Next-generation sequencing study reveals the broader variant spectrum of hereditary spastic paraplegia and related phenotypes

Abstract

Hereditary spastic paraplegias (HSPs) are clinically and genetically heterogeneous neurodegenerative disorders. Numerous genes linked to HSPs, overlapping phenotypes between HSP subtypes and other neurodegenerative disorders and the HSPs' dual mode of inheritance (both dominant and recessive) make the genetic diagnosis of HSPs complex and difficult. Out of the original HSP cohort comprising 306 index cases (familial and isolated) who had been tested according to "traditional workflow/guidelines" by Multiplex Ligation-dependent Probe Amplification (MLPA) and Sanger sequencing, 30 unrelated patients (all familial cases) with unsolved genetic diagnoses were tested using next-generation sequencing (NGS). One hundred thirty-two genes associated with spastic paraplegias, hereditary ataxias and related movement disorders were analysed using the Illumina TruSight™ One Sequencing Panel. The targeted NGS data showed pathogenic variants, likely pathogenic variants and those of uncertain significance (VUS) in the following genes: SPAST (spastin, SPG4), ATL1 (atlastin 1, SPG3), WASHC5 (SPG8), KIF5A (SPG10), KIF1A (SPG30), SPG11 (spatacsin), CYP27A1, SETX and ITPR1. Out of the nine genes mentioned above, three have not been directly associated with the HSP phenotype to date. Considering the phenotypic overlap and joint cellular pathways of the HSP, spinocerebellar ataxia (SCA) and amyotrophic lateral sclerosis (ALS) genes, our findings provide further evidence that common genetic testing may improve the diagnostics of movement disorders with a spectrum of ataxia-spasticity signs.

Keywords: Ataxia-spasticity; Hereditary spastic paraplegia; Movement disorders; Next-generation sequencing..

Fig. 1

Analysed cohort and methods used during HSP diagnostics. Detailed description of the identified variants is presented in tables

Fig. 2

A ITPR1 protein scheme. Localization of three identified variants interrupting coupling/regulatory domain is showed by: “*”, p.(Ala896Val); “♦”, p.(Met1138Val); “•”, p.(Ala2102Ser). IRBIT, Inositol 1,4,5-trisphosphate (IP₃) receptor binding domain; CARP, Carbonic anhydrase–related protein (CA8) binding domain. B Pedigrees of three families with ITPR1 variants. Families SPG0303 and SPG0401 are marked with “*” which indicates ITPR1: c. 2687C>T (p.Ala896Val); family SPG1203 is marked with “♦” and “•” which indicate ITPR1: c.3412A>G (p.Met1138Val) and c.6304G>T (p.Ala2102Ser), respectively. The “+” points out family members, in whom the DNA samples were tested; “-“affected individuals without DNA testing