The Effect of SMN Gene Dosage on ALS Risk and Disease Severity

Abstract

Objective: The role of the survival of motor neuron (SMN) gene in amyotrophic lateral sclerosis (ALS) is unclear, with several conflicting reports. A decisive result on this topic is needed, given that treatment options are available now for SMN deficiency.

Methods: In this largest multicenter case control study to evaluate the effect of SMN1 and SMN2 copy numbers in ALS, we used whole genome sequencing data from Project MinE data freeze 2. SMN copy numbers of 6,375 patients with ALS and 2,412 controls were called from whole genome sequencing data, and the reliability of the calls was tested with multiplex ligation-dependent probe amplification data.

Results: The copy number distribution of SMN1 and SMN2 between cases and controls did not show any statistical differences (binomial multivariate logistic regression SMN1 p = 0.54 and SMN2 p = 0.49). In addition, the copy number of SMN did not associate with patient survival (Royston-Parmar; SMN1 p = 0.78 and SMN2 p = 0.23) or age at onset (Royston-Parmar; SMN1 p = 0.75 and SMN2 p = 0.63).

Interpretation: In our well-powered study, there was no association of SMN1 or SMN2 copy numbers with the risk of ALS or ALS disease severity. This suggests that changing SMN protein levels in the physiological range may not modify ALS disease course. This is an important finding in the light of emerging therapies targeted at SMN deficiencies. ANN NEUROL 2021;89:686-697.

FIGURE 1

Raw data plots for discordant MLPA call. MPLA called 3 CNs for SMN1 in sample LP6008185‐DNA_A08, whereas SMNCNC called 4 CNs for SMN1. Closer inspection revealed SMNCNC to be correct. (A) Raw CN of full length SMN1 estimated by exon 7 and 8, histogram indicating the estimated CN of a large control cohort, vertical blue line indicates the discordant sample. (B) SMN1 and SMN2 raw CN values at the 8 loci used to determine the consensus CN. (C) SMN1 and SMN2 CNs normalized against coverage depth at 8 the loci. (D) Scatterplot of the raw CN calls by MLPA, on the x‐axis raw CN for SMN1, on the y‐axis raw CN for SMN2, discordant sample indicated with a line. (E) Scatter plot of the raw CN calls by SMNCNC, on the x‐axis raw CN for SMN1, and on the y‐axis raw CN for SMN2, discordant sample indicated with a line. CN = copy number; MLPA = multiplexed ligation‐dependent probe amplification; SMN = survival of motor neuron; SMNCNC = SMNCopyNumberCaller; WGS = whole genome sequencing.

FIGURE 2

Raw data plots for discordant SMNCNC call. MPLA called 3 CNs for SMN1 in sample LP6005947‐DNA_D01, whereas SMNCNC called 2 CNs for SMN1. Closer inspection revealed MLPA to be correct. (A) Raw CN of full length SMN1 estimated by exon 7 and 8, histogram indicating the estimated CN of a large control cohort, vertical blue line indicates the discordant sample. (B) SMN1 and SMN2 raw CN values at the 8 loci used to determine the consensus CN. (C) SMN1 and SMN2 CN normalized against coverage depth at the 8 loci. (D) Scatterplot of the raw CN calls by MLPA, on the x‐axis raw CN for SMN1, and on the y‐axis raw CN for SMN2, discordant sample indicated with a line. (E) Scatter plot of the raw CN calls by SMNCNC, on the x‐axis raw CN for SMN1, and on the y‐axis raw CN for SMN2, discordant sample indicated with a line. CN = copy number; MLPA = multiplexed ligation‐dependent probe amplification; SMN = survival of motor neuron; SMNCNC = SMNCopyNumberCaller; WGS = whole genome sequencing.

FIGURE 3

Frequency of the CNs of the SMN1 and 2 genes. Frequency of (A) SMN1 and (B) SMN2 copy number in control individuals of this study (MinE), Feng Y. et al. (White, Hispanic, Ashkenazi Jewish, Asian, and African American), Blauw HM. et al. (The Netherlands), Corcia P. et al. (France), Yoon S. et al. (Korea), and Fang P. et al. (China). Comparisons of the different cohort toward this study for SMN1 (lbl p value): White (0.16), Netherlands (3.2 × 10^‐3), France (1.3 × 10^‐3), Hispanic (3.4 × 10^‐5), Ashkenazi Jewish (0.20), Asian (0.83), Korea (0.07), China (0.25), and African American (<1 × 10^‐16); and SMN2: Netherlands (1.1 × 10^‐2), France (0.63), Korea (2.3 × 10^‐4), and China (7.6 × 10^‐6). Frequency of (C) SMN1 and (D) SMN2 copy numbers in patients with ALS and control individuals in this study. ALS = amyotrophic lateral sclerosis; CN = copy number; lbl = linear‐by‐linear.

FIGURE 4

SMN frequencies by country. Frequency of SMN1 (A) and SMN2 (B) CN in ALS patients and control individuals in this study by cohort. Lighter colors indicate controls. Comparisons of the different ALS cohort toward the Turkish cohort for SMN1 (lbl p value): BE (0.41), NL (0.75), IE (0.86), SE (0.67), US (0.79), GB (0.55), ES (0.96), PT (0.90), FR (0.21), IT (0.83), IL (1.1 × 10^‐2) and CH (0.42); and SMN2: BE (7.1 × 10^‐5), NL (2.5e‐5), IE (1.6 × 10^‐4), SE (0.19), US (0.4.0 × 10^‐6), GB (9.9 × 10^‐5), ES (5.9 × 10^‐3), PT (0.73), FR (2.3 × 10^‐4), IT (0.44), IL (0.05), and CH (0.81). ALS = amyotrophic lateral sclerosis; BE = Belgium; CH = Switzerland; CN = copy number; GB = United Kingdom; ES = Spain; FR = France; IE = Ireland; IL = Israel; IT = Italy; lbl = linear‐by‐linear; NL = The Netherlands; PT = Portugal; SE = Sweden; SMN = survival of motor neuron; TR = Turkey; US = United States.

FIGURE 5

Survival and onset of patients, stratified by SMN CN. Kaplan Meier survival curves and risk table for (A) SMN1 and (B) SMN2 CNs. Kaplan Meier age at onset curves and cumulative events table for (C) SMN1 and (D) SMN2. CN = copy number; SMN = survival of motor neuron.