Early complement genes are associated with visual system degeneration in multiple sclerosis

Abstract

Multiple sclerosis is a heterogeneous disease with an unpredictable course and a wide range of severity; some individuals rapidly progress to a disabled state whereas others experience only mild symptoms. Though genetic studies have identified variants that are associated with an increased risk of developing multiple sclerosis, no variants have been consistently associated with multiple sclerosis severity. In part, the lack of findings is related to inherent limitations of clinical rating scales; these scales are insensitive to early degenerative changes that underlie disease progression. Optical coherence tomography imaging of the retina and low-contrast letter acuity correlate with and predict clinical and imaging-based outcomes in multiple sclerosis. Therefore, they may serve as sensitive phenotypes to discover genetic predictors of disease course. We conducted a set of genome-wide association studies of longitudinal structural and functional visual pathway phenotypes in multiple sclerosis. First, we assessed genetic predictors of ganglion cell/inner plexiform layer atrophy in a discovery cohort of 374 patients with multiple sclerosis using mixed-effects models adjusting for age, sex, disease duration, optic neuritis and genetic ancestry and using a combination of single-variant and network-based analyses. For candidate variants identified in discovery, we conducted a similar set of analyses of ganglion cell/inner plexiform layer thinning in a replication cohort (n = 376). Second, we assessed genetic predictors of sustained loss of 5-letters in low-contrast letter acuity in discovery (n = 582) using multivariable-adjusted Cox proportional hazards models. We then evaluated candidate variants/pathways in a replication cohort. (n = 253). Results of both studies revealed novel subnetworks highly enriched for connected genes in early complement activation linked to measures of disease severity. Within these networks, C3 was the gene most strongly associated with ganglion cell/inner plexiform layer atrophy (P = 0.004) and C1QA and CR1 were top results in analysis of sustained low-contrast letter acuity loss. Namely, variant rs158772, linked to C1QA, and rs61822967, linked to CR1, were associated with 71% and 40% increases in risk of sustained LCLA loss, respectively, in meta-analysis pooling discovery and replication cohorts (rs158772: hazard ratio: 1.71; 95% confidence interval 1.30-2.25; P = 1.3 × 10-4; rs61822967: hazard ratio: 1.40; 95% confidence interval: 1.16-1.68; P = 4.1 × 10-4). In conclusion, early complement pathway gene variants were consistently associated with structural and functional measures of multiple sclerosis severity. These results from unbiased analyses are strongly supported by several prior reports that mechanistically implicated early complement factors in neurodegeneration.

Trial registration: ClinicalTrials.gov NCT00211887.

Keywords: early complement pathway genes; genome-wide association studies; multiple sclerosis; optical coherence tomography.

© The Author(s) (2019). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Figures

Figure 1

Summary of results for GWAS of GCIP decline in multiple sclerosis. (A) Manhattan plot of P-values from analyses assessing the association between genetic variants and rate of GCIP decline in the discovery JHU OCT cohort. One variant (rs2497800) achieved genome-wide significance. (B) Results for known multiple sclerosis HLA susceptibility variants. The left panel demonstrates the association between a given HLA allele and age of onset of multiple sclerosis. Values are displayed in years. The right panel demonstrates the association between a given HLA allele and difference in rate of change in GCIP. Values are displayed as difference in rate of change in µm/year. The HLA risk score is calculated as the linear combination of previously identified HLA risk alleles where each allele is weighted by its effect on multiple sclerosis susceptibility. (C) Composition of identified networks from HotNet2 analyses that were identified in both primary and secondary analyses. (D) Enrichment results of the HotNet2 network analyses of networks identified in both primary and secondary analyses. The plotted network reflects the identified network from the sensitivity analyses (where low-confidence genes are assigned a heat score of 0). The identified network was highly enriched in early complement pathway genes (P = 1.38 × 10−8). The left (red) portion of the plot denotes the proportion of a given pathway that is composed of the genes in the network. The middle (blue) portion of the plot denotes the −log(P-value) of the tests for enrichment in the pathway using the identified network of genes. The right (orange) portion of the plot denotes the genes in the network which are included in the given pathway.

Figure 2

Summary of results for GWAS of loss of visual function in multiple sclerosis. (A) Manhattan plot depicting P-values from analyses assessing the pooled association between genetic variants and risk of sustained LCLA from the discovery (CombiRx) and replication (JHU-LCLA). One variant (rs72830848) was potentially associated with sustained LCLA at the 5 × 10−8 significance level in the pooled analysis. (B) Kaplan Meier plot comparing rate of sustained LCLA for individuals with the CC genotype relative to individuals with TC or TT genotype. Individuals with the CT or TT genotype were at an over 2-fold increase risk of sustained LCLA change relative to individuals with the CC genotype (HR: 2.25; 95% CI: 1.70 to 2.98; P-value = 3.98 × 10−8).

Figure 3

Summary of results of the network analyses related to loss of visual function in multiple sclerosis. (A) Composition of identified networks from HotNet2 analyses that were identified in both primary and secondary analyses. (B) Enrichment results of the HotNet2 network analyses of networks identified in both primary and secondary analyses. The identified network was highly enriched in early complement pathway genes (P = 9.15 × 10−16). The plotted network reflects the identified network from the sensitivity analyses (where low-confidence genes are assigned a heat score of 0). (C) Kaplan Meier plot comparing rate of sustained LCLA for individuals with the CC genotype relative to individuals with TC or TT genotype for the variant rs158772, which is the top variant annotated to C1QA. Individuals with the CT or TT genotype were at a 71% increased risk of sustained LCLA change relative to individuals with the CC genotype (HR: 1.71; 95% CI: 1.30 to 2.25; P-value = 10−4). For CombiRx, the imputation R2 for rs158772 is 0.98; for JHU, the imputation R2 for rs158772 is 0.99. (D) Kaplan Meier plot comparing rate of sustained LCLA for individuals with the AA genotype relative to individuals with AG or GG genotype for the variant rs61822967, which is the top variant annotated to CR1. Individuals with the AG or GG genotype were at a 40% increased risk of sustained LCLA change relative to individuals with the AA genotype (HR: 1.40; 95% CI: 1.16 to 1.68; P-value = 4 × 10−4). For CombiRx, the imputation R2 for rs61822967is 0.96; for JHU, the imputation R2 for rs61822967 is 0.99.