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Genotype Phenotype Correlations Inform Therapeutic Approach in Serine Palmitoyltransferase (SPT)-related Disorders

Biochemical/Metabolic and Therapeutics
  • Primary Categories:
    • Metabolic Genetics
  • Secondary Categories:
    • Metabolic Genetics
Introduction:
Serine palmitoyltransferase (SPT) catalyzes the initial and rate-limiting step in sphingolipid synthesis involving the condensation of an acyl-CoA with L-serine to form a sphingoid or long-chain base. SPT is comprised of multiple subunits including SPTLC1 (SPT long chain base subunit-1), SPTLC2, and the activating subunit SPTSSA (SPT small subunit A) which increases catalytic activity of the SPTLC1/SPTLC2 heterodimer by more than 25-fold. ORMDL proteins bind to SPT, provide feedback inhibition and thereby regulate activity of the enzyme.



Pathogenic missense variants in SPTLC1 and SPTLC2 localized to the substrate binding pocket allows for alanine and glycine incorporation which ultimately results in the synthesis of the atypical and neurotoxic 1-deoxysphingolipids. This leads to a predominantly sensory neuropathy termed Hereditary Sensory and Autonomic Neuropathy Type I (HSAN1). In contrast, pathogenic gain of function variants in SPTLC1 and SPTLC2  impact ORMDL binding, cause an excess in canonical sphingolipids and lead to juvenile amyotrophic lateral sclerosis. We care for a 7 year old girl with a de novo pathogenic variant (c.152 C>T, p.Thr51Ile) in the SPTSSA gene. This variant also causes loss of ORMDL mediated feedback inhibition and excessive de novo sphingolipid synthesis leading to neurotoxicity and a complex hereditary spastic paraplegia (HSP).



We present data on a SPTSSA T51I/+ mouse model and pilot studies of our SPT inhibitor D-Cycloserine in a human patient with this SPTSSA-related complex HSP.

Methods:
A mouse model of our patient's pathogenic variant in SPTSSA (T51I/+) was given chow supplemented with L-serine and the effects on weight, hind limb clasping, survival, sphingolipid levels, and biomarkers of nervous system function were studied. Subsequently mice receiving this supplementation were treated with the SPT inhibitor myriocin after which comparative studies were performed. Due to the GI toxicity of myriocin, D-Cycloserine was chosen to inhibit SPT in our human studies. We designed an N=1 investigational protocol approved by our center's IRB.

 

Results:
T51I/+ mice exhibit increased sphingolipid production in plasma and nervous system. Supplementing the mouse chow with L-serine caused sphingolipid excess, aggravation of hind limb spasticity, and early death by 2 months of age. These T51I/+ mice were found to have aberrant myelination. By contrast mice treated with myriocin demonstrated a dose dependent decrease in sphingolipid levels, improved survival and no hind limb clasping up to 5 months of age. In our patient with SPTSSA-related complex HSP receiving D-Cycloserine we observed improved appendicular spasticity which led to a 71% reduction in the patient's daily dose of Baclofen.

Conclusion:
L-serine exacerbates the clinical and biochemical phenotypes of T51I/+ mice which is consistent with predictions based on the literature. SPT inhibition with myriocin reduced sphingolipid levels, improved survival and improves hind limb clasping up to 5 months. In our patient with SPTSSA-related complex HSP, treatment with the SPT inhibitor D-Cycloserine has had modest effects upon sphingolipid levels but impacted spasticity. Our studies highlight that SPT-related inborn errors of metabolism may require different treatment approaches depending on the specific gene defect. For example, missense variants in SPTLC1 and SPTLC2 lead to the primary sensory neuropathy observed in HSAN1 in which L-serine supplementation is beneficial. In contrast, gain of function variants in SPTLC1 and SPTLC2 cause juvenile ALS in which L-serine supplementation is toxic. This observation demonstrates the principle of phenotypic heterogeneity. One could also argue that SPTLC1/SPTLC2-related juvenile ALS and SPTSSA-related complex HSP demonstrate the principle of locus heterogeneity in that variants in different genes produce the same biochemical phenotype of sphingolipid excess, although admittedly the clinical phenotypes differ somewhat.  Thus, understanding genotype phenotype correlations is critically important for devising therapeutic approaches to treating disorders of sphingolipid synthesis.

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