HSAN1 mutations in serine palmitoyltransferase reveal a close structure–function–phenotype relationship

Abstract

Hereditary sensory and autonomic neuropathy type 1 (HSAN1) is a rare autosomal dominant inherited peripheral neuropathy caused by mutations in the SPTLC1 and SPTLC2 subunits of serine palmitoyltransferase (SPT). The mutations induce a permanent shift in the substrate preference from L-serine to L-alanine, which results in the pathological formation of atypical and neurotoxic 1-deoxy-sphingolipids (1-deoxySL). Here we compared the enzymatic properties of 11 SPTLC1 and six SPTLC2 mutants using a uniform isotope labelling approach. In total, eight SPT mutants (STPLC1p.C133W, p.C133Y, p.S331F, p.S331Y and SPTLC2p.A182P, p.G382V, p.S384F, p.I504F) were associated with increased 1-deoxySL synthesis. Despite earlier reports, canonical activity with l-serine was not reduced in any of the investigated SPT mutants. Three variants (SPTLC1p.S331F/Y and SPTLC2p.I505Y) showed an increased canonical activity and increased formation of C20 sphingoid bases. These three mutations are associated with an exceptionally severe HSAN1 phenotype, and increased C20 sphingosine levels were also confirmed in plasma of patients. A principal component analysis of the analysed sphingoid bases clustered the mutations into three separate entities. Each cluster was related to a distinct clinical outcome (no, mild and severe HSAN1 phenotype). A homology model based on the protein structure of the prokaryotic SPT recapitulated the same grouping on a structural level. Mutations associated with the mild form clustered around the active site, whereas mutations associated with the severe form were located on the surface of the protein. In conclusion, we showed that HSAN1 mutations in SPT have distinct biochemical properties, which allowed for the prediction of the clinical symptoms on the basis of the plasma sphingoid base profile.

Hereditary sensory and autonomic neuropathy type IC accompanied by upper motor neuron abnormalities and type II juxtafoveal retinal telangiectasias

“…The expression of the Ser384Phe mutation in HEK293 cells resulting in increased 1‐deoxySLs confirmed the mutations pathogenesis; however, the mutations full impact remains unknown as it may also regulate SPT substrate specificity . A comparison of genotype, phenotype, and 1‐deoxySL levels in HSAN1 patients showed the Ser384Phe mutation to have moderate increases in 1‐deoxySL levels . The mutation was typically associated with a late onset primarily sensory phenotype, accompanied by mild motor impairments .…”

“…A comparison of genotype, phenotype, and 1‐deoxySL levels in HSAN1 patients showed the Ser384Phe mutation to have moderate increases in 1‐deoxySL levels . The mutation was typically associated with a late onset primarily sensory phenotype, accompanied by mild motor impairments . SPTLC2‐Ser384 was identified previously as a protein phosphorylation site in SPT, and the expression of a phosphorylation mimicking mutant (S384D) in HEK293 cells was associated with increased 1‐deoxySL formation …”

Sphingolipid metabolism in cancer signalling and therapy

“…Specific missense mutations in the human SPTLC1 gene, which result in the accumulation of 1-deoxysphingoid bases owing to the utilization of L-alanine instead of L-serine as a substrate by the mutant SPT, are associated with hereditary sensory neuropathy type I (REF. 27). SPT-mediated elevation of cellular 1-deoxysphingoid base levels has been linked to paclitaxel-induced peripheral neuropathy in cell culture models as well as in serum samples from patients with breast cancer who received paclitaxel treatment 28 , which presents a major dose-limiting toxicity for paclitaxel treatment in patients with breast cancer.…”

“…SPT-mediated elevation of cellular 1-deoxysphingoid base levels has been linked to paclitaxel-induced peripheral neuropathy in cell culture models as well as in serum samples from patients with breast cancer who received paclitaxel treatment 28 , which presents a major dose-limiting toxicity for paclitaxel treatment in patients with breast cancer. The metabolic switch from SPT-dependent generation of 1-deoxysphingoid bases to conventional sphingolipids, such as (dihydro)sphingosine and/or ceramide, by use of L-serine might be a potential therapeutic intervention to alleviate paclitaxel-induced neurotoxicity in various cancer settings 27,28 . However, this strategy requires testing in future clinical trials.…”

“…Mutations in the genes encoding SPT subunits, such as SPTLC1 , are associated with hereditary sensory neuropathy type I (REF. 27). GCDase, galactosylceramidase; GlcCDase, glucosylceramidase; SGPP, S1P phosphatase.…”