting variant, c.203T>G [p.Met68Arg]. All patients presented with early-childhood onset progressive weakness, with signs and symptoms of upper and lower motor neuron degeneration and without a component of sensory neuropathy. Three patients had progressive academic difficulties, and the most severely affected patient (neonatal onset, died at age 7 years) was also diagnosed with an autism spectrum disorder. In silico mapping based on the cryo-EM structure of SPT shows that the SPTLC2 E260 residue and the M68 residue interact with the SPT negative regulatory subunit ORMDL3. Biochemical investigations in patients’ plasma and fibroblasts showed excess canonical sphingolipid biosynthesis, similar to SPTLC1-associated ALS. SPTLC2 is thus the second SPT-associated gene that underlies monogenic, childhood-onset ALS and further establishes alterations of sphingolipid metabolism in motor neuron disease pathogenesis. Understanding the common pathogenesis of these two SPT-related forms paves the way for targeted therapeutic approaches to dampen SPT overactivity. Of note, serine supplementation should be avoided as it would exacerbate the excess sphingolipid synthesis.