Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2

Abstract

Muscle bulk in adult healthy humans is highly variable even after height, age, and sex are accounted for. Low muscle mass, due to fewer and/or smaller constituent muscle fibers, would exacerbate the impact of muscle loss occurring in aging or disease. Genetic variability substantially influences muscle mass differences, but causative genes remain largely unknown. In a genome-wide association study (GWAS) on appendicular lean mass (ALM) in a population of 85,750 middle-aged (aged 38-49 years) individuals from the UK Biobank (UKB), we found 182 loci associated with ALM (p < 5 × 10^-8). We replicated associations for 78% of these loci (p < 5 × 10^-8) with ALM in a population of 181,862 elderly (aged 60-74 years) individuals from UKB. We also conducted a GWAS on hindlimb skeletal muscle mass of 1,867 mice from an advanced intercross between two inbred strains (LG/J and SM/J); this GWAS identified 23 quantitative trait loci. Thirty-eight positional candidates distributed across five loci overlapped between the two species. In vitro studies of positional candidates confirmed CPNE1 and STC2 as modifiers of myogenesis. Collectively, these findings shed light on the genetics of muscle mass variability in humans and identify targets for the development of interventions for treatment of muscle loss. The overlapping results between humans and the mouse model GWAS point to shared genetic mechanisms across species.

Keywords: UK Biobank; human and mouse GWAS; sarcopenia; skeletal muscle.

Figure 1

Map of Genome Associations with the Appendicular Lean Mass (ALM) of Humans Genome-wide association study on the ALM of middle-aged adults from the UK Biobank. Significance level is presented on the vertical axis, while the chromosomal position of each genetic marker is shown on the horizontal axis. Red line across the plot represents the genome-wide threshold of significance (p < 5 × 10⁻⁸). This plot shows the association of variants with minor allele frequency >0.001.

Figure 2

Genetic Lean Mass Score Affects the Appendicular Lean Mass (ALM) in Elderly Humans The plot shows the ALM (kg) of the elderly cohort on the vertical axis. The elderly cohort was ranked by genetic lean mass score and clustered in five quantiles (Q1–Q5) (horizontal axis). The average genetic lean mass score (±standard error) of each quantile is shown in parentheses below the horizontal axis. The overall quantile effect of the genetic lean mass score on ALM was tested with the Kruskal-Wallis test, and the resulting p value is presented on the top horizontal line above the bars. The ALM median differences between the groups were tested using a Wilcoxon test; the significance level of each comparison is presented above the horizontal lines with a Holm adjusted p value.

Figure 3

Muscle Weight Quantitative Trait Loci (QTLs) Identified in Mice of the LGSM AIL and Density Plot of the Genotypes The circle plot (A) shows from the outer to the inner ring the GWAS of the tibialis anterior, extensor digitorium longus (EDL), gastrocnemius, and soleus muscle weights. The chromosomal position of each SNP is shown in the outer black circle of the plot; chromosome names are shown outside as “Chr.” Dots within each chromosome space represent the association (–log₁₀ p value) of each SNP tested. Dotted blue lines represent the genome-wide threshold (p < 6.45 × 10⁻⁰⁶) of significance, and red dots above the genome-wide threshold are significantly associated SNPs. (B) Plots of the allelic effect of the Skmw34, Skmw55, and Skmw46 QTLs on the EDL muscle mass. These QTLs were identified for the four muscles investigated. The vertical axis represents the residual muscle mass adjusted for sex, age, dissector, and long bone length of the hindlimb, and the horizontal axis shows the genotypes (LG/J homozygote, heterozygote, and SM/J homozygote). Below the horizontal axis, the number of individuals with a given genotype is provided. The violin shapes within the plot area represent the distribution of individuals with the genotypes. Box whiskers represent minimum and maximum values, distance between a whisker and the top or bottom of the box contains 25% of the distribution, the box captures 50% of the distribution, and the bold horizontal line represents the median. Pairwise comparison p value (t test) is shown above horizontal lines at the top of the plots.

Figure 4

Gene Knockdown Effect on C2C12 Myotube Length This figure shows the gene knockdown effect of the Cpne1, Sbf2, and Stc2 genes on myotube length. The overall effect of the gene knockdown on myotube length was tested through the use of ANOVA, and the resulting p value was 0.00017 (F_{3, 34985} = 6.63). The vertical axis represents the myotube length (quantile normalized) residuals (adjusted for area analyzed and batch of cells), and the horizontal axis shows control and knockdown gene groups. Boxes represent the distribution of the myotube length for each group. Box whiskers represent minimum and maximum values within 1.5-fold interquartile range above the 75^th percentile and below the 25^th percentile; the box captures 50% of the distribution, and the bold horizontal line represents the median value of the myotube length normalized residuals distribution for each knockdown group. Each dot represents a single cell culture sample for each knockdown group. Statistically significant t–test p values between control and knockdown genes are presented above horizontal lines. Effects without a statistically significant difference between the control and gene knockdown are presented as “ns.” Cpne1 and Stc2 knockdown groups were not different from each other (p > 0.05). Sbf2 knockdown differed from Cpne1 (p = 0.002) and Stc2 (p = 0.043).