Mutations in PCYT2 disrupt etherlipid biosynthesis and cause a complex hereditary spastic paraplegia

Frédéric M Vaz ,Michel Van Weeghel,Marc Engelen,Rebecca Yarwood,John H Mcdermott,Henk Van Lenthe,Kay Metcalfe,Stefan Kölker,Sacha Ferdinandusse,Mariëlle Alders,Siddharth Banka,Sara Cuvertino,Saskia B Wortmann ,Peter E Clayton ,Angela C M Luyf ,J P N Ruiter ,Antoine H C Van Kampen ,Ronald J A Wanders ,R Curtis Rogers ,Mia L Pras‐Raves ,Deciphering Developmental Disorders Study ,Hyung L Elfrink ,Martin A T Vervaart ,Martin Lowe ,Simon C Lovell

doi:10.1093/brain/awz291

Abstract

CTP:phosphoethanolamine cytidylyltransferase (ET), encoded by PCYT2, is the rate-limiting enzyme for phosphatidylethanolamine synthesis via the CDP-ethanolamine pathway. Phosphatidylethanolamine is one of the most abundant membrane lipids and is particularly enriched in the brain. We identified five individuals with biallelic PCYT2 variants clinically characterized by global developmental delay with regression, spastic para- or tetraparesis, epilepsy and progressive cerebral and cerebellar atrophy. Using patient fibroblasts we demonstrated that these variants are hypomorphic, result in altered but residual ET protein levels and concomitant reduced enzyme activity without affecting mRNA levels. The significantly better survival of hypomorphic CRISPR-Cas9 generated pcyt2 zebrafish knockout compared to a complete knockout, in conjunction with previously described data on the Pcyt2 mouse model, indicates that complete loss of ET function may be incompatible with life in vertebrates. Lipidomic analysis revealed profound lipid abnormalities in patient fibroblasts impacting both neutral etherlipid and etherphospholipid metabolism. Plasma lipidomics studies also identified changes in etherlipids that have the potential to be used as biomarkers for ET deficiency. In conclusion, our data establish PCYT2 as a disease gene for a new complex hereditary spastic paraplegia and confirm that etherlipid homeostasis is important for the development and function of the brain.

Highlights

Phosphatidylethanolamine (PE) is one of the most abundant membrane lipids and is enriched in the human brain where it represents $45% of the phospholipid fraction
Pathogenic SACS variants cause autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS; OMIM 270550). These patients did not have the cranial MRI features or the characteristic retinal striations seen in ARSACS
To understand the effects of the ET deficiency on plasmalogen synthesis we investigated whether the accumulating PE[O] and PC[O] species were plasmalogens or non-plasmalogen etherphospholipids

Summary

Introduction

Phosphatidylethanolamine (PE) is one of the most abundant membrane lipids and is enriched in the human brain where it represents $45% of the phospholipid fraction. The CDP-ethanolamine pathway is important for the synthesis of PE etherphospholipids (PE[O]) (Fig. 1A). Plasmenyl-PEs, together with their phosphatidylcholine (PC) counterparts, are collectively called plasmalogens. Both plasmanyl- and plasmenyl-PE species are synthesized from the precursors 1-alkyl-2-acylglycerol (DG[O]). Plasmalogens are an important class of etherphospholipids and PE plasmalogens are by far the most abundant species (when compared to PC-plasmalogens) in the brain (Braverman and Moser, 2012). Several neurodevelopmental defects have been described where disturbed etherphospholipid metabolism is part of the pathological mechanism, including Zellweger syndrome and rhizomelic chondrodysplasia punctata (Braverman and Moser, 2012; Waterham et al, 2016). Reduced levels of PE plasmalogens have been demonstrated for Alzheimer’s disease, Parkinson’s disease, trisomy 21 and schizophrenia (Horibata et al, 2018)

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Conclusion