The advent of gene therapies, which can target specific variants, means pinpointing the genetic roots of each patient’s disease has taken on new importance, researchers said.
A team of researchers developed an approach that may provide a more accurate diagnosis of limb-girdle muscular dystrophy (LGMD) type R4/2E, according to findings published in The Journal of Clinical Investigation.
LGMD is a rare genetic muscle disease that causes weakness in the hips and shoulders, which can lead to difficulty walking and lifting the arms. Individuals with the most severe symptoms of the disease may need to start using wheelchairs as young as age seven.
Although in the past it has not been crucial to differentiate between different subtypes of LGMD, the advent of gene therapies, which can target specific variants, means pinpointing the genetic roots of each patient’s disease has taken on new importance, researchers said.
In an effort to help resolve inconclusive diagnoses, investigators at Washington University School of Medicine in St. Louis have taken a step toward creating a catalog of variants of genes linked with LGMD.
“Limb-girdle muscular dystrophy (LGMD) type R4/2E is caused by mutations in β-sarcoglycan (SGCB),” they explained. “β-sarcoglycan in association with α-, γ-, and δ-sarcoglycan form a four protein transmembrane complex (SGC) that localizes to the sarcolemma. Biallelic loss of function mutations in any subunit can lead to LGMD.”
Specifically, researchers performed deep mutational scanning (DMS) of SGCB and assessed SGC cell-surface localization for all possible amino acid changes. From this, they found variants with less severe functional scores appeared more often in patients with slower disease progression, suggesting there may be a relationship between variant function and disease severity.
Variants known to cause LGMD also scored low in functional activity and all known benign variants scored high.
In addition, “positions intolerant to variation mapped to points of predicted SGC interactions, validated in silico structural models and enabled accurate prediction of pathogenic variants in other SGC genes,” researchers wrote.
Results may not only be useful for the clinical interpretation of SGCB variants, but could also improve LGMD diagnoses, and potentially enable wider use of gene therapies.
“Twenty percent of the variants of unknown significance turned out to be pathogenic, which means they could be amenable to potential therapies,” said co-author Conrad Weihl, MD, PhD, in a release.
The study marks the first time a full-length muscular dystrophy gene has undergone DMS. Findings also suggest pooled functional screens are a viable method of large-scale functional assessment of protein-coding genetic variation in other muscular dystrophy genes, authors added.
“My dream is that one day we’ll be able to give people a genetic test report that says, ‘You have this variant, and it’s amenable to this type of therapy,’ and we can start them on the best therapy right away. Or we tell them, ‘Your variant is benign,’ and we keep looking until we find the variant that is responsible for the patient’s disease,” Weihl said.
More research could probe whether the functional scores measured in the current study correlate with more subtle muscle traits, like exercise intolerance, in the general population.
Investigators were unable to measure the effects of the variants on endogenous mRNA or protein levels, marking a limitation to the study. They also did not measure the effect of coding and non-coding genetic variation on splicing.
“In the future, splicing effects could be measured by mutagenizing splice regions in the endogenous locus and measuring cell-surface expression of the SGC complex in primary muscle cells,” they wrote.
Their assay did not measure muscle integrity or atrophy over time.
Li C, Wilborn J, Pittman S, et al. Comprehensive functional characterization of SGCB coding variants predict pathogenicity in limb-girdle muscular dystrophy type R4/2E. J Clin Invest. Published online June 15, 2023. doi:10.1172/JCI168156