Genome sequencing uncovers phenocopies in primary progressive multiple sclerosis

Abstract

Objective: Primary progressive multiple sclerosis (PPMS) causes accumulation of neurological disability from disease onset without clinical attacks typical of relapsing multiple sclerosis (RMS). However, whether genetic variation influences the disease course remains unclear. We aimed to determine whether mutations causative of neurological disorders that share features with multiple sclerosis (MS) contribute to risk for developing PPMS.

Methods: We examined whole-genome sequencing (WGS) data from 38 PPMS and 81 healthy subjects of European ancestry. We selected pathogenic variants exclusively found in PPMS patients that cause monogenic neurological disorders and performed two rounds of replication genotyping in 746 PPMS, 3,049 RMS, and 1,000 healthy subjects. To refine our findings, we examined the burden of rare, potentially pathogenic mutations in 41 genes that cause hereditary spastic paraplegias (HSPs) in PPMS (n = 314), secondary progressive multiple sclerosis (SPMS; n = 587), RMS (n = 2,248), and healthy subjects (n = 987) genotyped using the MS replication chip.

Results: WGS and replication studies identified three pathogenic variants in PPMS patients that cause neurological disorders sharing features with MS: KIF5A p.Ala361Val in spastic paraplegia 10; MLC1 p.Pro92Ser in megalencephalic leukodystrophy with subcortical cysts, and REEP1 c.606 + 43G>T in Spastic Paraplegia 31. Moreover, we detected a significant enrichment of HSP-related mutations in PPMS patients compared to controls (risk ratio [RR] = 1.95; 95% confidence interval [CI], 1.27-2.98; p = 0.002), as well as in SPMS patients compared to controls (RR = 1.57; 95% CI, 1.18-2.10; p = 0.002). Importantly, this enrichment was not detected in RMS.

Interpretation: This study provides evidence to support the hypothesis that rare Mendelian genetic variants contribute to the risk for developing progressive forms of MS. Ann Neurol 2018;83:51-63.

Figure 1

Summary of study cohorts, genotyping platforms, and variant selection. (A) Schematic of study design used for identifying MS phenocopy variants. The WGS discovery cohort included 38 PPMS patients (who met 2010 International Panel Criteria) and 81 ethnicity‐matched controls sequenced using the Complete Genomics Inc. (CGI) platform. Fifteen candidate variants were selected for Phase 1 replication genotyping in 411 PPMS and 460 RMS patients using OpenArray. Four top candidate variants exclusively found in PPMS and not RMS patients were selected for Phase 2 replication in 335 PPMS and 340 RMS patients from an Italian cohort and in 2,249 RMS and 1,000 controls from UCSF. (B) Schematic of study design used for determining the burden of HSP‐related mutations in PPMS. The discovery cohort comprised of 48 PPMS patients (who met 2010 International Panel Criteria) and 100 controls genotyped on the MS replication chip. Replication patients included an additional 266 PPMS, 1,702 RMS, and 887 control subjects from three additional cohorts (NARCOMS, Australian, and Italian) genotyped on the same platform. All subjects examined were of European ancestry. CADD = Combined Annotation Dependent Depletion; CNS = central nervous system; GWAS = genome‐wide association studies; HGMD = Human Gene Mutation Database; HSP = hereditary spastic paraplegia; MS = multiple sclerosis; NARCOMS = North America Research Committee on Multiple Sclerosis; PhyloP = phylogenetic conservation p value; PPMS = primary progressive multiple sclerosis; RMS = relapsing multiple sclerosis; SNVs = single‐nucleotide variants; SPMS = secondary progressive multiple sclerosis; UCSF = University of California San Francisco; WGS = whole‐genome sequencing.

Figure 2

Burden of spastic paraplegia mutations in PPMS. (A) Forty‐eight PPMS patients genotyped on the MS replication chip are enriched for rare (MAF < 1% in public data sets), functionally deleterious (missense and splice site), and potentially pathogenic (CADD score, > 10; PhyloP conservation, p < 0.01) variants in 41 genes known to cause spastic paraplegias, and the relative risk for PPMS increases with the number of HSP‐related variants carried by an individual (cases mean = 0.29; controls mean = 0.11; RR = 2.7; logistic regression, p = 0.028). (B) Random permutation of PPMS case and control status shows that the 2.7‐fold enrichment of pathogenic variants in 41 HSP‐related genes is greater than in 98.5% of 10,000 permutations (p = 0.015). HSP = hereditary spastic paraplegia; LR = likelihood ratio; MAF = minor allele frequency; MS = multiple sclerosis; PhyloP = phylogenetic conservation p value; PPMS = primary progressive multiple sclerosis; RR = risk ratio.

Figure 3

Meta‐analysis of HSP‐related mutations across multiple cohorts. Examination of 314 PPMS patients and 987 controls genotyped on the MS Replication Chip across four cohorts (UCSF, NARCOMS, Australian, and Italian) confirmed the observation that PPMS patients harbor significantly more potentially pathogenic HSP mutations compared to controls (RR = 1.95; random effects model, p = 0.002). HSP = hereditary spastic paraplegia; MS = multiple sclerosis; NARCOMS = North America Research Committee on Multiple Sclerosis; PPMS = primary progressive multiple sclerosis; RR = risk ratio; UCSF = University of California San Francisco; RE = random effects.

Figure 4

HSP‐related mutation burden in PPMS, SPMS, RMS, and controls. Examination of 314 PPMS, 2,248 RMS, 587 SPMS, and 987 control subjects from four cohorts (UCSF, NARCOMS, Australian, and Italian) showed that PPMS patients (0.23 variants per individual) on average harbored a significantly higher number of potentially pathogenic HSP‐related mutations compared to RMS (0.14) and controls (0.12; t test, p = 3.8 × 10⁻⁴ for PPMS vs controls; p = 9.6 × 10⁻⁴ for PPMS vs RMS). Moreover, SPMS patients (0.17), on average, also harbored a higher number of HSP‐related mutations compared to RMS (0.14) and controls (0.12; p = 0.018 for SPMS vs controls, p = 0.048 for SPMS vs RMS). Importantly, no significant enrichment was detected in RMS patients compared to healthy controls (p = 0.4). HSP = hereditary spastic paraplegia; NS = not significant; PPMS = primary progressive multiple sclerosis; RMS = relapsing multiple sclerosis; SPMS = secondary progressive multiple sclerosis.