Association Study of Exon Variants in the NF-κB and TGFβ Pathways Identifies CD40 as a Modifier of Duchenne Muscular Dystrophy

Abstract

The expressivity of Mendelian diseases can be influenced by factors independent from the pathogenic mutation: in Duchenne muscular dystrophy (DMD), for instance, age at loss of ambulation (LoA) varies between individuals whose DMD mutations all abolish dystrophin expression. This suggests the existence of trans-acting variants in modifier genes. Common single nucleotide polymorphisms (SNPs) in candidate genes (SPP1, encoding osteopontin, and LTBP4, encoding latent transforming growth factor β [TGFβ]-binding protein 4) have been established as DMD modifiers. We performed a genome-wide association study of age at LoA in a sub-cohort of European or European American ancestry (n = 109) from the Cooperative International Research Group Duchenne Natural History Study (CINRG-DNHS). We focused on protein-altering variants (Exome Chip) and included glucocorticoid treatment as a covariate. As expected, due to the small population size, no SNPs displayed an exome-wide significant p value (< 1.8 × 10). Subsequently, we prioritized 438 SNPs in the vicinities of 384 genes implicated in DMD-related pathways, i.e., the nuclear-factor-κB and TGFβ pathways. The minor allele at rs1883832, in the 5'-untranslated region of CD40, was associated with earlier LoA (p = 3.5 × 10). This allele diminishes the expression of CD40, a co-stimulatory molecule for T cell polarization. We validated this association in multiple independent DMD cohorts (United Dystrophinopathy Project, Bio-NMD, and Padova, total n = 660), establishing this locus as a DMD modifier. This finding points to cell-mediated immunity as a relevant pathogenetic mechanism and potential therapeutic target in DMD.

Long‐range genomic regulators of THBS1 and LTBP4 modify disease severity in duchenne muscular dystrophy

“…However, even without dystrophin protein, there is variability in clinical progression of disease symptoms suggesting that genetic background may play a role in modulating the disease process. Consistent with observations of genetic modifiers of muscle disease severity in animal models 3,4 , several human candidate gene associations with age at loss of ambulation (LOA) have identified variants in SPP1 5 , LTBP4 6 , and CD40 7 as genetic modifiers of DMD.…”

“…The LTBP4 and THBS1 regulatory SNPs reported here join additional examples of expression levels ameliorating the DMD phenotype, including Jagged1 overexpression in the golden retriever muscular dystrophy model 4 , and in human, rs28357094 in the SPP1 promoter 5 and rs1883832 in the CD40 Kozak consensus sequence 7 . As in previous candidate modifier gene studies with LOA in human DMD cohorts, these new associations show non-additive (recessive) protective effects of the modifier variants on the expressivity of DMD mutations.…”

Genetic modifiers of respiratory function in Duchenne muscular dystrophy

“…Other than glucocorticoid (GC) treatment and standards of care, 6,8,9 several genetic factors have been called into play as modifiers of DMD severity. These include “cis‐acting” modifiers, such as specific DMD mutations which may lead to the expression of minimal, but clinically relevant quantities of dystrophin 10–13 ; and “trans‐acting” modifiers, that is, polymorphisms in genes different from DMD , that may influence the pathological consequences of dystrophin deficiency 14–17 . As specific DMD mutations are now amenable to targeted molecular treatments, 18 such as “exon skipping” antisense oligonucleotides, or small molecules promoting stop codon readthrough, delineating “natural history” trajectories in corresponding subgroups are useful.…”

Outside in: The matrix as a modifier of muscular dystrophy

“…This SNP falls in the 5′-UTR of CD40 , which modulates T cell activation and can be found also on the surface of myofibers. Intriguingly, the same group reported a similar effect of the minor SNP haplotype (T) on loss of ambulation in other three independent cohorts of DMD patients [41]. Although the molecular mechanisms and the cell context of CD40-mediated effects on dystrophic degeneration must still be elucidated, these results reinforce the focus on the link between DMD genetic modifiers and immune system modulation.…”

“…Recently, a hypothesis-driven exome screening on DMD patients of European or European-American ancestry identified the rs1883832C>T as modifier of age of loss of ambulation, with the C haplotype associating with earlier age [41]. This SNP falls in the 5′-UTR of CD40 , which modulates T cell activation and can be found also on the surface of myofibers.…”